Mercurial > repos > galaxyp > openms_accuratemasssearch

comparison AccurateMassSearch.xml @ 11:96acf893530c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty
author galaxyp
date Fri, 17 May 2019 10:24:05 -0400
parents a7ef3b2f3621
children 40e0709178a5
comparison
equal deleted inserted replaced
10:d14681186aba 11:96acf893530c
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>AccurateMassSearch 13 <command detect_errors="aggressive"><![CDATA[AccurateMassSearch
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
66 #if $adv_opts.adv_opts_selector=='advanced': 66 #if $adv_opts.adv_opts_selector=='advanced':
67 #if $adv_opts.param_force: 67 #if $adv_opts.param_force:
68 -force 68 -force
69 #end if 69 #end if
70 #end if 70 #end if
71 </command> 71 ]]></command>
72 <inputs> 72 <inputs>
73 <param name="param_in" type="data" format="featurexml,consensusxml" optional="False" label="featureXML or consensusXML file" help="(-in) "/> 73 <param name="param_in" type="data" format="featurexml,consensusxml" optional="False" label="featureXML or consensusXML file" help="(-in) "/>
74 <param name="param_positive_adducts" type="data" format="tabular" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database" help="(-positive_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/> 74 <param name="param_positive_adducts" type="data" format="tabular" optional="False" value="CHEMISTRY/PositiveAdducts.tsv" label="This file contains the list of potential positive adducts that will be looked for in the database" help="(-positive_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
75 <param name="param_negative_adducts" type="data" format="tabular" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database" help="(-negative_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/> 75 <param name="param_negative_adducts" type="data" format="tabular" optional="False" value="CHEMISTRY/NegativeAdducts.tsv" label="This file contains the list of potential negative adducts that will be looked for in the database" help="(-negative_adducts) Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used! If empty, the default will be used"/>
76 <param name="param_db_mapping" type="data" format="tabular" multiple="true" optional="False" size="30" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="(-mapping) If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used"> 76 <param name="param_db_mapping" type="data" format="tabular" multiple="true" optional="False" size="30" value="CHEMISTRY/HMDBMappingFile.tsv" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="(-mapping) If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used">
111 <data name="param_out_annotation" metadata_source="param_in" format="input"/> 111 <data name="param_out_annotation" metadata_source="param_in" format="input"/>
112 </outputs> 112 </outputs>
113 <help>Match MS signals to molecules from a database by mass. 113 <help>Match MS signals to molecules from a database by mass.
114 114
115 115
116 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html</help> 116 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_AccurateMassSearch.html</help>
117 </tool> 117 </tool>