annotate rename_tracks.xml @ 0:8b19a698d90e draft

planemo upload commit b615ca3bfed9f2115f62d1af30d4726fe8ba08d8

<tool id="rename_tracks" name="rename the tracks" version="1.2">
<description>a Galaxy tool to rename the scaffold names in the custom track files</description>
    <requirements>
        <requirement type="package" version="1.2">samtools</requirement>
        <requirement type="package" version="340">ucsc_rename_bigwig</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        python $__tool_directory__/rename_tracks.py "${format_select.input}" "${mapping}" $format_select.format "${output}"
        #if $format_select.format == "bigwig"
            "${format_select.reference}"
        #end if


    ]]></command>
    <inputs>
        <conditional name="format_select">
            <param name="format" type="select" label="Select the format of your custom track file">
                <option value="bed">BED</option>
                <option value="gff3">GFF3</option>
                <option value="gtf">GTF</option>
                <option value="bam">BAM</option>
                <option value="bigwig">BigWig</option>
            </param>
            <when value="bed">
                <param name="input" type="data" format="bed" label="Custom track file" />
            </when>
            <when value="gff3">
                <param name="input" type="data" format="gff3" label="Custom track file" />
            </when>
            <when value="gtf">
                <param name="input" type="data" format="gtf" label="Custom track file" />
            </when>
            <when value="bam">
                <param name="input" type="data" format="bam" label="Custom track file" />
            </when>
            <when value="bigwig">
                <param name="input" type="data" format="bigwig" label="Custom track file" />
                <param name="reference" type="data" format="fasta" label="Provide the renamed the reference file from 'renamed the scaffolds' tool" />
            </when>
        </conditional>
        <param name="mapping" type="data" format="csv" label="Provide the name mapping file from 'renamed the scaffolds' tool"/>
    </inputs>
    <outputs>
        <data name="output" format_source="input" label="${tool.name} on ${on_string}: renamed_track" />
    </outputs>
    <tests>
        <test>
            <!-- Test with GFF3 -->
            <param name="input" value="Augustus.gff3" />
            <param name="format" value="gff3" />
            <param name="mapping" value="name_mapping.csv" />
            <output name="output" file="rename_Augustus.gff3"/>
        </test>
        <test>
            <!-- Test with BED -->
            <param name="input" value="TrfBig.bed" />
            <param name="format" value="bed" />
            <param name="mapping" value="name_mapping.csv" />
            <output name="output" file="rename_TrfBig.bed"/>
        </test>
        <test>
            <!-- Test with GTF -->
            <param name="input" value="StringTie_assembled_transcripts.gtf" />
            <param name="format" value="gtf" />
            <param name="mapping" value="name_mapping.csv" />
            <output name="output" file="rename_StringTie.gtf" />
        </test>
        <test>
            <!-- Test with BAM -->
            <param name="input" value="HISAT.bam" />
            <param name="format" value="bam" />
            <param name="mapping" value="name_mapping.csv" />
            <output name="output" file="rename_HISAT.bam" />
        </test>
        <test>
            <!-- Test with BigWig -->
            <param name="input" value="sequence_cov.bigwig" />
            <param name="format" value="bigwig" />
            <param name="mapping" value="name_mapping.csv" />
            <param name="reference" value="renamed_reference.fasta" />
            <output name="output" file="rename_sequence_cov.bigwig" />
        </test>
    </tests>
    <help><![CDATA[
    This tool is to rename scaffold names in the custom track files, so that the tracks use the same scaffold names as the reference genome renamed by "rename the scaffolds" tool
    ]]></help>
    <citations>
    </citations>
</tool>