view spectrast_filter.xml @ 4:c9bfe6adb7cd draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 592d86797e58318bad77de7c7de253056218cd1e-dirty

<tool id="spectrast_filter" name="SpectraST Filter" version="@VERSION@.0">
    <description>Filter and Manipulate Spectral Libraries</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/spectrast_params.py 
           --mode=filter
           #if $spectrastParams:
               '$spectrastParams'
           #end if
           '$spectrast_params' -o spectrast_create.params &&
        mkdir -p outdir &&
        spectrast -cFspectrast_create.params -cN'outdir/library' 
        #for $splib_file in $splib_files:
            ${splib_file.extra_files_path}/library.splib
        #end for
        &&
        mkdir -p '$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_MANIPULATION_OPTIONS@
        </configfile>
    </configfiles>
    <inputs>
        <param name="splib_files" multiple="true" type="data" format="splib" label="Spectral Libraries to operate on" help=""/>
        <param name="spectrastParams" type="data" format="txt" optional="true" label="SpectraST param file" help=""/>
        <expand macro="library_create_options"/>
        <expand macro="library_manipulation_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 format="splib" name="output"/>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Filter and Manipulate Spectral Libraries

]]>
    </help>
</tool>