comparison encyclopedia_encyclopedia.xml @ 1:b4f1a49ff3b5 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 81e7c4d3d6066b99ad50374292f340302dc4f02d"

0:36f9910c85c4

        -o gxpedia
    ]]></command>
    <inputs>
        <expand macro="scan_input"/>
        <expand macro="fasta_input"/>
        <expand macro="lib_input" token_optional="false" token_help="Chromatogram elib from SearchToLib"/>
        <expand macro="common_options"/>
        <expand macro="mass_library_tolerance"/>
        <expand macro="percolator_options"/>
        <expand macro="peak_options"/>
        <expand macro="window_options"/>

                <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
            </actions>
        </data>
    </outputs>
    <help><![CDATA[
EncyclopeDIA is a library search engine for DIA data.
You should prefix your arguments with a high memory setting, e.g. "-Xmx8g" for 8gb

Required Parameters:
	-i	input .DIA or .MZML file
	-f	protein .FASTA database
	-l	library .ELIB file

Other Parameters:
	-o	output report file (default: [input file].encyclopedia.txt)
	-acquisition                          (default: Non-Overlapping DIA)
	-enzyme                               (default: trypsin)
	-expectedPeakWidth                    (default: 25)
	-filterPeaklists                      (default: false)
	-fixed                                (default: C=57.0214635)
	-foffset                              (default: 0)
	-frag                                 (default: CID)
	-ftol                                 (default: 10)
	-ftolunits                            (default: ppm)
	-lftol                                (default: 10)
	-lftolunits                           (default: ppm)
	-localizationModification             (default: none)
	-minIntensity                         (default: -1.0)
	-minNumOfQuantitativePeaks            (default: 3)
	-minQuantitativeIonNumber             (default: 3)
	-numberOfExtraDecoyLibrariesSearched  (default: 0.0)
	-numberOfQuantitativePeaks            (default: 5)
	-percolatorProteinThreshold           (default: 0.01)
	-percolatorThreshold                  (default: 0.01)
	-percolatorVersionNumber              (default: 3)
	-poffset                              (default: 0)
	-precursorIsolationMargin             (default: 0)
	-precursorWindowSize                  (default: -1)
	-ptol                                 (default: 10)
	-ptolunits                            (default: ppm)
	-rtWindowInMin                        (default: -1.0)
	-scoringBreadthType                   (default: window)
	-verifyModificationIons               (default: true)

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

1:b4f1a49ff3b5

        -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="common_options"/>
        <expand macro="mass_library_tolerance"/>
        <expand macro="percolator_options"/>
        <expand macro="peak_options"/>
        <expand macro="window_options"/>

                <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>