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annotate IDMapper.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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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: [ID Processing]-->
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4 <tool id="IDMapper" name="IDMapper" version="2.0.0">
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5 <description>Assigns protein/peptide identifications to features or consensus features.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDMapper</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>IDMapper
0
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14
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15 #if $param_id:
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16 -id $param_id
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17 #end if
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18 #if $param_in:
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19 -in $param_in
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_rt_tolerance:
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25 -rt_tolerance $param_rt_tolerance
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26 #end if
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27 #if $param_mz_tolerance:
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28 -mz_tolerance $param_mz_tolerance
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29 #end if
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30 #if $param_mz_measure:
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31 -mz_measure
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32 #if &quot; &quot; in str($param_mz_measure):
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33 &quot;$param_mz_measure&quot;
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34 #else
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35 $param_mz_measure
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36 #end if
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37 #end if
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38 #if $param_mz_reference:
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39 -mz_reference
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40 #if &quot; &quot; in str($param_mz_reference):
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41 &quot;$param_mz_reference&quot;
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42 #else
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43 $param_mz_reference
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44 #end if
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45 #end if
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46 #if $param_ignore_charge:
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47 -ignore_charge
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48 #end if
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49 -threads \${GALAXY_SLOTS:-24}
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50 #if $param_feature_use_centroid_rt:
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51 -feature:use_centroid_rt
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52 #end if
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53 #if $param_feature_use_centroid_mz:
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54 -feature:use_centroid_mz
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55 #end if
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56 #if $param_consensus_use_subelements:
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57 -consensus:use_subelements
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58 #end if
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59 #if $adv_opts.adv_opts_selector=='advanced':
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60 #if $adv_opts.param_force:
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61 -force
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62 #end if
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63 #if $adv_opts.param_consensus_annotate_ids_with_subelements:
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64 -consensus:annotate_ids_with_subelements
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65 #end if
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66 #end if
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67 </command>
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68 <inputs>
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69 <param format="xml,txt" help="(-id) " label="Protein/peptide identifications file" name="param_id" optional="False" type="data"/>
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70 <param format="xml,consensusxml,mzq" help="(-in) " label="Feature map/consensus map file" name="param_in" optional="False" type="data"/>
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71 <param help="(-rt_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" min="0.0" name="param_rt_tolerance" optional="True" type="float" value="5.0"/>
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72 <param help="(-mz_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" min="0.0" name="param_mz_tolerance" optional="True" type="float" value="20.0"/>
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73 <param help="(-mz_measure) " label="Unit of 'mz_tolerance'" name="param_mz_measure" optional="True" type="select" value="ppm">
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74 <option value="ppm">ppm</option>
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75 <option value="Da">Da</option>
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76 </param>
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77 <param help="(-mz_reference) If 'precursor', the precursor-m/z from the idXML is used. If 'peptide', &lt;br&gt;masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches. &lt;br&gt;('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)" label="Source of m/z values for peptide identifications" name="param_mz_reference" optional="True" type="select" value="precursor">
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78 <option value="precursor">precursor</option>
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79 <option value="peptide">peptide</option>
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80 </param>
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81 <param checked="false" falsevalue="" help="(-ignore_charge) " label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" name="param_ignore_charge" optional="True" truevalue="-ignore_charge" type="boolean"/>
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82 <param checked="false" falsevalue="" help="(-use_centroid_rt) " label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces" name="param_feature_use_centroid_rt" optional="True" truevalue="-feature:use_centroid_rt" type="boolean"/>
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83 <param checked="false" falsevalue="" help="(-use_centroid_mz) &lt;br&gt;(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces" name="param_feature_use_centroid_mz" optional="True" truevalue="-feature:use_centroid_mz" type="boolean"/>
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84 <param checked="false" falsevalue="" help="(-use_subelements) A consensus feature matches if any of its sub-features matches" label="Match using RT and m/z of sub-features instead of consensus RT and m/z" name="param_consensus_use_subelements" optional="True" truevalue="-consensus:use_subelements" type="boolean"/>
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85 <expand macro="advanced_options">
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86 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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87 <param checked="false" falsevalue="" help="(-annotate_ids_with_subelements) " label="Store the map index of the sub-feature in the peptide ID" name="param_consensus_annotate_ids_with_subelements" optional="True" truevalue="-consensus:annotate_ids_with_subelements" type="boolean"/>
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88 </expand>
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89 </inputs>
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90 <outputs>
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91 <data format="input" metadata_source="param_in" name="param_out"/>
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92 </outputs>
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93 <help>Assigns protein/peptide identifications to features or consensus features.
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94
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95
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96 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html</help>
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97 </tool>