comparison jbrowse_hub.xml @ 60:ed17bb465bde draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 8386544cbce1efb5e9dd1f805a2099b3e214363f-dirty

59:caf649fc310b

    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/jbrowse_hub.py 
        --fasta '$reference' 
        --genome_name '$genome_name'

        ## json metadata recording from Remi's hub-archive-creator.xml
        #import json
        #set global data_parameter_dict = {}

        ## Function to retrieve the data of the inputs

       -o '$output'

    ]]></command>

    <inputs>
        <param name="reference" type="data" format="fasta" label="Reference Genome" />
        <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" />
        <repeat name="group" title="New group">
            <param type="text" name="group_name" label="Group name" value="Default group"/>
            <repeat name="format" title="New track">

60:ed17bb465bde

    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/jbrowse_hub.py 
        --fasta '$reference' 
        --genome_name '$genome_name'

        #set galaxy_url = str($GALAXY_URL)
        #set $jbrowse_url = galaxy_url.replace("8080", "80")
        --jbrowse_host '$jbrowse_url'
        
        ## json metadata recording from Remi's hub-archive-creator.xml
        #import json
        #set global data_parameter_dict = {}

        ## Function to retrieve the data of the inputs

       -o '$output'

    ]]></command>

    <inputs>
        <param name="GALAXY_URL" type="baseurl" value="" />
        <param name="reference" type="data" format="fasta" label="Reference Genome" />
        <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" />
        <repeat name="group" title="New group">
            <param type="text" name="group_name" label="Group name" value="Default group"/>
            <repeat name="format" title="New track">