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comparison ProteinResolver.xml @ 9:814d6f4706e3 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:51:43 +0000
parents 6cf5aa34e245
children 95f90fab5ce8
comparison
equal deleted inserted replaced
8:3901b7a1747c 9:814d6f4706e3
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 CTDConverter.--> 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: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="ProteinResolver" name="ProteinResolver" version="2.3.0"> 4 <tool id="ProteinResolver" name="ProteinResolver" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>protein inference</description> 5 <description>protein inference</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ProteinResolver</token> 7 <token name="@EXECUTABLE@">ProteinResolver</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[ProteinResolver 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_fasta: 18 ## Preprocessing
16 -fasta $param_fasta 19 mkdir fasta &&
20 ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
21 #if $in:
22 mkdir in &&
23 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
17 #end if 24 #end if
18 -in 25 #if $design:
19 #for token in $param_in: 26 mkdir design &&
20 $token 27 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
21 #end for
22 #if $param_in_path:
23 -in_path "$param_in_path"
24 #end if 28 #end if
25 #if $param_design: 29 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
26 -design $param_design 30 mkdir protein_groups &&
27 #end if 31 #end if
28 #if $param_protein_groups: 32 #if "peptide_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
29 -protein_groups $param_protein_groups 33 mkdir peptide_table &&
30 #end if 34 #end if
31 #if $param_peptide_table: 35 #if "protein_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
32 -peptide_table $param_peptide_table 36 mkdir protein_table &&
33 #end if 37 #end if
34 #if $param_protein_table: 38 #if "additional_info_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
35 -protein_table $param_protein_table 39 mkdir additional_info &&
36 #end if 40 #end if
37 #if $param_additional_info: 41
38 -additional_info $param_additional_info 42 ## Main program call
43
44 set -o pipefail &&
45 @EXECUTABLE@ -write_ctd ./ &&
46 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
47 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
48 -fasta
49 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)'
50 #if $in:
51 -in
52 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
39 #end if 53 #end if
40 #if $param_resolver_missed_cleavages: 54 #if $design:
41 -resolver:missed_cleavages $param_resolver_missed_cleavages 55 -design
56 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
42 #end if 57 #end if
43 #if $param_resolver_min_length: 58 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
44 -resolver:min_length $param_resolver_min_length 59 -protein_groups
60 'protein_groups/output.${gxy2omsext("csv")}'
45 #end if 61 #end if
46 #if $param_resolver_enzyme: 62 #if "peptide_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
47 -resolver:enzyme 63 -peptide_table
48 #if " " in str($param_resolver_enzyme): 64 'peptide_table/output.${gxy2omsext("csv")}'
49 "$param_resolver_enzyme"
50 #else
51 $param_resolver_enzyme
52 #end if
53 #end if 65 #end if
54 #if $param_designer_experiment: 66 #if "protein_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
55 -designer:experiment "$param_designer_experiment" 67 -protein_table
68 'protein_table/output.${gxy2omsext("csv")}'
56 #end if 69 #end if
57 #if $param_designer_file: 70 #if "additional_info_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
58 -designer:file "$param_designer_file" 71 -additional_info
72 'additional_info/output.${gxy2omsext("csv")}'
59 #end if 73 #end if
60 #if $param_designer_separator: 74 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
61 -designer:separator 75 | tee '$stdout'
62 #if " " in str($param_designer_separator):
63 "$param_designer_separator"
64 #else
65 $param_designer_separator
66 #end if
67 #end if 76 #end if
68 #if $adv_opts.adv_opts_selector=='advanced': 77
69 #if $adv_opts.param_force: 78 ## Postprocessing
70 -force 79 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
80 && mv 'protein_groups/output.${gxy2omsext("csv")}' '$protein_groups'
71 #end if 81 #end if
82 #if "peptide_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
83 && mv 'peptide_table/output.${gxy2omsext("csv")}' '$peptide_table'
72 #end if 84 #end if
73 ]]></command> 85 #if "protein_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
86 && mv 'protein_table/output.${gxy2omsext("csv")}' '$protein_table'
87 #end if
88 #if "additional_info_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
89 && mv 'additional_info/output.${gxy2omsext("csv")}' '$additional_info'
90 #end if
91 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
92 && mv '@EXECUTABLE@.ctd' '$ctd_out'
93 #end if]]></command>
94 <configfiles>
95 <inputs name="args_json" data_style="paths"/>
96 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
97 </configfiles>
74 <inputs> 98 <inputs>
75 <param name="param_fasta" type="data" format="fasta" optional="False" label="Input database file" help="(-fasta) "/> 99 <param name="fasta" argument="-fasta" type="data" format="fasta" optional="false" label="Input database file" help=" select fasta data sets(s)"/>
76 <param name="param_in" type="data" format="idxml,consensusxml" multiple="true" optional="True" size="30" label="Input file(s) holding experimental data" help="(-in) "> 100 <param name="in" argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/>
77 <sanitizer> 101 <param name="in_path" argument="-in_path" type="text" optional="true" value="" label="Path to idXMLs or consensusXMLs files" help="Ignored if 'in' is given">
78 <valid initial="string.printable"> 102 <expand macro="list_string_san"/>
79 <remove value="'"/>
80 <remove value="&quot;"/>
81 </valid>
82 </sanitizer>
83 </param> 103 </param>
84 <param name="param_in_path" type="text" size="30" label="Path to idXMLs or consensusXMLs files" help="(-in_path) Ignored if 'in' is given"> 104 <param name="design" argument="-design" type="data" format="txt" optional="true" label="Text file containing the experimental design" help="See documentation for specific format requirements select txt data sets(s)"/>
85 <sanitizer> 105 <section name="resolver" title="Additional options for algorithm" help="" expanded="false">
86 <valid initial="string.printable"> 106 <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" optional="true" min="0" value="2" label="Number of allowed missed cleavages" help=""/>
87 <remove value="'"/> 107 <param name="min_length" argument="-resolver:min_length" type="integer" optional="true" min="1" value="6" label="Minimum length of peptide" help=""/>
88 <remove value="&quot;"/> 108 <param name="enzyme" argument="-resolver:enzyme" display="radio" type="select" optional="false" label="Digestion enzyme" help="">
89 </valid> 109 <option value="Trypsin" selected="true">Trypsin</option>
90 </sanitizer> 110 <expand macro="list_string_san"/>
111 </param>
112 </section>
113 <section name="designer" title="Additional options for quantitative experimental design" help="" expanded="false">
114 <param name="experiment" argument="-designer:experiment" type="text" optional="true" value="ExperimentalSetting" label="Identifier for the experimental design" help="">
115 <expand macro="list_string_san"/>
116 </param>
117 <param name="file" argument="-designer:file" type="text" optional="true" value="File" label="Identifier for the file name" help="">
118 <expand macro="list_string_san"/>
119 </param>
120 <param name="separator" argument="-designer:separator" display="radio" type="select" optional="false" label="Separator, which should be used to split a row into columns" help="">
121 <option value="tab" selected="true">tab</option>
122 <option value="semi-colon">semi-colon</option>
123 <option value="comma">comma</option>
124 <option value="whitespace">whitespace</option>
125 <expand macro="list_string_san"/>
126 </param>
127 </section>
128 <expand macro="adv_opts_macro">
129 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
130 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
131 <expand macro="list_string_san"/>
132 </param>
133 </expand>
134 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
135 <option value="protein_groups_FLAG">protein_groups (Separator, which should be used to split a row into columns)</option>
136 <option value="peptide_table_FLAG">peptide_table (Separator, which should be used to split a row into columns)</option>
137 <option value="protein_table_FLAG">protein_table (Separator, which should be used to split a row into columns)</option>
138 <option value="additional_info_FLAG">additional_info (Separator, which should be used to split a row into columns)</option>
139 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
91 </param> 140 </param>
92 <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"/>
93 <param name="param_resolver_missed_cleavages" type="integer" min="0" optional="True" value="2" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/>
94 <param name="param_resolver_min_length" type="integer" min="1" optional="True" value="6" label="Minimum length of peptide" help="(-min_length) "/>
95 <param name="param_resolver_enzyme" display="radio" type="select" optional="False" value="Trypsin" label="Digestion enzyme" help="(-enzyme) ">
96 <option value="Trypsin" selected="true">Trypsin</option>
97 </param>
98 <param name="param_designer_experiment" type="text" size="30" value="ExperimentalSetting" label="Identifier for the experimental design" help="(-experiment) ">
99 <sanitizer>
100 <valid initial="string.printable">
101 <remove value="'"/>
102 <remove value="&quot;"/>
103 </valid>
104 </sanitizer>
105 </param>
106 <param name="param_designer_file" type="text" size="30" value="File" label="Identifier for the file name" help="(-file) ">
107 <sanitizer>
108 <valid initial="string.printable">
109 <remove value="'"/>
110 <remove value="&quot;"/>
111 </valid>
112 </sanitizer>
113 </param>
114 <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) ">
115 <option value="tab" selected="true">tab</option>
116 <option value="semi-colon">semi-colon</option>
117 <option value="comma">comma</option>
118 <option value="whitespace">whitespace</option>
119 </param>
120 <expand macro="advanced_options">
121 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
122 </expand>
123 </inputs> 141 </inputs>
124 <outputs> 142 <outputs>
125 <data name="param_protein_groups" format="tabular"/> 143 <data name="protein_groups" label="${tool.name} on ${on_string}: protein_groups" format="csv">
126 <data name="param_peptide_table" format="tabular"/> 144 <filter>OPTIONAL_OUTPUTS is not None and "protein_groups_FLAG" in OPTIONAL_OUTPUTS</filter>
127 <data name="param_protein_table" format="tabular"/> 145 </data>
128 <data name="param_additional_info" format="tabular"/> 146 <data name="peptide_table" label="${tool.name} on ${on_string}: peptide_table" format="csv">
147 <filter>OPTIONAL_OUTPUTS is not None and "peptide_table_FLAG" in OPTIONAL_OUTPUTS</filter>
148 </data>
149 <data name="protein_table" label="${tool.name} on ${on_string}: protein_table" format="csv">
150 <filter>OPTIONAL_OUTPUTS is not None and "protein_table_FLAG" in OPTIONAL_OUTPUTS</filter>
151 </data>
152 <data name="additional_info" label="${tool.name} on ${on_string}: additional_info" format="csv">
153 <filter>OPTIONAL_OUTPUTS is not None and "additional_info_FLAG" in OPTIONAL_OUTPUTS</filter>
154 </data>
155 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
156 <filter>OPTIONAL_OUTPUTS is None</filter>
157 </data>
158 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
159 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
160 </data>
129 </outputs> 161 </outputs>
130 <help>protein inference 162 <tests>
163 <expand macro="autotest_ProteinResolver"/>
164 <expand macro="manutest_ProteinResolver"/>
165 </tests>
166 <help><![CDATA[protein inference
131 167
132 168
133 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ProteinResolver.html</help> 169 For more information, visit http://www.openms.de/documentation/TOPP_ProteinResolver.html]]></help>
170 <expand macro="references"/>
134 </tool> 171 </tool>