http://wiki.biouml.org/index.php?title=Creating_Galaxy_tool&feed=atom&action=historyCreating Galaxy tool - Revision history2024-03-29T00:54:31ZRevision history for this page on the wikiMediaWiki 1.20.3http://wiki.biouml.org/index.php?title=Creating_Galaxy_tool&diff=7550&oldid=prevIvan@dote.ru: /* BioUML extensions to Galaxy standard */2018-01-17T07:04:27Z<p><span dir="auto"><span class="autocomment">BioUML extensions to Galaxy standard</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><code>&lt;command&gt;cat $inputs > out&lt;command&gt;</code></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><code>&lt;command&gt;cat $inputs > out&lt;command&gt;</code></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">=== Output name templates ===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Allow to generate output file names based on other parameter values, such as names of input files.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Example:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><code>&lt;data format="vcf" name="output" label="Mapped coordinates" template="$input$_mapped"&gt;</code></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">where "input" is the name of input parameter.</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td></tr>
</table>Ivan@dote.ruhttp://wiki.biouml.org/index.php?title=Creating_Galaxy_tool&diff=5486&oldid=prevIvan@dote.ru at 09:13, 5 December 20132013-12-05T09:13:10Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Multiselect parameter type ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Multiselect parameter type ===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Example:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Example:</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><code><del class="diffchange diffchange-inline"><</del>param name="inputs" type="data-multi" format="tabular" label="Input tables"/<del class="diffchange diffchange-inline">></del><code></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><code><ins class="diffchange diffchange-inline">&lt;</ins>param name="inputs" type="data-multi" format="tabular" label="Input tables"/<ins class="diffchange diffchange-inline">&gt;</ins><<ins class="diffchange diffchange-inline">/</ins>code></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In Cheetah template this parameter will be expanded to *.tabular (depending on the format), that can be used in the bash script to get the list of files.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In Cheetah template this parameter will be expanded to *.tabular (depending on the format), that can be used in the bash script to get the list of files.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For example, to concatenate input files use:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For example, to concatenate input files use:</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><code><del class="diffchange diffchange-inline"><</del>command<del class="diffchange diffchange-inline">></del>cat $inputs > out<del class="diffchange diffchange-inline"><</del>command<del class="diffchange diffchange-inline">></del><code></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><code><ins class="diffchange diffchange-inline">&lt;</ins>command<ins class="diffchange diffchange-inline">&gt;</ins>cat $inputs > out<ins class="diffchange diffchange-inline">&lt;</ins>command<ins class="diffchange diffchange-inline">&gt;</ins><<ins class="diffchange diffchange-inline">/</ins>code></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td></tr>
</table>Ivan@dote.ruhttp://wiki.biouml.org/index.php?title=Creating_Galaxy_tool&diff=5485&oldid=prevIvan@dote.ru: /* Multiselect parameter type */2013-12-05T09:10:08Z<p><span dir="auto"><span class="autocomment">Multiselect parameter type</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Multiselect parameter type ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Multiselect parameter type ===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Example:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Example:</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><code></ins><param name="inputs" type="data-multi" format="tabular" label="Input tables"/<ins class="diffchange diffchange-inline">><code</ins>></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><param name="inputs" type="data-multi" format="tabular" label="Input tables"/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In Cheetah template this parameter will be expanded to *.tabular (depending on the format), that can be used in the bash script to get the list of files.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In Cheetah template this parameter will be expanded to *.tabular (depending on the format), that can be used in the bash script to get the list of files.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For example, to concatenate input files use:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For example, to concatenate input files use:</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><command>cat $inputs > out<command></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><code></ins><command>cat $inputs > out<command<ins class="diffchange diffchange-inline">><code</ins>></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td></tr>
</table>Ivan@dote.ruhttp://wiki.biouml.org/index.php?title=Creating_Galaxy_tool&diff=5484&oldid=prevIvan@dote.ru: /* Multiselect parameter type */2013-12-05T09:09:35Z<p><span dir="auto"><span class="autocomment">Multiselect parameter type</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Multiselect parameter type ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Multiselect parameter type ===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Example:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Example:</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><param name="inputs" type="data-multi" format="tabular" label="Input tables"/></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><param name="inputs" type="data-multi" format="tabular" label="Input tables"/></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In Cheetah template this parameter will be expanded to *.tabular (depending on the format), that can be used in the bash script to get the list of files.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In Cheetah template this parameter will be expanded to *.tabular (depending on the format), that can be used in the bash script to get the list of files.</div></td></tr>
</table>Ivan@dote.ruhttp://wiki.biouml.org/index.php?title=Creating_Galaxy_tool&diff=5483&oldid=prevIvan@dote.ru at 09:09, 5 December 20132013-12-05T09:09:17Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>set the names of additional columns in the [[Interval format]].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>set the names of additional columns in the [[Interval format]].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In general format options can be changed by adding format.$OptionName="$OptionValue" attributes, the list of possible options for each format is defined by properties of corresponding {{Class|ru.biosoft.access.DataElementImporter}} or {{Class|ru.biosoft.access.DataElementExporter}}.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In general format options can be changed by adding format.$OptionName="$OptionValue" attributes, the list of possible options for each format is defined by properties of corresponding {{Class|ru.biosoft.access.DataElementImporter}} or {{Class|ru.biosoft.access.DataElementExporter}}.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">=== Multiselect parameter type ===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Example:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><param name="inputs" type="data-multi" format="tabular" label="Input tables"/></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">In Cheetah template this parameter will be expanded to *.tabular (depending on the format), that can be used in the bash script to get the list of files.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">For example, to concatenate input files use:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><command>cat $inputs > out<command></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td></tr>
</table>Ivan@dote.ruhttp://wiki.biouml.org/index.php?title=Creating_Galaxy_tool&diff=5120&oldid=prevLan@dote.ru: Formatting /* Configurable file format */2013-08-14T04:07:54Z<p>Formatting - <span dir="auto"><span class="autocomment">Configurable file format</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML extends Galaxy tool configuration syntax [http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Galaxy Wiki] that allow closer interaction between Galaxy and BioUML systems.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML extends Galaxy tool configuration syntax [http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Galaxy Wiki] that allow closer interaction between Galaxy and BioUML systems.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Configurable file format ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Configurable file format ===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In Galaxy to define output (<data name="out1" format="tabular" />) or input parameter (<param type='data' format="tabular" />) you should set "format" attribute. The list of predefined formats is contained in the $GALAXY_DIST/datatypes_conf.xml and the mapping of these formats to BioUML element types in [[Types (extension point)|ru.biosoft.galaxy.types]]. For more flexibility BioUML allows to change format options "on the fly" when you specify parameter format. For example:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In Galaxy to define output (<<ins class="diffchange diffchange-inline">code>&lt;</ins>data name="out1" format="tabular"/<ins class="diffchange diffchange-inline">&gt;</code</ins>>) or input parameter (<<ins class="diffchange diffchange-inline">code>&lt;</ins>param type='data' format="tabular"/<ins class="diffchange diffchange-inline">&gt;</code</ins>>) you should set "format" attribute. The list of predefined formats is contained in the <ins class="diffchange diffchange-inline"><code></ins>$GALAXY_DIST/datatypes_conf.xml<ins class="diffchange diffchange-inline"></code> </ins>and the mapping of these formats to BioUML element types in [[Types (extension point)|ru.biosoft.galaxy.types]] <ins class="diffchange diffchange-inline">(currently all these mappings are registered in [[Ru.biosoft.galaxy (plugin)|ru.biosoft.galaxy plugin]])</ins>. For more flexibility BioUML allows to change format options "on the fly" when you specify parameter format. For example:</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">  </del><data name="outTable" format="tabular" format.commentString="#" /></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins><data name="outTable" format="tabular" format.commentString="#" /></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>means that lines starting with "#" are comments and should be ignored,</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>means that lines starting with "#" are comments and should be ignored,</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">  </del><data name="outTrack" format="interval" format.fieldNames="pValue,FDR" /></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins><data name="outTrack" format="interval" format.fieldNames="pValue,FDR" /></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>set the names of additional columns in the [[Interval format]].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>set the names of additional columns in the [[Interval format]].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In general format options can be changed by adding format.$OptionName="$OptionValue" attributes, the list of possible options for each format is defined by properties of corresponding {{Class|ru.biosoft.access.DataElementImporter}} or {{Class|ru.biosoft.access.DataElementExporter}}.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In general format options can be changed by adding format.$OptionName="$OptionValue" attributes, the list of possible options for each format is defined by properties of corresponding {{Class|ru.biosoft.access.DataElementImporter}} or {{Class|ru.biosoft.access.DataElementExporter}}.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td></tr>
</table>Lan@dote.ruhttp://wiki.biouml.org/index.php?title=Creating_Galaxy_tool&diff=4171&oldid=prevLan@dote.ru: Type link|folder /* Customizing tools menu */2013-06-04T09:33:36Z<p>Type link|folder - <span dir="auto"><span class="autocomment">Customizing tools menu</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>  </section></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>  </section></div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In BioUML interface section is transformed into folder and label is rendered as a separator between tools. You can freely add, delete or rearrange sections, labels or tools here. To add new tool you should specify a path to the tool description XML file relative to <code>$GALAXY_DIST/tools</code> directory.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In BioUML interface section is transformed into <ins class="diffchange diffchange-inline">{{Type link|</ins>folder<ins class="diffchange diffchange-inline">}} </ins>and label is rendered as a separator between tools. You can freely add, delete or rearrange sections, labels or tools here. To add new tool you should specify a path to the tool description XML file relative to <code>$GALAXY_DIST/tools</code> directory.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Creating your own tool ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Creating your own tool ==</div></td></tr>
</table>Lan@dote.ruhttp://wiki.biouml.org/index.php?title=Creating_Galaxy_tool&diff=3817&oldid=prevIvan@dote.ru at 05:55, 24 May 20132013-05-24T05:55:50Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Creating your own tool ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Creating your own tool ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>When you added a link to new tool description XML file, you should create that file. Refer to [http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Galaxy Wiki] to learn how to create such files. Please note that not all Galaxy features are supported by BioUML. Ask for technical support if you have any doubts.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>When you added a link to new tool description XML file, you should create that file. Refer to [http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Galaxy Wiki] to learn how to create such files. Please note that not all Galaxy features are supported by BioUML. Ask for technical support if you have any doubts.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">== BioUML extensions to Galaxy standard ==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">BioUML extends Galaxy tool configuration syntax [http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Galaxy Wiki] that allow closer interaction between Galaxy and BioUML systems.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">=== Configurable file format ===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">In Galaxy to define output (<data name="out1" format="tabular" />) or input parameter (<param type='data' format="tabular" />) you should set "format" attribute. The list of predefined formats is contained in the $GALAXY_DIST/datatypes_conf.xml and the mapping of these formats to BioUML element types in [[Types (extension point)|ru.biosoft.galaxy.types]]. For more flexibility BioUML allows to change format options "on the fly" when you specify parameter format. For example:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">  <data name="outTable" format="tabular" format.commentString="#" /></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">means that lines starting with "#" are comments and should be ignored,</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">  <data name="outTrack" format="interval" format.fieldNames="pValue,FDR" /></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">set the names of additional columns in the [[Interval format]].</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">In general format options can be changed by adding format.$OptionName="$OptionValue" attributes, the list of possible options for each format is defined by properties of corresponding {{Class|ru.biosoft.access.DataElementImporter}} or {{Class|ru.biosoft.access.DataElementExporter}}.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Reloading tool configuration ==</div></td></tr>
</table>Ivan@dote.ruhttp://wiki.biouml.org/index.php?title=Creating_Galaxy_tool&diff=1546&oldid=prevLan@dote.ru: +Category:Galaxy2013-04-19T05:42:40Z<p>+<a href="/index.php/Category:Galaxy" title="Category:Galaxy">Category:Galaxy</a></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Development]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Development]]</div></td></tr>
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</table>Lan@dote.ruhttp://wiki.biouml.org/index.php?title=Creating_Galaxy_tool&diff=1541&oldid=prevLan@dote.ru: +Category:Development2013-04-19T05:39:04Z<p>+<a href="/index.php/Category:Development" title="Category:Development">Category:Development</a></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>  galaxy.reload();</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>  galaxy.reload();</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Please note that for security reasons this command is available for BioUML server administrators only.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Please note that for security reasons this command is available for BioUML server administrators only.</div></td></tr>
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