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

"planemo upload for repository commit 3500c1e606a902b492180db3e2e0c2ee07c90e8b"
author gga
date Tue, 27 Apr 2021 12:49:22 +0000
parents 11033bdad2ca
line wrap: on
line source

<?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>
    <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;

        rm -rf "@DATA_DIR@/"*


        #for $org in $organisms:
            #if $org.advanced.unique_id:
                #set dataset_name = $org.advanced.unique_id
                #set dataset_name = $
            #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_BASE_URL@ > $output
        <configfile name="trackList">
#for $org in $organisms:
#if $org.advanced.unique_id:
#set dataset_name = $org.advanced.unique_id
#set dataset_name = $
#end if
url  = ?data=data/${dataset_name}
name = $
#end for
        <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>
        <data format="html" name="output"/>
**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.

    <expand macro="citations"/>