Mercurial > repos > galaxyp > openms_proteinresolver

comparison ProteinResolver.xml @ 0:154998956e7a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:38:04 -0500
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children b09b5ecc297d
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-1:000000000000 0:154998956e7a
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.-->
3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="ProteinResolver" name="ProteinResolver" version="2.1.0">
5 <description>protein inference</description>
6 <macros>
7 <token name="@EXECUTABLE@">ProteinResolver</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>ProteinResolver
14
15 #if $param_fasta:
16 -fasta $param_fasta
17 #end if
18 -in
19 #for token in $param_in:
20 $token
21 #end for
22 #if $param_in_path:
23 -in_path "$param_in_path"
24 #end if
25 #if $param_design:
26 -design $param_design
27 #end if
28 #if $param_protein_groups:
29 -protein_groups $param_protein_groups
30 #end if
31 #if $param_peptide_table:
32 -peptide_table $param_peptide_table
33 #end if
34 #if $param_protein_table:
35 -protein_table $param_protein_table
36 #end if
37 #if $param_additional_info:
38 -additional_info $param_additional_info
39 #end if
40 #if $param_resolver_missed_cleavages:
41 -resolver:missed_cleavages $param_resolver_missed_cleavages
42 #end if
43 #if $param_resolver_min_length:
44 -resolver:min_length $param_resolver_min_length
45 #end if
46 #if $param_resolver_enzyme:
47 -resolver:enzyme $param_resolver_enzyme
48 #end if
49 #if $param_designer_experiment:
50 -designer:experiment "$param_designer_experiment"
51 #end if
52 #if $param_designer_file:
53 -designer:file "$param_designer_file"
54 #end if
55 #if $param_designer_separator:
56 -designer:separator $param_designer_separator
57 #end if
58 #if $adv_opts.adv_opts_selector=='advanced':
59 #if $adv_opts.param_force:
60 -force
61 #end if
62 #end if
63 </command>
64 <inputs>
65 <param name="param_fasta" type="data" format="fasta" optional="False" label="Input database file" help="(-fasta) "/>
66 <param name="param_in" type="data" format="consensusxml,idxml" multiple="true" optional="True" size="30" label="Input file(s) holding experimental data" help="(-in) ">
67 <sanitizer>
68 <valid initial="string.printable">
69 <remove value="'"/>
70 <remove value="&quot;"/>
71 </valid>
72 </sanitizer>
73 </param>
74 <param name="param_in_path" type="text" size="30" label="Path to idXMLs or consensusXMLs files" help="(-in_path) Ignored if 'in' is given">
75 <sanitizer>
76 <valid initial="string.printable">
77 <remove value="'"/>
78 <remove value="&quot;"/>
79 </valid>
80 </sanitizer>
81 </param>
82 <param name="param_design" type="data" format="txt" optional="True" label="Text file containing the experimental design" help="(-design) See documentation for specific format requirements"/>
83 <param name="param_resolver_missed_cleavages" type="integer" min="0" optional="True" value="2" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/>
84 <param name="param_resolver_min_length" type="integer" min="1" optional="True" value="6" label="Minimum length of peptide" help="(-min_length) "/>
85 <param name="param_resolver_enzyme" display="radio" type="select" optional="False" value="Trypsin" label="Digestion enzyme" help="(-enzyme) ">
86 <option value="Trypsin" selected="true">Trypsin</option>
87 </param>
88 <param name="param_designer_experiment" type="text" size="30" value="ExperimentalSetting" label="Identifier for the experimental design" help="(-experiment) ">
89 <sanitizer>
90 <valid initial="string.printable">
91 <remove value="'"/>
92 <remove value="&quot;"/>
93 </valid>
94 </sanitizer>
95 </param>
96 <param name="param_designer_file" type="text" size="30" value="File" label="Identifier for the file name" help="(-file) ">
97 <sanitizer>
98 <valid initial="string.printable">
99 <remove value="'"/>
100 <remove value="&quot;"/>
101 </valid>
102 </sanitizer>
103 </param>
104 <param name="param_designer_separator" display="radio" type="select" optional="False" value="tab" label="Separator, which should be used to split a row into columns" help="(-separator) ">
105 <option value="tab" selected="true">tab</option>
106 <option value="semi-colon">semi-colon</option>
107 <option value="comma">comma</option>
108 <option value="whitespace">whitespace</option>
109 </param>
110 <expand macro="advanced_options">
111 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
112 </expand>
113 </inputs>
114 <outputs>
115 <data name="param_protein_groups" format="tabular"/>
116 <data name="param_peptide_table" format="tabular"/>
117 <data name="param_protein_table" format="tabular"/>
118 <data name="param_additional_info" format="tabular"/>
119 </outputs>
120 <help>protein inference
121
122
123 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinResolver.html</help>
124 </tool>