Mercurial > repos > galaxyp > idpqonvert
annotate idpQonvertEmbedder.xml @ 10:2ec9bd69259e draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 66973ea01088c809c3f7c3daa54233674c67fa45"
| author | galaxyp |
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| date | Fri, 12 Jun 2020 17:02:53 -0400 |
| parents | fb6ce5041417 |
| children |
| rev | line source |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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1 <?xml version="1.0"?> |
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10
2ec9bd69259e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 66973ea01088c809c3f7c3daa54233674c67fa45"
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2 <tool id="idpqonvertEmbedder" name="idpEmbedder" version="@VERSION@.1"> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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3 <description>Embed human/mouse gene metadata into IDPicker files</description> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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4 <macros> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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5 <import>macros.xml</import> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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6 <xml name="IsobaricQuantitationOptions" token_tolerance="0.015"> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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7 <param argument="-ReporterIonMzTolerance" type="float" min="0.000001" value="@TOLERANCE@" label="Tolerance window to search for iTRAQ/TMT reporter ions" help="The most intense ion in the tolerance window is used as the reporter ion intensity." /> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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diff
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8 <param name="ReporterIonMzTolerance_units" type="select" label="Tolerance units"> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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9 <option value="ppm">Parts per million</option> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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10 <option value="daltons" selected="true">Daltons</option> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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11 </param> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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12 <param argument="-NormalizeReporterIons" type="boolean" value="false" label="Normalize reporter ion channels to match 1:1 ratio?" help="This option will adjust the intensity of each channel so that the total intensity of each channel across an entire source file is the same." /> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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diff
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13 </xml> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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14 </macros> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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15 <expand macro="requirements" /> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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16 <stdio> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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17 <exit_code range="1:" level="fatal" description="Job Failed" /> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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18 <regex match="\nError:.*\n" source="both" level="fatal" /> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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19 </stdio> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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20 <command> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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21 <![CDATA[ |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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22 #set $input_name = $input.display_name |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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23 cp '$input' output && |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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24 ln -s output output.idpDB && |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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25 ln -s \$(dirname \$(which idpQonvert))/gene2protein.db3 gene2protein.db3 && |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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26 |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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27 #if $use_raw_data_condition.use_raw_data |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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28 #for $i in $use_raw_data_condition.input_raw |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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29 ln -s '${i.file_name}' '${i.display_name}' && |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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30 #end for |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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31 #end if |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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32 |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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33 idpQonvert |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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34 -EmbedOnly true |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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35 -EmbedGeneMetadata $EmbedGeneMetadata |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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36 #if $use_raw_data_condition.use_raw_data |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
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37 -EmbedSpectrumScanTimes $use_raw_data_condition.EmbedSpectrumScanTimes |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
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38 -EmbedSpectrumSources $use_raw_data_condition.EmbedSpectrumSources |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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39 |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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40 #set $qm = $use_raw_data_condition.quantitation_method_condition.QuantitationMethod |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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41 -QuantitationMethod $qm |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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42 #if $qm != "None" and $qm != "LabelFree" |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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43 -ReporterIonMzTolerance '$use_raw_data_condition.quantitation_method_condition.ReporterIonMzTolerance $use_raw_data_condition.quantitation_method_condition.ReporterIonMzTolerance_units' |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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44 -NormalizeReporterIons $use_raw_data_condition.quantitation_method_condition.NormalizeReporterIons |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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45 #end if |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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46 #end if |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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47 output.idpDB |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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48 ]]> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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49 </command> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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50 <inputs> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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51 <param name="input" type="data" format="idpdb" label="Input idpDB file" /> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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52 <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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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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53 <conditional name="use_raw_data_condition"> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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54 <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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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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55 <when value="false"></when> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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56 <when value="true"> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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57 <param name="input_raw" type="data" format="mzml,mzxml,mgf,ms2,mz5" label="Input raw MS files" multiple="true" /> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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58 <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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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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59 <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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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
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60 <conditional name="quantitation_method_condition"> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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61 <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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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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62 <option value="None" selected="true">None</option> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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63 <option value="LabelFree">Label-free (XIC)</option> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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64 <option value="ITRAQ4plex">iTRAQ 4-plex</option> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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65 <option value="ITRAQ8plex">iTRAQ 8-plex</option> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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66 <option value="TMT2plex">TMT 2-plex</option> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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67 <option value="TMT6plex">TMT 6-plex</option> |
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fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
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68 <option value="TMT10plex">TMT 10-plex</option> |
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2ec9bd69259e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 66973ea01088c809c3f7c3daa54233674c67fa45"
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69 <option value="TMT11plex">TMT 11-plex</option> |
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2ec9bd69259e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 66973ea01088c809c3f7c3daa54233674c67fa45"
galaxyp
parents:
8
diff
changeset
|
70 <option value="TMTpro16plex">TMTpro 16-plex</option> |
|
8
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
71 </param> |
|
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
72 <when value="ITRAQ4plex"><expand macro="IsobaricQuantitationOptions" /></when> |
|
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
73 <when value="ITRAQ8plex"><expand macro="IsobaricQuantitationOptions" /></when> |
|
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
74 <when value="TMT2plex"><expand macro="IsobaricQuantitationOptions" /></when> |
|
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
75 <when value="TMT6plex"><expand macro="IsobaricQuantitationOptions" /></when> |
|
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
76 <when value="TMT10plex"><expand macro="IsobaricQuantitationOptions" tolerance="0.003" /></when> |
|
10
2ec9bd69259e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 66973ea01088c809c3f7c3daa54233674c67fa45"
galaxyp
parents:
8
diff
changeset
|
77 <when value="TMT11plex"><expand macro="IsobaricQuantitationOptions" tolerance="0.003" /></when> |
|
2ec9bd69259e
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 66973ea01088c809c3f7c3daa54233674c67fa45"
galaxyp
parents:
8
diff
changeset
|
78 <when value="TMTpro16plex"><expand macro="IsobaricQuantitationOptions" tolerance="0.003" /></when> |
|
8
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
79 |
|
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
80 <when value="None"></when> |
|
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
81 <when value="LabelFree"></when> |
|
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
82 </conditional> |
|
3
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
83 </when> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
84 </conditional> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
85 </inputs> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
86 <outputs> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
87 <data format="idpdb" name="output" from_work_dir="output" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
88 </outputs> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
89 <tests> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
90 <test> |
|
6
aec819a9068b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
galaxyp
parents:
3
diff
changeset
|
91 <param name="input" value="201208-378803.idpDB" /> |
|
3
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
92 <param name="EmbedGeneMetadata" value="false" /> |
|
6
aec819a9068b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
galaxyp
parents:
3
diff
changeset
|
93 <output name="output" file="201208-378803.idpDB" compare="sim_size" delta="500000" /> |
|
3
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
94 </test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
95 <test> |
|
6
aec819a9068b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
galaxyp
parents:
3
diff
changeset
|
96 <param name="input" value="201208-378803.idpDB" /> |
|
3
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
97 <param name="EmbedGeneMetadata" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
98 <output name="output" file="201208-378803-embeddedGenes.idpDB" compare="sim_size" delta="500000" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
99 </test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
100 <test> |
|
6
aec819a9068b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
galaxyp
parents:
3
diff
changeset
|
101 <param name="input" value="201208-378803.idpDB" /> |
|
3
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
102 <param name="EmbedGeneMetadata" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
103 <param name="use_raw_data" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
104 <param name="input_raw" value="input/201208-378803.mzML" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
105 <param name="EmbedSpectrumSources" value="false" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
106 <param name="EmbedSpectrumScanTimes" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
107 <param name="QuantitationMethod" value="None" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
108 <output name="output" file="201208-378803-embeddedGenesAndScanTimes.idpDB" compare="sim_size" delta="500000" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
109 </test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
110 <test> |
|
6
aec819a9068b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
galaxyp
parents:
3
diff
changeset
|
111 <param name="input" value="201208-378803.idpDB" /> |
|
3
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
112 <param name="EmbedGeneMetadata" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
113 <param name="use_raw_data" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
114 <param name="input_raw" value="input/201208-378803.mzML" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
115 <param name="EmbedSpectrumSources" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
116 <param name="EmbedSpectrumScanTimes" value="false" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
117 <param name="QuantitationMethod" value="None" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
118 <output name="output" file="201208-378803-embeddedGenesAndSpectra.idpDB" compare="sim_size" delta="500000" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
119 </test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
120 <test> |
|
6
aec819a9068b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 1e51bed3a1c10c67ef0404216608e9333db04c64
galaxyp
parents:
3
diff
changeset
|
121 <param name="input" value="201208-378803.idpDB" /> |
|
3
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
122 <param name="EmbedGeneMetadata" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
123 <param name="use_raw_data" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
124 <param name="input_raw" value="input/201208-378803.mzML" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
125 <param name="EmbedSpectrumSources" value="false" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
126 <param name="EmbedSpectrumScanTimes" value="true" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
127 <param name="QuantitationMethod" value="ITRAQ4plex" /> |
|
8
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
128 <param name="ReporterIonMzTolerance" value="10" /> |
|
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
129 <param name="ReporterIonMzTolerance_units" value="ppm" /> |
|
fb6ce5041417
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit baf4379f0cf287238a4c988723611fe0983917db
galaxyp
parents:
6
diff
changeset
|
130 <param name="NormalizeReporterIons" value="true" /> |
|
3
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
131 <output name="output" file="201208-378803-embeddedGenesAndQuantitation.idpDB" compare="sim_size" delta="500000" /> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
132 </test> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
133 </tests> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
134 <help> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
135 <![CDATA[ |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
136 **What it does** |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
137 |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
138 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). |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
139 ]]> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
140 </help> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
141 <citations> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
parents:
diff
changeset
|
142 <citation type="doi">10.1021/pr900360j</citation> |
|
d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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143 <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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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
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144 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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145 </citations> |
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d1f7b2395bc2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/idpqonvert commit 0be0fd3f899ce64aa53e44117931fe1a7d8c52ab
galaxyp
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146 </tool> |