view rename_tracks.xml @ 1:72ccb2f848a0 draft default tip

planemo upload commit 869adf4bb92923a8a5cb0d62ae40cdab9bf6e1d7

<tool id="rename_tracks" name="rename the tracks" version="1.3">
<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>