Mercurial > repos > gga > jbrowse_to_container
view jbrowse_to_container.xml @ 0:11033bdad2ca draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268
author | gga |
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date | Mon, 11 Sep 2017 05:49:16 -0400 |
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<?xml version="1.0"?> <tool id="jbrowse_to_container" name="Add organisms to JBrowse container" version="@WRAPPER_VERSION@"> <description>will replace any existing organism</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ if [ -z "@DATA_DIR@" ]; then echo '@DATA_DIR@ variable must be set to use this tool'; exit 1; fi; rm -rf "@DATA_DIR@/"* && #for $org in $organisms: #if $org.advanced.unique_id: #set dataset_name = $org.advanced.unique_id #else: #set dataset_name = $org.jbrowse.id #end if cp -R '${org.jbrowse.extra_files_path}/data/' "@DATA_DIR@/${dataset_name}" && echo -e "[general]\ndataset_id = ${dataset_name}" >> "@DATA_DIR@/${dataset_name}/tracks.conf" && #end for cp $trackList "@DATA_DIR@/datasets.conf" && python $__tool_directory__/jbrowse_to_container.py @JBROWSE_BASE_URL@ > $output ]]></command> <configfiles> <configfile name="trackList"> <![CDATA[ #for $org in $organisms: #if $org.advanced.unique_id: #set dataset_name = $org.advanced.unique_id #else: #set dataset_name = $org.jbrowse.id #end if [datasets.$dataset_name] url = ?data=data/${dataset_name} name = $org.name #end for ]]> </configfile> </configfiles> <inputs> <repeat name="organisms" title="Organism"> <param name="jbrowse" type="data" format="html" label="JBrowse HTML Output" /> <param name="name" type="text" label="Display name" optional="False" /> <section name="advanced" title="Advanced" expanded="False"> <param name="unique_id" type="text" label="Unique ID" help="will be used in HTTP links (default=auto generated id). WARNING: If set, pay attention to have different ID for each dataset." optional="True"> <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> </param> </section> </repeat> </inputs> <outputs> <data format="html" name="output"/> </outputs> <help><![CDATA[ **What it does** Adds an organism to a JBrowse instance. The tool takes the output of a JBrowse run as that contains all of the necessary information for which tracks are appropriate for a given analysis. @ATTRIBUTION@ ]]></help> <expand macro="citations"/> </tool>