annotate encyclopedia_encyclopedia.xml @ 3:a3db9a8cf1b5 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit e3a6bfbf90e9ee3efeb6ff6517074bcc69f8d424"

<tool id="encyclopedia_encyclopedia" name="EncyclopeDIA" version="@VERSION@.0">
    <description>Library Searching Directly from Data-Independent Acquisition (DIA) MS/MS Data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @CMD_IMPORTS@
        @LINK_SCAN_INPUT@
        @LINK_FASTA_INPUT@
        @LINK_LIB_INPUT@
        EncyclopeDIA -Djava.awt.headless=true
        @SCAN_INPUT@
        @FASTA_INPUT@
        @LIB_INPUT@
        @COMMON_OPTIONS@
        @MASS_LIBRARY_TOLERANCE@
        @PERCOLATOR_OPTIONS@
        @PEAK_OPTIONS@
        @WINDOW_OPTIONS@
        @MODIFICATION_OPTIONS@
        -o gxpedia
    ]]></command>
    <inputs>
        <expand macro="scan_input"/>
        <expand macro="fasta_input"/>
        <expand macro="lib_input" optional="false" libhelp="Chromatogram elib from SearchToLib on pooled samples"/>
        <expand macro="options_section"/>
        <param name="select_outputs" type="select" label="Select outputs" multiple="true">
            <option value="log" selected="true">log</option>
            <option value="elib" selected="true">elib</option>
            <option value="first_delta_rt_pdf" selected="true">encyclopedia.txt.first.delta_rt.pdf</option>
            <option value="first_rt_fit_pdf" selected="true">encyclopedia.txt.first.rt_fit.pdf</option>
            <option value="first_rt_fit_txt" selected="true">encyclopedia.txt.first.rt_fit.txt</option>
            <option value="final_delta_rt_pdf" selected="true">encyclopedia.txt.final.delta_rt.pdf</option>
            <option value="final_rt_fit_pdf" selected="true">encyclopedia.txt.final.rt_fit.pdf</option>
            <option value="final_rt_fit_txt" selected="true">encyclopedia.txt.final.rt_fit.txt</option>
            <option value="features" selected="true">features.txt</option>
            <option value="encyclopedia" selected="true">encyclopedia.txt</option>
            <option value="encyclopedia_decoy" selected="true">encyclopedia.decoy.txt</option>
        </param>
    </inputs>
    <outputs>
        <data name="log" format="txt" label="${tool.name} ${on_string} log" from_work_dir="gxpedia.log">
            <filter>'log' in select_outputs</filter>
        </data>
        <data name="elib" format="elib" label="${tool.name} ${on_string} elib" from_work_dir="gxpedia.elib">
            <filter>'elib' in select_outputs</filter>
        </data>
        <data name="first_delta_rt_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.first.delta_rt.pdf" from_work_dir="gxpedia.encyclopedia.txt.first.delta_rt.pdf">
            <filter>'first_delta_rt_pdf' in select_outputs</filter>
        </data>
        <data name="first_rt_fit_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.first.rt_fit.pdf" from_work_dir="gxpedia.encyclopedia.txt.first.rt_fit.pdf">
            <filter>'first_rt_fit_pdf' in select_outputs</filter>
        </data>
        <data name="first_rt_fit_txt" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt.first.rt_fit.txt" from_work_dir="gxpedia.encyclopedia.txt.first.rt_fit.txt">
            <filter>'first_rt_fit_txt' in select_outputs</filter>
            <actions>
                <action name="column_names" type="metadata" default="library,actual,warpToActual,delta,fitProb,isDecoy,sequence" />
            </actions>
        </data>
        <data name="final_delta_rt_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.final.delta_rt.pdf" from_work_dir="gxpedia.encyclopedia.txt.final.delta_rt.pdf">
            <filter>'final_delta_rt_pdf' in select_outputs</filter>
        </data>
        <data name="final_rt_fit_pdf" format="pdf" label="${tool.name} ${on_string} encyclopedia.txt.final.rt_fit.pdf" from_work_dir="gxpedia.encyclopedia.txt.final.rt_fit.pdf">
            <filter>'final_rt_fit_pdf' in select_outputs</filter>
        </data>
        <data name="final_rt_fit_txt" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt.final.rt_fit.txt" from_work_dir="gxpedia.encyclopedia.txt.final.rt_fit.txt">
            <filter>'final_rt_fit_txt' in select_outputs</filter>
            <actions>
                <action name="column_names" type="metadata" default="library,actual,warpToActual,delta,fitProb,isDecoy,sequence" />
            </actions>
        </data>
        <data name="features" format="tabular" label="${tool.name} ${on_string} features.txt" from_work_dir="gxpedia.features.txt">
            <filter>'features' in select_outputs</filter>
            <actions>
                <action name="column_names" type="metadata" default="id,TD,ScanNr,topN,deltaCN,primary,xCorrLib,xCorrModel,LogDotProduct,logWeightedDotProduct,sumOfSquaredErrors,weightedSumOfSquaredErrors,numberOfMatchingPeaks,numberOfMatchingPeaksAboveThreshold,averageAbsFragmentDeltaMass,averageFragmentDeltaMasses,isotopeDotProduct,averageAbsParentDeltaMass,averageParentDeltaMass,eValue,deltaRT,pepLength,charge2,charge3,precursorMz,RTinMin,sequence,protein" />
            </actions>
        </data>
        <data name="encyclopedia" format="tabular" label="${tool.name} ${on_string} encyclopedia.txt" from_work_dir="gxpedia.encyclopedia.txt">
            <filter>'encyclopedia' in select_outputs</filter>
            <actions>
                <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
            </actions>
        </data>
        <data name="encyclopedia_decoy" format="tabular" label="${tool.name} ${on_string} encyclopedia.decoy.txt" from_work_dir="gxpedia.encyclopedia.decoy.txt">
            <filter>'encyclopedia_decoy' in select_outputs</filter>
            <actions>
                <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
            </actions>
        </data>
    </outputs>
    <help><![CDATA[
**EncyclopeDIA**

@ENCYCLOPEDIA_WIKI@

EncyclopeDIA extracts peptide fragmentation chromatograms from MZML files, matches them to spectra in libraries, and calculates various scoring features. These features are interpreted by Percolator to identify peptides.


**Inputs**


  - A spectrum file in mzML format
  - A chromatogram library that can be generated by SearchToLib 
  - A protein data base in fasta format


@MSCONVERT_HELP@

**Outputs**

  - A log file
  - The identified features in tabular format 

    ]]></help>
    <expand macro="citations" />
</tool>