Mercurial > repos > galaxyp > openms_openswathrewritetofeaturexml
annotate OpenSwathRewriteToFeatureXML.xml @ 2:12ead45c5820 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author | galaxyp |
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date | Wed, 18 Oct 2017 15:43:50 -0400 |
parents | 62cc5897c340 |
children | 27dc92c6a49b |
rev | line source |
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1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 <!--Proposed Tool Section: [Targeted Experiments]--> |
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62cc5897c340
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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4 <tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.2.0"> |
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1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 <import>macros.xml</import> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 </macros> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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10 <expand macro="references"/> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 <expand macro="stdio"/> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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12 <expand macro="requirements"/> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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13 <command>OpenSwathRewriteToFeatureXML |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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14 |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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15 #if $param_csv: |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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16 -csv $param_csv |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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17 #end if |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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18 #if $param_featureXML: |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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19 -featureXML $param_featureXML |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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20 #end if |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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21 #if $param_out: |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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22 -out $param_out |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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23 #end if |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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24 #if $param_FDR_cutoff: |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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25 -FDR_cutoff $param_FDR_cutoff |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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26 #end if |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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27 #if $adv_opts.adv_opts_selector=='advanced': |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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28 #if $adv_opts.param_force: |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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29 -force |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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30 #end if |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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31 #end if |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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32 </command> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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33 <inputs> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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34 <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: "all_peakgroups.xls"" help="(-csv) "/> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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35 <param name="param_featureXML" type="data" format="featurexml" optional="False" label="input featureXML file" help="(-featureXML) "/> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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36 <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (" help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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37 <expand macro="advanced_options"> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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38 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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39 </expand> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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40 </inputs> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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41 <outputs> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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42 <data name="param_out" format="featurexml"/> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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43 </outputs> |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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44 <help>Combines featureXML and mProphet tsv to FDR filtered featureXML. |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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45 |
1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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46 |
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62cc5897c340
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathRewriteToFeatureXML.html</help> |
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1e14ca98808b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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48 </tool> |