view spectrast_filter.xml @ 11:cf953fb3f0c0 draft

Fix cheetah

<tool id="spectrast_filter_1" name="SpectraST Filter" version="1.0.0">
    <requirements>
        <container type="docker">iracooke/protk-1.4.2</container>
        <requirement type="package" version="1.4">protk</requirement>
        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
   </requirements>
   
	<description>Filter and Manipulate Spectral Libraries</description>

    <stdio>
        <exit_code range="1:" level="fatal" description="Job Failed" />
    </stdio>

	<command>
        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.extra_files_path};

        cp library.splib library.spidx library.pepidx  ${output.extra_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>

</tool>