comparison spectrast_create.xml @ 12:f6fd2798879a draft default tip

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

11:cf953fb3f0c0

<tool id="spectrast_create_1" name="SpectraST Create" 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>Create Spectral Libraries</description>

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

	<command>
        spectrast_create.rb --galaxy 

        #for $pepxml_file in $pepxml_files:
        ${pepxml_file}
        #end for

        --spectrum-files='$spectrum_files'

        --predicate 'Protein!~$decoy_prefix_string'

        --p-thresh $p_thresh

        --instrument-acquisition $instrument_acquisition

        -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="pepxml_files" multiple="true" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml" label="PepXML Files to use in library generation" help=""/>
	
        <param name="spectrum_files" multiple="true" type="data" format="mzml" label="Data files containing spectra referred to in pepxml files" help=""/>

        <param name="decoy_prefix_string" help="String to identify decoys. All decoys wil be excluded" type="text" value="decoy" label="Decoy String" size="20"/> 

        <param name="instrument_acquisition" help="Set the instrument and acquisition settings of the spectra (in case not specified in data files).
                                 Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra." type="text" value="CID-QTOF" label="Decoy String" size="20"/>

        <param name="p_thresh" help="Matches scoring less than this value are discarded" type="float" value="0.99" min="0" max="1" label="Probability Threshold"/>
	
    </inputs>

      <outputs>
        <data format="splib" name="output"/>
      </outputs>

</tool>

12:f6fd2798879a

<tool id="spectrast_create_1" name="SpectraST Create" version="1.0.0">
    <description>Create 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_create.rb --galaxy

        #for $pepxml_file in $pepxml_files:
            ${pepxml_file}
        #end for

        --spectrum-files='$spectrum_files'
        --predicate 'Protein!~$decoy_prefix_string'
        --p-thresh $p_thresh
        --instrument-acquisition $instrument_acquisition
        -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="pepxml_files" multiple="true" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml" label="PepXML Files to use in library generation" help=""/>
        <param name="spectrum_files" multiple="true" type="data" format="mzml" label="Data files containing spectra referred to in pepxml files" help=""/>
        <param name="decoy_prefix_string" help="String to identify decoys. All decoys wil be excluded" type="text" value="decoy" label="Decoy String" size="20"/> 
        <param name="instrument_acquisition" type="text" value="CID-QTOF" label="Decoy String" size="20" 
            help="Set the instrument and acquisition settings of the spectra (in case not specified in data files).
            Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra."/>
        <param name="p_thresh" type="float" value="0.99" min="0" max="1" label="Probability Threshold"
            help="Matches scoring less than this value are discarded" />
    </inputs>
    <outputs>
        <data format="splib" name="output"/>
    </outputs>
    <help>
<![CDATA[
**What it does**

Create Spectral Libraries.

]]>
    </help>
</tool>