Mercurial > repos > galaxyp > openms_idmapper

annotate IDMapper.xml @ 0:026dbe52de09 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:31:09 -0500
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026dbe52de09 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'?>
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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="2.1.0">
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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
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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 $param_mz_measure
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32 #end if
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33 #if $param_mz_reference:
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34 -mz_reference $param_mz_reference
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35 #end if
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36 #if $param_ignore_charge:
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37 -ignore_charge
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38 #end if
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39 #if $param_feature_use_centroid_rt:
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40 -feature:use_centroid_rt
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41 #end if
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42 #if $param_feature_use_centroid_mz:
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43 -feature:use_centroid_mz
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44 #end if
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45 #if $param_consensus_use_subelements:
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46 -consensus:use_subelements
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47 #end if
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48 #if $adv_opts.adv_opts_selector=='advanced':
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49 #if $adv_opts.param_force:
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50 -force
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51 #end if
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52 #if $adv_opts.param_consensus_annotate_ids_with_subelements:
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53 -consensus:annotate_ids_with_subelements
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54 #end if
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55 #end if
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56 </command>
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57 <inputs>
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58 <param name="param_id" type="data" format="mzid,idxml" optional="False" label="Protein/peptide identifications file" help="(-id) "/>
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59 <param name="param_in" type="data" format="featurexml,consensusxml,mzq" optional="False" label="Feature map/consensus map file" help="(-in) "/>
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60 <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) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
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61 <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) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
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62 <param name="param_mz_measure" display="radio" type="select" optional="False" value="ppm" label="Unit of 'mz_tolerance'" help="(-mz_measure) ">
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63 <option value="ppm" selected="true">ppm</option>
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64 <option value="Da">Da</option>
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65 </param>
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66 <param name="param_mz_reference" display="radio" type="select" optional="False" 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', &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.)">
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67 <option value="precursor" selected="true">precursor</option>
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68 <option value="peptide">peptide</option>
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69 </param>
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70 <param name="param_ignore_charge" display="radio" 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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71 <param name="param_feature_use_centroid_rt" display="radio" 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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72 <param name="param_feature_use_centroid_mz" display="radio" 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) &lt;br&gt;(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)"/>
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73 <param name="param_consensus_use_subelements" display="radio" 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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74 <expand macro="advanced_options">
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75 <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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76 <param name="param_consensus_annotate_ids_with_subelements" display="radio" 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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77 </expand>
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78 </inputs>
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79 <outputs>
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80 <data name="param_out" metadata_source="param_in" format="input"/>
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81 </outputs>
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82 <help>Assigns protein/peptide identifications to features or consensus features.
026dbe52de09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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83
026dbe52de09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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84
026dbe52de09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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85 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html</help>
026dbe52de09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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86 </tool>