Mercurial > repos > galaxyp > openms_idmapper

comparison IDMapper.xml @ 9:d29bb4c9831e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 08:16:23 -0400
parents f9dbe4e67097
children 138a734e21a1
comparison
equal deleted inserted replaced
8:a3960e7c2d1d 9:d29bb4c9831e
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"/>
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>