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comparison ProteinResolver.xml @ 14:c2612cb89529 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:31:23 +0000
parents 851f7c252d66
children
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13:851f7c252d66 14:c2612cb89529
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="ProteinResolver" name="ProteinResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="ProteinResolver" name="ProteinResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>protein inference</description> 4 <description>protein inference</description>
6 <macros> 5 <macros>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir fasta && 16 mkdir fasta &&
18 ln -s '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' && 17 cp '$fasta' 'fasta/${re.sub("[^\w\-_]", "_", $fasta.element_identifier)}.$gxy2omsext($fasta.ext)' &&
19 #if $in_cond.in: 18 #if $in_cond.in:
20 mkdir in_cond.in && 19 mkdir in_cond.in &&
21 #if $in_cond.in_select == "no" 20 #if $in_cond.in_select == "no"
22 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 21 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
23 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} 22 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
24 #else 23 #else
25 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && 24 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
26 #end if 25 #end if
27 #end if 26 #end if
28 #if $design: 27 #if $design:
29 mkdir design && 28 mkdir design &&
30 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && 29 cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
31 #end if 30 #end if
32 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 31 #if "protein_groups_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
33 mkdir protein_groups && 32 mkdir protein_groups &&
34 #end if 33 #end if
35 #if "peptide_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 34 #if "peptide_table_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
101 <configfiles> 100 <configfiles>
102 <inputs name="args_json" data_style="paths"/> 101 <inputs name="args_json" data_style="paths"/>
103 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 102 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
104 </configfiles> 103 </configfiles>
105 <inputs> 104 <inputs>
106 <param argument="-fasta" type="data" format="fasta" optional="false" label="Input database file" help=" select fasta data sets(s)"/> 105 <param argument="-fasta" type="data" format="fasta" label="Input database file" help=" select fasta data sets(s)"/>
107 <conditional name="in_cond"> 106 <conditional name="in_cond">
108 <param name="in_select" type="select" label="Run tool in batch mode for -in"> 107 <param name="in_select" type="select" label="Run tool in batch mode for -in">
109 <option value="no">No: process all datasets jointly</option> 108 <option value="no">No: process all datasets jointly</option>
110 <option value="yes">Yes: process each dataset in an independent job</option> 109 <option value="yes">Yes: process each dataset in an independent job</option>
111 </param> 110 </param>
112 <when value="no"> 111 <when value="no">
113 <param 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)"/> 112 <param 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)"/>
114 </when> 113 </when>
115 <when value="yes"> 114 <when value="yes">
116 <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/> 115 <param argument="-in" type="data" format="consensusxml,idxml" optional="true" label="Input file(s) holding experimental data" help=" select consensusxml,idxml data sets(s)"/>
117 </when> 116 </when>
118 </conditional> 117 </conditional>
119 <param argument="-in_path" type="text" optional="true" value="" label="Path to idXMLs or consensusXMLs files" help="Ignored if 'in' is given"> 118 <param argument="-in_path" type="text" optional="true" value="" label="Path to idXMLs or consensusXMLs files" help="Ignored if 'in' is given">
120 <expand macro="list_string_san" name="in_path"/> 119 <expand macro="list_string_san" name="in_path"/>
121 </param> 120 </param>
122 <param 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)"/> 121 <param 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)"/>
123 <section name="resolver" title="Additional options for algorithm" help="" expanded="false"> 122 <section name="resolver" title="Additional options for algorithm" help="" expanded="false">
124 <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" optional="true" min="0" value="2" label="Number of allowed missed cleavages" help=""/> 123 <param name="missed_cleavages" argument="-resolver:missed_cleavages" type="integer" min="0" value="2" label="Number of allowed missed cleavages" help=""/>
125 <param name="min_length" argument="-resolver:min_length" type="integer" optional="true" min="1" value="6" label="Minimum length of peptide" help=""/> 124 <param name="min_length" argument="-resolver:min_length" type="integer" min="1" value="6" label="Minimum length of peptide" help=""/>
126 <param name="enzyme" argument="-resolver:enzyme" type="select" optional="true" label="Digestion enzyme" help=""> 125 <param name="enzyme" argument="-resolver:enzyme" type="select" label="Digestion enzyme" help="">
127 <option value="Trypsin" selected="true">Trypsin</option> 126 <option value="Trypsin" selected="true">Trypsin</option>
128 <expand macro="list_string_san" name="enzyme"/> 127 <expand macro="list_string_san" name="enzyme"/>
129 </param> 128 </param>
130 </section> 129 </section>
131 <section name="designer" title="Additional options for quantitative experimental design" help="" expanded="false"> 130 <section name="designer" title="Additional options for quantitative experimental design" help="" expanded="false">
132 <param name="experiment" argument="-designer:experiment" type="text" optional="true" value="ExperimentalSetting" label="Identifier for the experimental design" help=""> 131 <param name="experiment" argument="-designer:experiment" type="text" value="ExperimentalSetting" label="Identifier for the experimental design" help="">
133 <expand macro="list_string_san" name="experiment"/> 132 <expand macro="list_string_san" name="experiment"/>
134 </param> 133 </param>
135 <param name="file" argument="-designer:file" type="text" optional="true" value="File" label="Identifier for the file name" help=""> 134 <param name="file" argument="-designer:file" type="text" value="File" label="Identifier for the file name" help="">
136 <expand macro="list_string_san" name="file"/> 135 <expand macro="list_string_san" name="file"/>
137 </param> 136 </param>
138 <param name="separator" argument="-designer:separator" type="select" optional="true" label="Separator, which should be used to split a row into columns" help=""> 137 <param name="separator" argument="-designer:separator" type="select" label="Separator, which should be used to split a row into columns" help="">
139 <option value="tab" selected="true">tab</option> 138 <option value="tab" selected="true">tab</option>
140 <option value="semi-colon">semi-colon</option> 139 <option value="semi-colon">semi-colon</option>
141 <option value="comma">comma</option> 140 <option value="comma">comma</option>
142 <option value="whitespace">whitespace</option> 141 <option value="whitespace">whitespace</option>
143 <expand macro="list_string_san" name="separator"/> 142 <expand macro="list_string_san" name="separator"/>
144 </param> 143 </param>
145 </section> 144 </section>
146 <expand macro="adv_opts_macro"> 145 <expand macro="adv_opts_macro">
147 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 146 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
148 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 147 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
149 <expand macro="list_string_san" name="test"/> 148 <expand macro="list_string_san" name="test"/>
150 </param> 149 </param>
151 </expand> 150 </expand>
152 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 151 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
153 <option value="protein_groups_FLAG">protein_groups (output file. Contains all protein groups)</option> 152 <option value="protein_groups_FLAG">protein_groups (output file. Contains all protein groups)</option>
175 </data> 174 </data>
176 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 175 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
177 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 176 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
178 </data> 177 </data>
179 </outputs> 178 </outputs>
180 <tests><!-- TOPP_ProteinResolver_1 --> 179 <tests>
180 <!-- TOPP_ProteinResolver_1 -->
181 <test expect_num_outputs="4"> 181 <test expect_num_outputs="4">
182 <section name="adv_opts"> 182 <section name="adv_opts">
183 <param name="force" value="false"/> 183 <param name="force" value="false"/>
184 <param name="test" value="true"/> 184 <param name="test" value="true"/>
185 </section> 185 </section>
186 <param name="fasta" value="ProteinResolver_1_input.fasta"/> 186 <param name="fasta" value="ProteinResolver_1_input.fasta"/>
187 <conditional name="in_cond"> 187 <conditional name="in_cond">
188 <param name="in" value="ProteinResolver_1_input.consensusXML"/> 188 <param name="in" value="ProteinResolver_1_input.consensusXML"/>
189 </conditional> 189 </conditional>
190 <param name="in_path" value=""/> 190 <param name="in_path" value=""/>
191 <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 191 <output name="protein_groups" value="ProteinResolver_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
192 <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 192 <output name="peptide_table" value="ProteinResolver_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
193 <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 193 <output name="protein_table" value="ProteinResolver_1_output3.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
194 <section name="resolver"> 194 <section name="resolver">
195 <param name="missed_cleavages" value="2"/> 195 <param name="missed_cleavages" value="2"/>
196 <param name="min_length" value="6"/> 196 <param name="min_length" value="6"/>
197 <param name="enzyme" value="Trypsin"/> 197 <param name="enzyme" value="Trypsin"/>
198 </section> 198 </section>
205 <output name="ctd_out" ftype="xml"> 205 <output name="ctd_out" ftype="xml">
206 <assert_contents> 206 <assert_contents>
207 <is_valid_xml/> 207 <is_valid_xml/>
208 </assert_contents> 208 </assert_contents>
209 </output> 209 </output>
210 <assert_stdout>
211 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
212 </assert_stdout>
210 </test> 213 </test>
211 </tests> 214 </tests>
212 <help><![CDATA[protein inference 215 <help><![CDATA[protein inference
213 216
214 217
215 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinResolver.html]]></help> 218 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ProteinResolver.html]]></help>
216 <expand macro="references"/> 219 <expand macro="references"/>
217 </tool> 220 </tool>