view spectrast_create.xml @ 3:7f02fc51bddf draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty

<tool id="specrast_create" name="SpectraST Create" version="@VERSION@.0">
    <description>Spectral Library from Search Results</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        ## Need to symlink to data using name with extension that spectrast recognizes 
        #import re
        ## pepxml datasets
        #set $input_files = []
        #for $px in $pepxml_files:
            #set $input_name = $re.sub('[.]?pep[.]?xml$','',$re.sub('[ ]','_',$input.display_name.split('/')[-1])) + '.pep.xml' 
            #silent $input_files.append($input_name)
            ln -s -f '${px}' '${input_name}' &&
        #end for
        #set $input_names = ' '.join($input_files)
        python $__tool_directory__/link_scan_datasets.py
            #for spectrum_file in spectrum_files:
                -n '$spectrum_file.display_name' -f '$spectrum_file'
            #end for
            $input_names &&
        python $__tool_directory__/spectrast_params.py 
           --mode=create
           #if $spectrastParams:
               '$spectrastParams'
           #end if
           '$spectrast_params' -o spectrast_create.params &&
        mkdir -p libdir &&
        spectrast -cFspectrast_create.params -cN'libdir/library' $input_names &&
        mkdir -p '$output.files_path' &&
        for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/${i} ]; then cp -p outdir/${i} '$output.files_path'; fi; done
    ]]></command>
    <configfiles>
        <configfile name="spectrast_params"><![CDATA[#slurp
]]>
@LIBRARY_CREATE_OPTIONS@
@LIBRARY_IMPORT_OPTIONS@
        </configfile>
    </configfiles>
    <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="mzxml" label="Data files containing spectra referred to in pepxml files" help=""/>
        <param name="spectrastParams" type="data" format="txt" optional="true" label="SpectraST param file" help=""/>
        <expand macro="library_create_options"/>
        <expand macro="library_import_options"/>
    </inputs>
    <outputs>
        <data name="log" format="txt" label="spectrast.log" from_work_dir="spectrast.log"/>
        <data name="params" format="txt" label="spectrast_create.params" from_work_dir="spectrast_create.params"/>
        <expand macro="library_create_outputs"/>
        <data name="output" format="splib" label="libary.splib" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help><![CDATA[
**Create Libraries from Sequence Search Results**

Note: As per TPP convention, the spectrum query must be named:
<mzXML file name>.<start scan>.<end scan>.<charge>
in the .pepXML file, so that SpectraST knows where to find the corresponding experimental spectrum. (If the .pepXML file is created with TPP tools, this should not be an issue.)

SpectraST can create a spectral library from a .pepXML file, which contains peptide identifications from a previous shotgun proteomics experiment. For this purpose, it is preferable that the .pepXML has been processed with PeptideProphet and/or iProphet, such that all the search hits have probabilities assigned. (iProphet probabilities are used over PeptideProphet ones if both are present.)

When importing from a .pepXML file, SpectraST scans through the .pepXML file for confident identifications, and attempts to extract the corresponding experimental spectra from .mzXML files. 
    ]]></help>
    <expand macro="citations" />
</tool>