Mercurial > repos > galaxyp > idpqonvert
annotate idpQonvertEmbedder.xml @ 6:4a4059471054 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
| author | galaxyp |
|---|---|
| date | Thu, 15 Dec 2016 17:20:42 -0500 |
| parents | eab42d2eace6 |
| children | 43c73fd96ce0 |
| rev | line source |
|---|---|
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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1 <?xml version="1.0"?> |
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4
eab42d2eace6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 2a4b1c0e842f356239c141ea7cad867d91607c6a
galaxyp
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2 <tool id="idpqonvertEmbedder" name="idpEmbedder" version="@VERSION@.0"> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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3 <description>Embed human/mouse gene metadata into IDPicker files</description> |
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4
eab42d2eace6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 2a4b1c0e842f356239c141ea7cad867d91607c6a
galaxyp
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4 <macros> |
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eab42d2eace6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 2a4b1c0e842f356239c141ea7cad867d91607c6a
galaxyp
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5 <import>macros.xml</import> |
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eab42d2eace6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 2a4b1c0e842f356239c141ea7cad867d91607c6a
galaxyp
parents:
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6 </macros> |
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eab42d2eace6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 2a4b1c0e842f356239c141ea7cad867d91607c6a
galaxyp
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7 <expand macro="requirements" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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8 <stdio> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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9 <exit_code range="1:" level="fatal" description="Job Failed" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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10 <regex match="\nError:.*\n" source="both" level="fatal" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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11 </stdio> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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12 <command> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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13 <![CDATA[ |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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14 #set $input_name = $input.display_name |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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15 cp '$input' output && |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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16 ln -s output output.idpDB && |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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17 ln -s \$(dirname \$(which idpQonvert))/gene2protein.db3 gene2protein.db3 && |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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18 |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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19 #if $use_raw_data_condition.use_raw_data |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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20 #for $i in $use_raw_data_condition.input_raw |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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21 ln -s '${i.file_name}' '${i.display_name}' && |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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22 #end for |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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23 #end if |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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24 |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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25 idpQonvert |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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26 -EmbedOnly true |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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27 -EmbedGeneMetadata $EmbedGeneMetadata |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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28 #if $use_raw_data_condition.use_raw_data |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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29 -EmbedSpectrumScanTimes $use_raw_data_condition.EmbedSpectrumScanTimes |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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30 -EmbedSpectrumSources $use_raw_data_condition.EmbedSpectrumSources |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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31 -QuantitationMethod $use_raw_data_condition.QuantitationMethod |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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32 #end if |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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33 output.idpDB |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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34 ]]> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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35 </command> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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36 <inputs> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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37 <param name="input" type="data" format="idpdb" label="Input idpDB file" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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38 <param argument="-EmbedGeneMetadata" type="boolean" value="true" label="Embed Gene Metadata?" help="Allows gene-centric analysis in IDPicker. The gene metadata embedding only works for human/mouse proteins from a RefSeq database. For best results, run idpQonvert with RefSeq no matter what database was used for the search: idpQonvert always remap the peptides anyway. Non-human/mouse proteins and any unmappable human/mouse proteins will get gene ids like "Unmapped_<protein accession>". This option, run by itself, is very fast." /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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39 <conditional name="use_raw_data_condition"> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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40 <param name="use_raw_data" type="boolean" label="Do you have the raw data (spectra)?" help="More embed options are available if the raw spectra are available." /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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41 <when value="false"></when> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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42 <when value="true"> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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43 <param name="input_raw" type="data" format="mzml,mzxml,mgf,ms2,mz5" label="Input raw MS files" multiple="true" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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44 <param argument="-EmbedSpectrumSources" type="boolean" value="false" label="Embed Spectrum Sources?" help="Allows visualizing peptide-spectrum-matches without downloading the raw data. Embedding spectra will greatly increase the size of the database, even though only spectra that passed the import FDR filter will be included. This option can take a LONG time to run." /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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45 <param argument="-EmbedSpectrumScanTimes" type="boolean" value="false" label="Embed Spectrum Scan Times?" help="If the pepXML/mzIdentML file did not contain scan time (retention time) information, this will look up that information in the raw data. This option, run by itself, will take some time (it has to open every raw file)." /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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46 <param argument="-QuantitationMethod" type="select" label="Quantitation Method" help="Enables quantitation methods other than spectral counting. For isobaric isotope labelling quantitation (iTRAQ/TMT) or intensity-based label-free quantitation (XIC), select the appropriate QuantitationMethod here. You have to keep iTRAQ/TMT and label-free data separate since you can only specify a single QuantitationMethod for the entire assembly. Like embedding spectrum sources, this option can take a LONG time to run, although not quite as long."> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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47 <option value="None" selected="true">None</option> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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48 <option value="LabelFree">Label-free (XIC)</option> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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49 <option value="ITRAQ4plex">iTRAQ 4-plex</option> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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50 <option value="ITRAQ8plex">iTRAQ 8-plex</option> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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51 <option value="TMT2plex">TMT 2-plex</option> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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52 <option value="TMT6plex">TMT 6-plex</option> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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53 <option value="TMT10plex">TMT 10-plex</option> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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54 </param> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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55 </when> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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56 </conditional> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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57 </inputs> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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58 <outputs> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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59 <data format="idpdb" name="output" from_work_dir="output" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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60 </outputs> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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61 <tests> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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62 <test> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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63 <param name="input" value="input/201208-378803.idpDB" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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64 <param name="EmbedGeneMetadata" value="false" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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65 <output name="output" file="input/201208-378803.idpDB" compare="sim_size" delta="500000" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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66 </test> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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changeset
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67 <test> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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68 <param name="input" value="input/201208-378803.idpDB" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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69 <param name="EmbedGeneMetadata" value="true" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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70 <output name="output" file="201208-378803-embeddedGenes.idpDB" compare="sim_size" delta="500000" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
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71 </test> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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72 <test> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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73 <param name="input" value="input/201208-378803.idpDB" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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74 <param name="EmbedGeneMetadata" value="true" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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75 <param name="use_raw_data" value="true" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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76 <param name="input_raw" value="input/201208-378803.mzML" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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77 <param name="EmbedSpectrumSources" value="false" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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78 <param name="EmbedSpectrumScanTimes" value="true" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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79 <param name="QuantitationMethod" value="None" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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80 <output name="output" file="201208-378803-embeddedGenesAndScanTimes.idpDB" compare="sim_size" delta="500000" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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81 </test> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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82 <test> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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83 <param name="input" value="input/201208-378803.idpDB" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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84 <param name="EmbedGeneMetadata" value="true" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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|
85 <param name="use_raw_data" value="true" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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86 <param name="input_raw" value="input/201208-378803.mzML" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
87 <param name="EmbedSpectrumSources" value="true" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
88 <param name="EmbedSpectrumScanTimes" value="false" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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changeset
|
89 <param name="QuantitationMethod" value="None" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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|
90 <output name="output" file="201208-378803-embeddedGenesAndSpectra.idpDB" compare="sim_size" delta="500000" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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|
91 </test> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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|
92 <test> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
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|
93 <param name="input" value="input/201208-378803.idpDB" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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changeset
|
94 <param name="EmbedGeneMetadata" value="true" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
diff
changeset
|
95 <param name="use_raw_data" value="true" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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|
96 <param name="input_raw" value="input/201208-378803.mzML" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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diff
changeset
|
97 <param name="EmbedSpectrumSources" value="false" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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98 <param name="EmbedSpectrumScanTimes" value="true" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
parents:
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99 <param name="QuantitationMethod" value="ITRAQ4plex" /> |
|
2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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100 <output name="output" file="201208-378803-embeddedGenesAndQuantitation.idpDB" compare="sim_size" delta="500000" /> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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101 </test> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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102 </tests> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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103 <help> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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104 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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105 **What it does** |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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106 |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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107 Embeds optional data and metadata into the IDPicker 3 idpDB files. This should be run after all idpDB files have been merged together (e.g. after idpAssemble). |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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108 ]]> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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109 </help> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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110 <citations> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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111 <citation type="doi">10.1021/pr900360j</citation> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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112 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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113 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
galaxyp
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114 </citations> |
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2eecd0b031d0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 3b8a4b0b93d2270f3a31fe67d7c09c73046ceb4c-dirty
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115 </tool> |