Mercurial > repos > galaxyp > idpquery
annotate idpquery.xml @ 0:4c1e8f2243ce draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
| author | galaxyp |
|---|---|
| date | Tue, 15 Sep 2015 17:10:20 -0400 |
| parents | |
| children | 9682d5d021ab |
| rev | line source |
|---|---|
|
0
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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1 <?xml version="1.0"?> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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2 <tool id="idpquery" name="idpQuery" version="0.1.0"> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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3 <description>Creates text reports from idpDB files.</description> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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4 <macros> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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5 <xml name="proteinGroupByColumns"> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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6 <param name="report_columns" type="select" label="Select report columns" display="checkboxes" multiple="true"> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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7 <option value="Accession" selected="true">Accession</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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8 <option value="GeneId">Gene Id</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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9 <option value="GeneGroup">Gene Group</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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10 <option value="DistinctPeptides">Distinct Peptides</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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11 <option value="DistinctMatches">Distinct Matches</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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12 <option value="FilteredSpectra">Filtered Spectra</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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13 <option value="IsDecoy">Is Decoy</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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14 <option value="Cluster">Cluster</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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15 <option value="ProteinGroup">Protein Group</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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16 <option value="Length">Length</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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17 <option value="PercentCoverage">Percent Coverage</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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18 <option value="Sequence">Sequence</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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19 <option value="Description">Description</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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20 <option value="TaxonomyId">Taxonomy Id</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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21 <option value="GeneName">Gene Name</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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22 <option value="GeneFamily">Gene Family</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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23 <option value="Chromosome">Chromosome</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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24 <option value="GeneDescription">Gene Description</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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25 <option value="PrecursorIntensity">Precursor Intensity</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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26 <option value="PrecursorArea">Precursor Area</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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27 <option value="PrecursorBestSNR">Precursor Best SNR</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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28 <option value="PrecursorMeanSNR">Precursor Mean SNR</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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29 <option value="iTRAQ4plex">iTRAQ 4-plex</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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30 <option value="iTRAQ8plex">iTRAQ 8-plex</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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31 <option value="TMT2plex">TMT 2-plex</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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32 <option value="TMT6plex">TMT 6-plex</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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33 <option value="TMT10plex">TMT 10-plex</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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34 <option value="PivotMatchesByGroup">Pivot Matches By Group</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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35 <option value="PivotMatchesBySource">Pivot Matches By Source</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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36 <option value="PivotPeptidesByGroup">Pivot Peptides By Group</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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37 <option value="PivotPeptidesBySource">Pivot Peptides By Source</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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38 <option value="PivotSpectraByGroup">Pivot Spectra By Group</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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39 <option value="PivotSpectraBySource">Pivot Spectra By Source</option> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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40 <option value="PivotPrecursorIntensityByGroup">Pivot Precursor Intensity By Group</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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41 <option value="PivotPrecursorIntensityBySource">Pivot Precursor Intensity By Source</option> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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42 <option value="PivotPrecursorAreaByGroup">Pivot Precursor Area By Group</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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43 <option value="PivotPrecursorAreaBySource">Pivot Precursor Area By Source</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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44 <option value="PivotPrecursorBestSNRByGroup">Pivot Precursor Best SNR By Group</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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45 <option value="PivotPrecursorBestSNRBySource">Pivot Precursor Best SNR By Source</option> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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46 <option value="PivotPrecursorMeanSNRByGroup">Pivot Precursor Mean SNR By Group</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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47 <option value="PivotPrecursorMeanSNRBySource">Pivot Precursor Mean SNR By Source</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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48 <option value="PivotITRAQByGroup">Pivot iTRAQ By Group</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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49 <option value="PivotITRAQBySource">Pivot iTRAQ By Source</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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50 <option value="PivotTMTByGroup">Pivot TMT By Group</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
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51 <option value="PivotTMTBySource">Pivot TMT By Source</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
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52 <option value="PeptideGroups">Peptide Groups</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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53 <option value="PeptideSequences">Peptide Sequences</option> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
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54 </param> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
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55 </xml> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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changeset
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56 </macros> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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changeset
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57 <requirements> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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changeset
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58 <requirement type="package" version="3.0.8789">bumbershoot</requirement> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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changeset
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59 </requirements> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
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60 <stdio> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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changeset
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61 <exit_code range="1:" level="fatal" description="Job Failed" /> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
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62 <regex match="^Error:.*$" source="both" level="fatal" /> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
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63 </stdio> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
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64 <command> |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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65 <![CDATA[ |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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66 #set $input_name = $input.display_name |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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67 #set $output_name = $input_name.split(".")[0] + ".tsv" |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
68 ln -s '$input' '${input_name}' && |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
69 |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
70 idpQuery $group_by.group_by_value $group_by.report_columns '${input_name}' && |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
71 mv '$output_name' output |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
72 ]]> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
73 </command> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
74 <inputs> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
75 <param name="input" type="data" format="idpdb" label="Input File" multiple="false" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
76 <conditional name="group_by"> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
77 <param name="group_by_value" type="select" label="What proteomic entity do you want to group by?" help="Only protein- and gene-centric entities are currently supported."> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
78 <option value="Protein" selected="true">Protein</option> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
79 <option value="ProteinGroup">Protein Group</option> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
80 <option value="Gene">Gene</option> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
81 <option value="GeneGroup">Gene Group</option> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
82 </param> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
83 <when value="Protein"> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
84 <expand macro="proteinGroupByColumns" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
85 </when> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
86 <when value="ProteinGroup"> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
87 <expand macro="proteinGroupByColumns" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
88 </when> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
89 <when value="Gene"> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
90 <expand macro="proteinGroupByColumns" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
91 </when> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
92 <when value="GeneGroup"> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
93 <expand macro="proteinGroupByColumns" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
94 </when> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
95 </conditional> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
96 </inputs> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
97 <outputs> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
98 <data format="tabular" name="output" from_work_dir="output" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
99 </outputs> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
100 <tests> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
101 <test> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
102 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
103 <param name="group_by_value" value="Protein" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
104 <param name="report_columns" value="Accession,FilteredSpectra,Description" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
105 <output name="output" file="201203-624176-12-mm-gui-test-Protein-Accession,FilteredSpectra,Description.tsv" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
106 </test> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
107 <test> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
108 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
109 <param name="group_by_value" value="ProteinGroup" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
110 <param name="report_columns" value="ProteinGroup,Accession,PercentCoverage" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
111 <output name="output" file="201203-624176-12-mm-gui-test-ProteinGroup-ProteinGroup,Accession,PercentCoverage.tsv" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
112 </test> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
113 <test> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
114 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
115 <param name="group_by_value" value="Gene" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
116 <param name="report_columns" value="GeneId,Accession,DistinctPeptides" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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|
117 <output name="output" file="201203-624176-12-mm-gui-test-Gene-GeneId,Accession,DistinctPeptides.tsv" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
118 </test> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
119 <test> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
120 <param name="input" value="201203-624176-12-mm-gui-test.idpDB" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
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|
121 <param name="group_by_value" value="GeneGroup" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
122 <param name="report_columns" value="GeneGroup,GeneId,DistinctMatches" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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diff
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|
123 <output name="output" file="201203-624176-12-mm-gui-test-GeneGroup-GeneGroup,GeneId,DistinctMatches.tsv" /> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
124 </test> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
125 </tests> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
126 <help> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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changeset
|
127 <![CDATA[ |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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128 **What it does** |
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4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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changeset
|
129 |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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parents:
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130 Creates user-configurable text reports from IDPicker 3 idpDB files. |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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parents:
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131 ]]> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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parents:
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132 </help> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
133 <citations> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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|
134 <citation type="doi">10.1021/pr900360j</citation> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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135 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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136 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
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|
137 </citations> |
|
4c1e8f2243ce
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpquery commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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138 </tool> |