view utils_fix-fasta-headers.xml @ 5:b7cf9b172cfe draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b97b90c692604239ed6e9423655c6c5d05798b32-dirty

<tool id="smf_utils_fix-fasta-headers" name="fix-fasta-headers" version="@VERSION@-1">
    <description>Replaces all spaces with underscores in the ">.."-sequence headers of a FASTA file</description>
    
    <macros>
        <import>macros.xml</import>
    </macros>
    
    <requirements>
        <requirement type="package" version="2.7.10">python</requirement>
        <requirement type="package" version="1.9">numpy</requirement>
        <requirement type="package" version="0.8.2.1">pysam</requirement>
        <requirement type="package" version="0.6.1">htseq</requirement>
        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>
    </requirements>
    
    <expand macro="stdio" />

    <version_command>@VERSION_COMMAND_UTILS@</version_command>
    
    <command><![CDATA[
        segmentation-fold-utils
            fix-fasta-headers
                '${fasta_input}'
                '${fasta_output}'
    ]]></command>

    <inputs>
        <param name="fasta_input"
               type="data"
               format="fasta"
               argument="-f"
               label="Fasta file with RNA-sequece" />
    </inputs>

    <outputs>
        <data format="fasta"
              name="fasta_output"
              label="${tool.name} on ${str($fasta_input.hid) + ': ' + $fasta_input.name}" />
    </outputs>

    <tests>
        <test>
            <param name="fasta_input" value="test_22.fa" format="fasta" />
            
            <output name="fasta_output" file="test_22.fixed.fa" />
        </test>
        <test>
            <param name="fasta_input" value="test_23.fa" format="fasta" />
            
            <output name="fasta_output" file="test_23.fixed.fa" />
        </test>
    </tests>
    
    <help><![CDATA[
Replaces all spaces with underscores in the ">.."-sequence headers of a FASTA file for compatibility with pysam indexing.
    ]]></help>
    
    <expand macro="citations" />
</tool>