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comparison ProteinResolver.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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3:ec62782f6c68 4:6ead64a594bd
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="2.0.0">
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 $param_in_path:
23 -in_path &quot;$param_in_path&quot;
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 -threads \${GALAXY_SLOTS:-24}
41 #if $param_resolver_missed_cleavages:
42 -resolver:missed_cleavages $param_resolver_missed_cleavages
43 #end if
44 #if $param_resolver_min_length:
45 -resolver:min_length $param_resolver_min_length
46 #end if
47 #if $param_resolver_enzyme:
48 -resolver:enzyme &quot;$param_resolver_enzyme&quot;
49 #end if
50 #if $param_designer_experiment:
51 -designer:experiment &quot;$param_designer_experiment&quot;
52 #end if
53 #if $param_designer_file:
54 -designer:file &quot;$param_designer_file&quot;
55 #end if
56 #if $param_designer_separator:
57 -designer:separator
58 #if &quot; &quot; in str($param_designer_separator):
59 &quot;$param_designer_separator&quot;
60 #else
61 $param_designer_separator
62 #end if
63 #end if
64 #if $adv_opts.adv_opts_selector=='advanced':
65 #if $adv_opts.param_force:
66 -force
67 #end if
68 #end if
69 </command>
70 <inputs>
71 <param format="fasta" help="(-fasta) " label="Input database file" name="param_fasta" optional="False" type="data"/>
72 <param format="xml,consensusxml" help="(-in) " label="Input file(s) holding experimental data" multiple="true" name="param_in" optional="True" size="30" type="data">
73 <sanitizer>
74 <valid initial="string.printable">
75 <remove value="'"/>
76 <remove value="&quot;"/>
77 </valid>
78 </sanitizer>
79 </param>
80 <param help="(-in_path) Ignored if 'in' is given" label="Path to idXMLs or consensusXMLs files" name="param_in_path" size="30" type="text">
81 <sanitizer>
82 <valid initial="string.printable">
83 <remove value="'"/>
84 <remove value="&quot;"/>
85 </valid>
86 </sanitizer>
87 </param>
88 <param format="txt" help="(-design) See documentation for specific format requirements" label="Text file containing the experimental design" name="param_design" optional="True" type="data"/>
89 <param help="(-missed_cleavages) " label="Number of allowed missed cleavages" min="0" name="param_resolver_missed_cleavages" optional="True" type="integer" value="2"/>
90 <param help="(-min_length) " label="Minimum length of peptide" min="1" name="param_resolver_min_length" optional="True" type="integer" value="6"/>
91 <param help="(-enzyme) " label="Digestion enzyme" name="param_resolver_enzyme" size="30" type="text" value="Trypsin">
92 <sanitizer>
93 <valid initial="string.printable">
94 <remove value="'"/>
95 <remove value="&quot;"/>
96 </valid>
97 </sanitizer>
98 </param>
99 <param help="(-experiment) " label="Identifier for the experimental design" name="param_designer_experiment" size="30" type="text" value="ExperimentalSetting">
100 <sanitizer>
101 <valid initial="string.printable">
102 <remove value="'"/>
103 <remove value="&quot;"/>
104 </valid>
105 </sanitizer>
106 </param>
107 <param help="(-file) " label="Identifier for the file name" name="param_designer_file" size="30" type="text" value="File">
108 <sanitizer>
109 <valid initial="string.printable">
110 <remove value="'"/>
111 <remove value="&quot;"/>
112 </valid>
113 </sanitizer>
114 </param>
115 <param help="(-separator) " label="Separator, which should be used to split a row into columns" name="param_designer_separator" optional="True" type="select" value="tab">
116 <option value="tab">tab</option>
117 <option value="semi-colon">semi-colon</option>
118 <option value="comma">comma</option>
119 <option value="whitespace">whitespace</option>
120 </param>
121 <expand macro="advanced_options">
122 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
123 </expand>
124 </inputs>
125 <outputs>
126 <data format="tabular" name="param_protein_groups"/>
127 <data format="tabular" name="param_peptide_table"/>
128 <data format="tabular" name="param_protein_table"/>
129 <data format="tabular" name="param_additional_info"/>
130 </outputs>
131 <help>protein inference
132
133
134 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinResolver.html</help>
135 </tool>