annotate jbrowse_to_container.xml @ 1:4065bcff8e85 draft default tip

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit 3500c1e606a902b492180db3e2e0c2ee07c90e8b"

<?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>