comparison hicup_digester.xml @ 4:a2f3a4129052 draft

planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3

3:f6f324d0bb27

    <description>cuts throughout a selected genome at one or two specified restriction sites.</description>
    <macros>
        <import>hicup_macros.xml</import>
    </macros>
    <expand macro="requirements_hicup" />
    <expand macro="stdio" />

    <command><![CDATA[
        hicup_digester --re1 '$re1' --genome '$genome'
        #if $advanced_options.re2:
            --re2 '$advanced_options.re2'
        #end if
        #for $file in $input_files_digest:
            $file
        #end for
        && mv *Digest_* digester_file.txt
    ]]></command>
    <inputs>
        <expand macro="digester_input" />
        <expand macro="re1" />   
        <section name="advanced_options" title="Advanced options">
            <expand macro="re2" />
        </section>
    </inputs>
    <outputs>
        <data name="digest_file" format="txt" from_work_dir="digester_file.txt" label="Digester File.txt"/>
    </outputs>
     <tests>
        <test>
            <param name="input_files_digest" value="chr1.fa"/>
            <param name="re1" value="A^AGCTT"/>
            <param name="genome" value="human"/>
            <output name="digest_file" file="digester_file.txt" lines_diff="4"/>
        </test>
    </tests>
    <help><![CDATA[

4:a2f3a4129052

    <description>cuts throughout a selected genome at one or two specified restriction sites.</description>
    <macros>
        <import>hicup_macros.xml</import>
    </macros>
    <expand macro="requirements_hicup" />
    <command detect_errors="exit_code"><![CDATA[
        hicup_digester --re1 '$re1' --genome '$genome'
        #if $advanced_options.re2:
            --re2 '$advanced_options.re2'
        #end if
        #for $file in $input_files_digest:
            $file
        #end for
    ]]></command>
    <inputs>
        <param name="input_files_digest" type="data" multiple="true" format="fasta" label="Input DNA sequence files that should be digested"/>
        <param argument="--genome" type="text" label="Genome name"
            help="Name of the genome to be digested."/>
        <expand macro="re1" />
        <section name="advanced_options" title="Advanced options">
            <expand macro="re2" />
        </section>
    </inputs>
    <outputs>
        <data name="digest_file" format="txt" from_work_dir="Digest_*" label="Digester File.txt"/>
    </outputs>
     <tests>
        <test>
            <param name="input_files_digest" value="chr21And22FromHg38.fasta"/>
            <param name="re1" value="A^AGCTT"/>
            <param name="genome" value="chr21And22FromHg38"/>
            <output name="digest_file" file="digester_file.txt" lines_diff="4"/>
        </test>
    </tests>
    <help><![CDATA[