comparison encyclopedia_encyclopedia.xml @ 6:61692bb2c78f draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 17dcc85ebd7507af5557a1aee4816ac437a3f27b"

5:aeda6093dd40

            <option value="first_rt_fit_pdf" selected="false">encyclopedia.txt.first.rt_fit.pdf</option>
            <option value="first_rt_fit_txt" selected="false">encyclopedia.txt.first.rt_fit.txt</option>
            <option value="final_delta_rt_pdf" selected="false">encyclopedia.txt.final.delta_rt.pdf</option>
            <option value="final_rt_fit_pdf" selected="false">encyclopedia.txt.final.rt_fit.pdf</option>
            <option value="final_rt_fit_txt" selected="false">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="false">encyclopedia.decoy.txt</option>
        </param>
    </inputs>
    <outputs>

    <tests>
        <test>
            <param name="scan_input" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML"/>
            <param name="library" ftype="elib" value="BCS_hela.elib"/>
            <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
            <output name="features" ftype="tabular">
                <assert_contents>
                    <has_text text="ESYDDVSSFR"/>
                </assert_contents>
            </output>

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 
  - The identified proteins in tabular format 

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

6:61692bb2c78f

            <option value="first_rt_fit_pdf" selected="false">encyclopedia.txt.first.rt_fit.pdf</option>
            <option value="first_rt_fit_txt" selected="false">encyclopedia.txt.first.rt_fit.txt</option>
            <option value="final_delta_rt_pdf" selected="false">encyclopedia.txt.final.delta_rt.pdf</option>
            <option value="final_rt_fit_pdf" selected="false">encyclopedia.txt.final.rt_fit.pdf</option>
            <option value="final_rt_fit_txt" selected="false">encyclopedia.txt.final.rt_fit.txt</option>
            <option value="features" selected="false">features.txt</option>
            <option value="encyclopedia" selected="true">encyclopedia.txt</option>
            <option value="encyclopedia_decoy" selected="false">encyclopedia.decoy.txt</option>
        </param>
    </inputs>
    <outputs>

    <tests>
        <test>
            <param name="scan_input" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML"/>
            <param name="library" ftype="elib" value="BCS_hela.elib"/>
            <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
            <param name="select_outputs" values="log,features,encyclopedia"/>
            <output name="features" ftype="tabular">
                <assert_contents>
                    <has_text text="ESYDDVSSFR"/>
                </assert_contents>
            </output>

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
  - A Chromatogram Library (.elib)
  - The identified features in tabular format
    Feature values of scans that are used by percolator to determine matches.
  - The identified Peptide Spectral Match results in tabular format
    Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
  - The identified peptides in tabular format
    Per peptide: the normalized intensity for each scan file.
    Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
  - The identified proteins in tabular format
    Per protein: the normalized intensity for each scan file.
    Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...

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