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comparison AccurateMassSearch.xml @ 9:a7ef3b2f3621 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:14:34 -0500
parents c869c0af9bca
children 96acf893530c
comparison
equal deleted inserted replaced
8:252ef1ffd08d 9:a7ef3b2f3621
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.2.0"> 4 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="2.3.0">
5 <description>Find potential HMDB ids within the given mass error window.</description> 5 <description>Match MS signals to molecules from a database by mass.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">AccurateMassSearch</token> 7 <token name="@EXECUTABLE@">AccurateMassSearch</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
19 -out $param_out 19 -out $param_out
20 #end if 20 #end if
21 #if $param_out_annotation: 21 #if $param_out_annotation:
22 -out_annotation $param_out_annotation 22 -out_annotation $param_out_annotation
23 #end if 23 #end if
24 #if $param_positive_adducts_file: 24 #if $param_positive_adducts:
25 -positive_adducts_file $param_positive_adducts_file 25 -positive_adducts $param_positive_adducts
26 #end if 26 #end if
27 #if $param_negative_adducts_file: 27 #if $param_negative_adducts:
28 -negative_adducts_file $param_negative_adducts_file 28 -negative_adducts $param_negative_adducts
29 #end if 29 #end if
30 -db:mapping 30 -db:mapping
31 #for token in $param_db_mapping: 31 #for token in $param_db_mapping:
32 $token 32 $token
33 #end for 33 #end for
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_file" 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_file) 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_file" 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_file) 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">
77 <sanitizer> 77 <sanitizer>
78 <valid initial="string.printable"> 78 <valid initial="string.printable">
79 <remove value="'"/> 79 <remove value="'"/>
80 <remove value="&quot;"/> 80 <remove value="&quot;"/>
108 </inputs> 108 </inputs>
109 <outputs> 109 <outputs>
110 <data name="param_out" format="tabular"/> 110 <data name="param_out" format="tabular"/>
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>Find potential HMDB ids within the given mass error window. 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 http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_AccurateMassSearch.html</help>
117 </tool> 117 </tool>