Creating Galaxy tool - Revision history

Ivan@dote.ru: /* BioUML extensions to Galaxy standard */

2018-01-17T07:04:27Z

‎BioUML extensions to Galaxy standard

Ivan@dote.ru at 09:13, 5 December 2013

2013-12-05T09:13:10Z

Ivan@dote.ru: /* Multiselect parameter type */

2013-12-05T09:10:08Z

‎Multiselect parameter type

Ivan@dote.ru: /* Multiselect parameter type */

2013-12-05T09:09:35Z

‎Multiselect parameter type

Ivan@dote.ru at 09:09, 5 December 2013

2013-12-05T09:09:17Z

Lan@dote.ru: Formatting /* Configurable file format */

2013-08-14T04:07:54Z

Formatting - ‎Configurable file format

Lan@dote.ru: Type link|folder /* Customizing tools menu */

2013-06-04T09:33:36Z

Type link|folder - ‎Customizing tools menu

Ivan@dote.ru at 05:55, 24 May 2013

2013-05-24T05:55:50Z

Lan@dote.ru: +Category:Galaxy

2013-04-19T05:42:40Z

+Category:Galaxy

Lan@dote.ru: +Category:Development

2013-04-19T05:39:04Z

+Category:Development

← Older revision		Revision as of 07:04, 17 January 2018
Line 35:		Line 35:

	<code><command>cat $inputs > out<command></code>		<code><command>cat $inputs > out<command></code>
		+
		+	=== Output name templates ===
		+	Allow to generate output file names based on other parameter values, such as names of input files.
		+	Example:
		+
		+	<code><data format="vcf" name="output" label="Mapped coordinates" template="$input$_mapped"></code>
		+
		+	where "input" is the name of input parameter.

	== Reloading tool configuration ==		== Reloading tool configuration ==

@@ Line 28: / Line 28: @@
 === Multiselect parameter type ===
 Example:
-<code><param name="inputs" type="data-multi" format="tabular" label="Input tables"/><code>
 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.
 For example, to concatenate input files use:
-<code><command>cat $inputs > out<command><code>
 == Reloading tool configuration ==

@@ Line 28: / Line 28: @@
 === Multiselect parameter type ===
 Example:
+<code><param name="inputs" type="data-multi" format="tabular" label="Input tables"/><code>
 <param name="inputs" type="data-multi" format="tabular" label="Input tables"/>
 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.
 For example, to concatenate input files use:
-<command>cat $inputs > out<command>
+<code><command>cat $inputs > out<command><code>
 == Reloading tool configuration ==

@@ Line 28: / Line 28: @@
 === Multiselect parameter type ===
 Example:
 <param name="inputs" type="data-multi" format="tabular" label="Input tables"/>
 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.

@@ Line 26: / Line 26: @@
 set the names of additional columns in the [[Interval format]].
 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}}.
 == Reloading tool configuration ==

@@ Line 20: / Line 20: @@
 BioUML extends Galaxy tool configuration syntax [http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Galaxy Wiki] that allow closer interaction between Galaxy and BioUML systems.
 === Configurable file format ===
-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 $GALAXY_DIST/datatypes_conf.xml and the mapping of these formats to BioUML element types in [[Types (extension point)|ru.biosoft.galaxy.types]]. For more flexibility BioUML allows to change format options "on the fly" when you specify parameter format. For example:
+In Galaxy to define output (<code>&lt;data name="out1" format="tabular"/&gt;</code>) or input parameter (<code>&lt;param type='data' format="tabular"/&gt;</code>) you should set "format" attribute. The list of predefined formats is contained in the <code>$GALAXY_DIST/datatypes_conf.xml</code> and the mapping of these formats to BioUML element types in [[Types (extension point)|ru.biosoft.galaxy.types]] (currently all these mappings are registered in [[Ru.biosoft.galaxy (plugin)|ru.biosoft.galaxy plugin]]). For more flexibility BioUML allows to change format options "on the fly" when you specify parameter format. For example:
-  <data name="outTable" format="tabular" format.commentString="#" />
+ <data name="outTable" format="tabular" format.commentString="#" />
 means that lines starting with "#" are comments and should be ignored,
-  <data name="outTrack" format="interval" format.fieldNames="pValue,FDR" />
+ <data name="outTrack" format="interval" format.fieldNames="pValue,FDR" />
 set the names of additional columns in the [[Interval format]].
 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}}.
 == Reloading tool configuration ==

@@ Line 11: / Line 11: @@
   </section>
-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>$GALAXY_DIST/tools</code> directory.
+In BioUML interface section is transformed into {{Type link|folder}} and label is rendered as a separator between tools. You can freely add, delete or rearrange sections, labels or tools here. To add new tool you should specify a path to the tool description XML file relative to <code>$GALAXY_DIST/tools</code> directory.
 == Creating your own tool ==

← Older revision		Revision as of 05:42, 19 April 2013
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	[[Category:Development]]		[[Category:Development]]
		+	[[Category:Galaxy]]

← Older revision		Revision as of 05:39, 19 April 2013
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	galaxy.reload();		galaxy.reload();
	Please note that for security reasons this command is available for BioUML server administrators only.		Please note that for security reasons this command is available for BioUML server administrators only.
		+
		+	[[Category:Development]]