view utils_fix-fasta-headers.xml @ 6:4d16cf9414cf draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/segmentation_fold commit 3a3c1d069e0a079d8ea7c0b4ac856ef24141b1aa

<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>
    
    <expand macro="requirements" />
    <expand macro="version_command" />
    
    <command detect_errors="aggressive"><![CDATA[
        segmentation-fold-utils
            fix-fasta-headers
                '${fasta_input}'
                '${fasta_output}'
    ]]></command>

    <inputs>
        <param name="fasta_input"
               type="data"
               format="fasta"
               label="Fasta file with RNA-sequece"
               argument="-f" />
    </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" ftype="fasta" />
            
            <output name="fasta_output" file="test_22.fixed.fa" />
        </test>
        <test>
            <param name="fasta_input" value="test_23.fa" ftype="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>