comparison encyclopedia_walnut.xml @ 5:4936de9f9024 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"

4:2f36eba0b877

            <actions>
                <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
            </actions>
        </data>
    </outputs>
    <help><![CDATA[
Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data.
Walnut uses PeCAn-style scoring to extract peptide fragmentation chromatograms from MZML files, assign peaks, and calculate various peak features. These features are interpreted by Percolator to identify peptides.

Required Parameters: 
	-i	input .DIA or .MZML file
	-f	background FASTA file

Other Parameters: 
	-t	target FASTA file (default: background FASTA file)
	-tp	true/false target FASTA file contains peptides (default: false)
	-o	output report file (default: [input file].pecan.txt)
	-acquisition                          (default: overlapping dia)
	-addDecoysToBackground                (default: false)
	-alpha                                (default: 1.8)
	-beta                                 (default: 0.4)
	-dontRunDecoys                        (default: false)
	-enzyme                               (default: trypsin)
	-filterPeaklists                      (default: false)
	-fixed                                (default: C=57.0214635)
	-foffset                              (default: 0)
	-frag                                 (default: YONLY)
	-ftol                                 (default: 10)
	-ftolunits                            (default: ppm)
	-maxCharge                            (default: 3)
	-maxLength                            (default: 100)
	-maxMissedCleavage                    (default: 1)
	-minCharge                            (default: 2)
	-minEluteTime                         (default: 12)
	-minIntensity                         (default: -1.0)
	-minLength                            (default: 5)
	-minNumOfQuantitativePeaks            (default: 3)
	-minQuantitativeIonNumber             (default: 3)
	-numberOfQuantitativePeaks            (default: 5)
	-numberOfReportedPeaks                (default: 1)
	-numberOfThreadsUsed                  (default: 12)
	-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)
	-requireVariableMods                  (default: false)
	-variable                             (default: -)

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

5:4936de9f9024

            <actions>
                <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" />
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="scan_input" ftype="mzml" value="BCS_hela_narrow_3_1.mzML"/>
            <param name="fasta" ftype="fasta" value="uniprot_tiny_human.fasta"/>
            <output name="features" ftype="tabular">
                <assert_contents>
                    <has_text text="LHYNEGLNIK"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

    <help><![CDATA[

**Walnut**

@ENCYCLOPEDIA_WIKI@

Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data.
Walnut uses PeCAn-style scoring to extract peptide fragmentation chromatograms from MZML files, assign peaks, and calculate various peak features. These features are interpreted by Percolator to identify peptides.


**Inputs**


  - A spectrum file in mzML format
  - A protein data base in fasta format


@MSCONVERT_HELP@

**Outputs**

  - A log file
  - The identified features in tabular format 
  - The identified proteins in tabular format 

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