comparison pep_match.xml @ 2:bf6acfb148a8 draft default tip

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper commit 040d09319fb0f43fafb1d3ebd99af41bce0f6bfd

1:c57d7d83f3f8

<tool id="peptimapper_pep_match" name="PepMatch" version="2.0">
    <description>align PSTs on sequence and cluster hits</description>
    <requirements>
        <container type="docker">dockerprotim/peptimapper</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
ln -s '$fastafile' 'in.fa' &&
ln -s '$tagsfile' 'in.tags' &&
LXRunPepMatch -D $D -t $t -T $T -d $d 'in.fa' 'in.tags' &&
mv 'in.tags.in.fa.trans.${D}.hit' ${hitsfile} &&
mv 'in.tags.in.fa.trans.${D}.hit.${t}.${T}.${d}.clust' '${clustersfile}'
    ]]></command>
    <inputs>
        <param name="tagsfile" type="data" format="txt" label="PSTs file (Text)" help="Peptide sequence tags file generated by PepnovoTag" />
        <param name="fastafile" type="data" format="fasta" label="Chromosome file (Fasta)" help="Chromosome file" />

        <param name="D" type="select" label="Mass tolerance" help="uma">
            <option value="0.5" selected="selected">0.5</option>
            <option value="0.25">0.25</option>
            <option value="0.025">0.025</option>
            <option value="0.0025">0.0025</option>
            <option value="0">0</option>
        </param>

        <param name="t" type="select" label="Min. hits" help="Minimal hits number per cluster">
            <option value="2" selected="selected">2</option>
            <option value="3">3</option>
            <option value="4">4</option>
        </param>

        <param name="T" type="select" label="Min. peptides" help="Minimal peptides number per cluster">
            <option value="2" selected="selected">2</option>
            <option value="3">3</option>
            <option value="4">4</option>
        </param>

        <param name="d" type="select" label="Distance" help="Maximum distance between two hits to be clustered">
            <option value="500">500</option>
            <option value="1000">1000</option>
            <option value="2000">2000</option>
            <option value="5000" selected="selected">5000</option>
            <option value="10000">10000</option>
            <option value="15000">15000</option>
            <option value="20000">20000</option>
            <option value="50000">50000</option>
            <option value="80000">80000</option>

2:bf6acfb148a8

<tool id="peptimapper_pep_match" name="PepMatch" version="2.1">
    <description>align PSTs on sequence and cluster hits</description>
    <requirements>
        <container type="docker">dockerprotim/peptimapper@sha256:d3eb807d7d5aa155f7b39d05a47420e0a0a9191d5fa867b6ca1be763f8a23bf1</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
ln -s '$fastafile' 'in.fa' &&
ln -s '$tagsfile' 'in.tags' &&
LXRunPepMatch -D $D -t $t -T $T -d $d 'in.fa' 'in.tags' &&
mv 'in.tags.in.fa.trans.${D}.hit' '${hitsfile}' &&
mv 'in.tags.in.fa.trans.${D}.hit.${t}.${T}.${d}.clust' '${clustersfile}'
    ]]></command>
    <inputs>
        <param name="tagsfile" type="data" format="txt" label="PSTs file (Text)" help="Peptide sequence tags file generated by PepnovoTag" />
        <param name="fastafile" type="data" format="fasta" label="Chromosome file (Fasta)" help="Chromosome file" />

        <param name="D" type="select" label="Mass tolerance" help="uma">
            <option value="0.5" selected="true">0.5</option>
            <option value="0.25">0.25</option>
            <option value="0.025">0.025</option>
            <option value="0.0025">0.0025</option>
            <option value="0">0</option>
        </param>

        <param name="t" type="select" label="Min. hits" help="Minimal hits number per cluster">
            <option value="2" selected="true">2</option>
            <option value="3">3</option>
            <option value="4">4</option>
        </param>

        <param name="T" type="select" label="Min. peptides" help="Minimal peptides number per cluster">
            <option value="2" selected="true">2</option>
            <option value="3">3</option>
            <option value="4">4</option>
        </param>

        <param name="d" type="select" label="Distance" help="Maximum distance between two hits to be clustered">
            <option value="500">500</option>
            <option value="1000">1000</option>
            <option value="2000">2000</option>
            <option value="5000" selected="true">5000</option>
            <option value="10000">10000</option>
            <option value="15000">15000</option>
            <option value="20000">20000</option>
            <option value="50000">50000</option>
            <option value="80000">80000</option>