Mercurial > repos > galaxyp > openms_targetedfileconverter

annotate TargetedFileConverter.xml @ 3:258a1cfd78f6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 26556c08813e892b4d1eed0e98012601870cae5f
author galaxyp
date Wed, 18 Oct 2017 10:21:53 -0400
parents 8d7da01e088a
children caf8fee30220
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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'?>
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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.-->
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3 <!--Proposed Tool Section: [Targeted Experiments]-->
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4 <tool id="TargetedFileConverter" name="TargetedFileConverter" version="2.2.0">
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5 <description>Converts different transition files for targeted proteomics / metabolomics analysis.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">TargetedFileConverter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>TargetedFileConverter
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_out_type:
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22 -out_type
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23 #if " " in str($param_out_type):
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24 "$param_out_type"
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25 #else
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26 $param_out_type
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27 #end if
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28 #end if
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29 #if $adv_opts.adv_opts_selector=='advanced':
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30 #if $adv_opts.param_legacy_traml_id:
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31 -legacy_traml_id
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32 #end if
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33 #if $adv_opts.param_force:
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34 -force
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35 #end if
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36 #if $adv_opts.param_algorithm_retentionTimeInterpretation:
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37 -algorithm:retentionTimeInterpretation
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38 #if " " in str($adv_opts.param_algorithm_retentionTimeInterpretation):
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39 "$adv_opts.param_algorithm_retentionTimeInterpretation"
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40 #else
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41 $adv_opts.param_algorithm_retentionTimeInterpretation
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42 #end if
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43 #end if
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44 #if $adv_opts.param_algorithm_override_group_label_check:
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45 -algorithm:override_group_label_check
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46 #end if
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47 #if $adv_opts.param_algorithm_force_invalid_mods:
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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>
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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) &lt;br&gt; See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file"/>
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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 &lt;br&gt;Note: that not all conversion paths work or make sense" help="(-out_type) ">
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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) "/>
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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"/>
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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) "/>
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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>
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74 <help>Converts different transition files for targeted proteomics / metabolomics analysis.
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75
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76
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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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78 </tool>