Mercurial > repos > galaxyp > openms_idmapper

comparison IDMapper.xml @ 12:29d6b012e395 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 05:33:34 -0400
parents fc1196abd955
children 26422c1360ea
comparison
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11:fc1196abd955 12:29d6b012e395
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 CTDConverter.-->
3 <!--Proposed Tool Section: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="IDMapper" name="IDMapper" version="2.2.0"> 4 <tool id="IDMapper" name="IDMapper" version="2.3.0">
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>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>IDMapper 13 <command detect_errors="aggressive"><![CDATA[IDMapper
14 14
15 #if $param_id: 15 #if $param_id:
16 -id $param_id 16 -id $param_id
17 #end if 17 #end if
18 #if $param_in: 18 #if $param_in:
64 #end if 64 #end if
65 #if $adv_opts.param_consensus_annotate_ids_with_subelements: 65 #if $adv_opts.param_consensus_annotate_ids_with_subelements:
66 -consensus:annotate_ids_with_subelements 66 -consensus:annotate_ids_with_subelements
67 #end if 67 #end if
68 #end if 68 #end if
69 </command> 69 ]]></command>
70 <inputs> 70 <inputs>
71 <param name="param_id" type="data" format="mzid,idxml" optional="False" label="Protein/peptide identifications file" help="(-id) "/> 71 <param name="param_id" type="data" format="mzid,idxml" optional="False" label="Protein/peptide identifications file" help="(-id) "/>
72 <param name="param_in" type="data" format="featurexml,consensusxml,mzq" optional="False" label="Feature map/consensus map file" help="(-in) "/> 72 <param name="param_in" type="data" format="featurexml,consensusxml,mzq" optional="False" label="Feature map/consensus map file" help="(-in) "/>
73 <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"/> 73 <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"/>
74 <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"/> 74 <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"/>
89 <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) "/>
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) "/> 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) "/>
91 </expand> 91 </expand>
92 </inputs> 92 </inputs>
93 <outputs> 93 <outputs>
94 <data name="param_out" metadata_source="param_in" format_source="param_in"/> 94 <data name="param_out" metadata_source="param_in" format_source="param_in" />
95 </outputs> 95 </outputs>
96 <help>Assigns protein/peptide identifications to features or consensus features. 96 <help>Assigns protein/peptide identifications to features or consensus features.
97 97
98 98
99 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html</help> 99 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDMapper.html</help>
100 </tool> 100 </tool>