Mercurial > repos > galaxyp > openms_targetedfileconverter
annotate TargetedFileConverter.xml @ 2:1f1ca90f5f48 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8d70dbb6c61659d5ced433b168a2a4e32c9af677
author | galaxyp |
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date | Fri, 18 Aug 2017 15:03:50 -0400 |
parents | 8d7da01e088a |
children | caf8fee30220 |
rev | line source |
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8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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1 <?xml version='1.0' encoding='UTF-8'?> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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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.--> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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3 <!--Proposed Tool Section: [Targeted Experiments]--> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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4 <tool id="TargetedFileConverter" name="TargetedFileConverter" version="2.2.0"> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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5 <description>Converts different transition files for targeted proteomics / metabolomics analysis.</description> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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6 <macros> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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7 <token name="@EXECUTABLE@">TargetedFileConverter</token> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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8 <import>macros.xml</import> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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9 </macros> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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10 <expand macro="references"/> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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11 <expand macro="stdio"/> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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12 <expand macro="requirements"/> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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13 <command>TargetedFileConverter |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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14 |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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15 #if $param_in: |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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16 -in $param_in |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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17 #end if |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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18 #if $param_out: |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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19 -out $param_out |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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20 #end if |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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21 #if $param_out_type: |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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22 -out_type |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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23 #if " " in str($param_out_type): |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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24 "$param_out_type" |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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25 #else |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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26 $param_out_type |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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27 #end if |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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28 #end if |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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29 #if $adv_opts.adv_opts_selector=='advanced': |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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30 #if $adv_opts.param_legacy_traml_id: |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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31 -legacy_traml_id |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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32 #end if |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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33 #if $adv_opts.param_force: |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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34 -force |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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35 #end if |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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36 #if $adv_opts.param_algorithm_retentionTimeInterpretation: |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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37 -algorithm:retentionTimeInterpretation |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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38 #if " " in str($adv_opts.param_algorithm_retentionTimeInterpretation): |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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39 "$adv_opts.param_algorithm_retentionTimeInterpretation" |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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40 #else |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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41 $adv_opts.param_algorithm_retentionTimeInterpretation |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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42 #end if |
8d7da01e088a
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43 #end if |
8d7da01e088a
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44 #if $adv_opts.param_algorithm_override_group_label_check: |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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45 -algorithm:override_group_label_check |
8d7da01e088a
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46 #end if |
8d7da01e088a
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47 #if $adv_opts.param_algorithm_force_invalid_mods: |
8d7da01e088a
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48 -algorithm:force_invalid_mods |
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49 #end if |
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50 #end if |
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51 </command> |
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52 <inputs> |
8d7da01e088a
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53 <param name="param_in" type="data" format="tabular,mrm,pqp,traml" optional="False" label="Input file to convert" help="(-in) <br> See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file"/> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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54 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content <br>Note: that not all conversion paths work or make sense" help="(-out_type) "> |
8d7da01e088a
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55 <option value="tsv">tsv</option> |
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56 <option value="pqp">pqp</option> |
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57 <option value="TraML">TraML</option> |
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58 </param> |
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59 <expand macro="advanced_options"> |
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60 <param name="param_legacy_traml_id" display="radio" type="boolean" truevalue="-legacy_traml_id" falsevalue="" checked="false" optional="True" label="PQP to TraML: Should legacy TraML IDs be used?" help="(-legacy_traml_id) "/> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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61 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> |
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62 <param name="param_algorithm_retentionTimeInterpretation" display="radio" type="select" optional="False" value="iRT" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="(-retentionTimeInterpretation) "> |
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63 <option value="iRT" selected="true">iRT</option> |
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64 <option value="seconds">seconds</option> |
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65 <option value="minutes">minutes</option> |
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66 </param> |
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67 <param name="param_algorithm_override_group_label_check" display="radio" type="boolean" truevalue="-algorithm:override_group_label_check" falsevalue="" checked="false" optional="True" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="(-override_group_label_check) Only turn this off if you know what you are doing"/> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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68 <param name="param_algorithm_force_invalid_mods" display="radio" type="boolean" truevalue="-algorithm:force_invalid_mods" falsevalue="" checked="false" optional="True" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help="(-force_invalid_mods) "/> |
8d7da01e088a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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69 </expand> |
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70 </inputs> |
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71 <outputs> |
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72 <data name="param_out" metadata_source="param_in" format="input"/> |
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73 </outputs> |
8d7da01e088a
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74 <help>Converts different transition files for targeted proteomics / metabolomics analysis. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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77 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_TargetedFileConverter.html</help> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d589f39067c2e8556273601a2b53b1b1ef2d88f4
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78 </tool> |