view spectrast_filter.xml @ 12:f6fd2798879a draft default tip

planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty

<tool id="spectrast_filter_1" name="SpectraST Filter" version="1.0.0">
    <description>Filter and Manipulate Spectral Libraries</description>
    <requirements>
        <container type="docker">iracooke/protk-1.4.3</container>
        <requirement type="package" version="1.4.3">protk</requirement>
        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Job Failed" />
    </stdio>
    <command>
<![CDATA[
        spectrast_filter.rb  --merge $merge

        #for $splib_file in $splib_files:
            ${splib_file.extra_files_path}/library.splib
        #end for

        --replicates $replicates
        -o library

        &&

        mkdir -p ${output.files_path}

        &&

        cp library.splib library.spidx library.pepidx  ${output.files_path}/

        &&

        echo "Spectral Library Primary File" > $output
]]>
    </command>
    <inputs>
        <param name="splib_files" multiple="true" type="data" format="splib" label="Spectral Libraries to operate on" help=""/>
        <param name="merge" type="select" format="text">
            <label>Merge Method</label>
            <option value="U">Union</option>
            <option value="S">Subtraction</option>
            <option value="H">Subtraction of homologs</option>
            <option value="A">Appending</option>
        </param>

        <param name="replicates" type="select" format="text">
            <label>How to deal with replicate spectra</label>
            <option value="None">Keep All</option>
            <option value="C">Consensus</option>
            <option value="B">Best replicate</option>
        </param>
    </inputs>
    <outputs>
        <data format="splib" name="output"/>
    </outputs>
    <help>
<![CDATA[
**What it does**

Filter and Manipulate Spectral Libraries

]]>
    </help>
</tool>