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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="IDMapper" name="IDMapper" version="2.0.0">
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3 <description>Assigns protein/peptide identifications to features or consensus features.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">IDMapper</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>IDMapper
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11
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12 #if $param_id:
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13 -id $param_id
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14 #end if
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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_rt_tolerance:
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22 -rt_tolerance $param_rt_tolerance
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23 #end if
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24 #if $param_mz_tolerance:
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25 -mz_tolerance $param_mz_tolerance
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26 #end if
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27 #if $param_mz_measure:
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28 -mz_measure
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29 #if " " in str($param_mz_measure):
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30 "$param_mz_measure"
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31 #else
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32 $param_mz_measure
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33 #end if
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34 #end if
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35 #if $param_mz_reference:
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36 -mz_reference
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37 #if " " in str($param_mz_reference):
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38 "$param_mz_reference"
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39 #else
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40 $param_mz_reference
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41 #end if
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42 #end if
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43 #if $param_ignore_charge:
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44 -ignore_charge
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45 #end if
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46 -threads \${GALAXY_SLOTS:-24}
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47 #if $param_feature_use_centroid_rt:
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48 -feature:use_centroid_rt
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49 #end if
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50 #if $param_feature_use_centroid_mz:
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51 -feature:use_centroid_mz
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52 #end if
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53 #if $param_consensus_use_subelements:
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54 -consensus:use_subelements
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55 #end if
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56 #if $adv_opts.adv_opts_selector=='advanced':
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57 #if $adv_opts.param_force:
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58 -force
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59 #end if
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60 #if $adv_opts.param_consensus_annotate_ids_with_subelements:
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61 -consensus:annotate_ids_with_subelements
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62 #end if
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63 #end if
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64 </command>
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65 <inputs>
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66 <param name="param_id" type="data" format="idxml" optional="False" label="Protein/peptide identifications file" help="(-id) "/>
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67 <param name="param_in" type="data" format="featurexml,consensusxml,mzq" optional="False" label="Feature map/consensus map file" help="(-in) "/>
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68 <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="(-rt_tolerance) <br>Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
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69 <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="(-mz_tolerance) <br>Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
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70 <param name="param_mz_measure" type="select" optional="True" value="ppm" label="Unit of 'mz_tolerance'" help="(-mz_measure) ">
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71 <option value="ppm">ppm</option>
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72 <option value="Da">Da</option>
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73 </param>
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74 <param name="param_mz_reference" type="select" optional="True" value="precursor" label="Source of m/z values for peptide identifications" help="(-mz_reference) If 'precursor', the precursor-m/z from the idXML is used. If 'peptide', <br>masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches. <br>('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)">
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75 <option value="precursor">precursor</option>
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76 <option value="peptide">peptide</option>
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77 </param>
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78 <param name="param_ignore_charge" type="boolean" truevalue="-ignore_charge" falsevalue="" checked="false" optional="True" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" help="(-ignore_charge) "/>
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79 <param name="param_feature_use_centroid_rt" type="boolean" truevalue="-feature:use_centroid_rt" falsevalue="" checked="false" optional="True" label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces" help="(-use_centroid_rt) "/>
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80 <param name="param_feature_use_centroid_mz" type="boolean" truevalue="-feature:use_centroid_mz" falsevalue="" checked="false" optional="True" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces" help="(-use_centroid_mz) <br>(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)"/>
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81 <param name="param_consensus_use_subelements" type="boolean" truevalue="-consensus:use_subelements" falsevalue="" checked="false" optional="True" label="Match using RT and m/z of sub-features instead of consensus RT and m/z" help="(-use_subelements) A consensus feature matches if any of its sub-features matches"/>
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82 <expand macro="advanced_options">
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83 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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84 <param name="param_consensus_annotate_ids_with_subelements" type="boolean" truevalue="-consensus:annotate_ids_with_subelements" falsevalue="" checked="false" optional="True" label="Store the map index of the sub-feature in the peptide ID" help="(-annotate_ids_with_subelements) "/>
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85 </expand>
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86 </inputs>
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87 <outputs>
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88 <data name="param_out" metadata_source="param_in" format="input"/>
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89 </outputs>
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90 <help>**What it does**
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91
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92 Assigns protein/peptide identifications to features or consensus features.
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93
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94
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95 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html</help>
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96 <expand macro="references"/>
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97 </tool>
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