comparison commet.xml @ 5:d03353742508 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"

4:8c53dc8b4adb

<?xml version='1.0' encoding='utf-8'?>
<tool profile="16.04" id="commet" name="Commet" version="24.7.14">
    <description>COmpare Multiple METagenomes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="24.7.14">commet</requirement>
    </requirements>
    <command><![CDATA[
        #for $i, $set in enumerate( $sets )
            echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt &&
        #end for
        Commet.py
        -k ${k}
        -t ${t}
        -l ${l}
        -e ${e}
        #if str( $options_advanced.options_advanced_selector ) == "advanced"
            -m ${options_advanced.m}
            -n ${options_advanced.n}
        #end if
        commet_input_sets.txt

    ]]></command>

    <inputs>
        <!-- Input data files -->
        <repeat name="sets" title="Read sets" min="1">
            <param name="reads" type="data" multiple="true" format="fasta, fastq" label="Dataset" help="Accept fasta/fastq"/>
        </repeat>
        <param argument="-k" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
        <param argument="-t" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
        <param argument="-l" type="integer" label="Read mini length" value="66" help="Minimal length a read should have to be kept." />
        <param argument="-e" type="float" label="Mini Shannon index" value="0" min="0" max="2.32" help="Minimal Shannon index a read should have to be kept." />

    </outputs>
    <tests>
        <test>
            <param name="input_type" value="list" />
            <repeat name="sets">
                <param name="reads" value="commet/A.fa" ftype="fasta" />
            </repeat>
            <repeat name="sets">
                <param name="reads" value="commet/B.fa,commet/C.fa" ftype="fasta" />
            </repeat>
            <repeat name="sets">
                <param name="reads" value="commet/D.fa" ftype="fasta" />
            </repeat>
            <param name="plain_outputs" value="True"/>
            <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/>
            <output name="matrix_plain" file="commet/matrix_plain.csv"/>
        </test>

5:d03353742508

<tool id="commet" name="Commet" version="24.7.14+galaxy0" profile="@PROFILE@">
    <description>COmpare Multiple METagenomes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="24.7.14">commet</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #for $i, $set in enumerate($sets):
            echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt &&
        #end for
        Commet.py
        -k ${k}
        -t ${t}
        -l ${l}
        -e ${e}
        #if str($options_advanced.options_advanced_selector) == "advanced":
            -m ${options_advanced.m}
            -n ${options_advanced.n}
        #end if
        commet_input_sets.txt
    ]]></command>
    <inputs>
        <repeat name="sets" title="Read sets" min="1">
            <param name="reads" type="data" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" label="Dataset" help="Accept fasta/fastq"/>
        </repeat>
        <param argument="-k" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
        <param argument="-t" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
        <param argument="-l" type="integer" label="Read mini length" value="66" help="Minimal length a read should have to be kept." />
        <param argument="-e" type="float" label="Mini Shannon index" value="0" min="0" max="2.32" help="Minimal Shannon index a read should have to be kept." />

    </outputs>
    <tests>
        <test>
            <param name="input_type" value="list" />
            <repeat name="sets">
                <param name="reads" value="commet/A.fa.gz" ftype="fasta.gz" />
            </repeat>
            <repeat name="sets">
                <param name="reads" value="commet/B.fa.gz,commet/C.fa.gz" ftype="fasta.gz" />
            </repeat>
            <repeat name="sets">
                <param name="reads" value="commet/D.fa.gz" ftype="fasta.gz" />
            </repeat>
            <param name="plain_outputs" value="True"/>
            <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/>
            <output name="matrix_plain" file="commet/matrix_plain.csv"/>
        </test>