Mercurial > repos > galaxyp > openms_idmapper

comparison IDMapper.xml @ 3:e0c599550478 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:18:09 -0400
parents 79186fbde4ea
children d92d43ce63ce
comparison
equal deleted inserted replaced
2:b5d0905419da 3:e0c599550478
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="IDMapper" name="IDMapper" version="2.1.0"> 4 <tool id="IDMapper" name="IDMapper" version="2.2.0">
5 <description>Assigns protein/peptide identifications to features or consensus features.</description> 5 <description>Assigns protein/peptide identifications to features or consensus features.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDMapper</token> 7 <token name="@EXECUTABLE@">IDMapper</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
53 -feature:use_centroid_mz 53 -feature:use_centroid_mz
54 #end if 54 #end if
55 #if $param_consensus_use_subelements: 55 #if $param_consensus_use_subelements:
56 -consensus:use_subelements 56 -consensus:use_subelements
57 #end if 57 #end if
58 #if $param_spectra_in:
59 -spectra:in $param_spectra_in
60 #end if
58 #if $adv_opts.adv_opts_selector=='advanced': 61 #if $adv_opts.adv_opts_selector=='advanced':
59 #if $adv_opts.param_force: 62 #if $adv_opts.param_force:
60 -force 63 -force
61 #end if 64 #end if
62 #if $adv_opts.param_consensus_annotate_ids_with_subelements: 65 #if $adv_opts.param_consensus_annotate_ids_with_subelements:
79 </param> 82 </param>
80 <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) "/> 83 <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) "/>
81 <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) "/> 84 <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) "/>
82 <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.)"/> 85 <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.)"/>
83 <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"/> 86 <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"/>
87 <param name="param_spectra_in" type="data" format="mzml" optional="True" label="MS run used to annotated unidentified spectra to features or consensus features" help="(-in) "/>
84 <expand macro="advanced_options"> 88 <expand macro="advanced_options">
85 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 89 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
86 <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) "/> 90 <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) "/>
87 </expand> 91 </expand>
88 </inputs> 92 </inputs>