comparison pep_pointer.xml @ 2:ac3494caea96 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer commit e70efe967398bc8d01f4847a5d22ae9f3575f4ef

1:e2340f69d224

<tool id="pep_pointer" name="PepPointer" version="0.1.1">
    <description>classify genomic location of peptides</description>
    <requirements>
        <requirement type="package" version="2.7.9">python</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf' '$bed' '$classified'
    ]]></command>
    <inputs>
        <conditional name="gtf_input">
            <param type="select" name="gtf_source" label="Choose the source of the GTF file">
                <option value="cached" selected="true">Built-in</option>
                <option value="history">From history</option>
            </param>
            <when value="cached">
                <param name="gtf" type="select" format="gtf" label="GTF file with the genome of interest">
                    <options from_data_table="pep_pointer"/>
                </param>
            </when>
            <when value="history">
                <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
            </when>

2:ac3494caea96

<tool id="pep_pointer" name="PepPointer" version="0.1.2">
    <description>classify genomic location of peptides</description>
    <requirements>
        <requirement type="package" version="2.7.9">python</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        #if $gtf_input.gtf_source == "cached":
            python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf.fields.path' '$bed' '$classified'
        #else
            python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf' '$bed' '$classified'
        #end if
    ]]></command>
    <inputs>
        <conditional name="gtf_input">
            <param type="select" name="gtf_source" label="Choose the source of the GTF file">
                <option value="cached" selected="true">Locally installed</option>
                <option value="history">From history</option>
            </param>
            <when value="cached">
                <param name="gtf" type="select" format="gtf" label="GTF file with the genome of interest">
                    <options from_data_table="gff_gene_annotations"/>
                </param>
            </when>
            <when value="history">
                <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
            </when>