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comparison MzTabExporter.xml @ 14:748dfbdf2201 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 21:34:36 +0000
parents 2735db4dd8d9
children
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13:2735db4dd8d9 14:748dfbdf2201
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: [File Handling]--> 2 <!--Proposed Tool Section: [File Converter]-->
4 <tool id="MzTabExporter" name="MzTabExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="MzTabExporter" name="MzTabExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Exports various XML formats to an mzTab file.</description> 4 <description>Exports various XML formats to an mzTab file</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MzTabExporter</token> 6 <token name="@EXECUTABLE@">MzTabExporter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 #if $in: 16 #if $in:
18 mkdir in && 17 mkdir in &&
19 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 18 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
20 #end if 19 #end if
21 mkdir out && 20 mkdir out &&
22 21
23 ## Main program call 22 ## Main program call
24 23
42 <inputs name="args_json" data_style="paths"/> 41 <inputs name="args_json" data_style="paths"/>
43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
44 </configfiles> 43 </configfiles>
45 <inputs> 44 <inputs>
46 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzid" optional="true" label="Input files used to generate the mzTab file" help=" select consensusxml,featurexml,idxml,mzid data sets(s)"/> 45 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzid" optional="true" label="Input files used to generate the mzTab file" help=" select consensusxml,featurexml,idxml,mzid data sets(s)"/>
47 <param argument="-opt_columns" display="checkboxes" multiple="true" type="select" optional="true" label="Add optional columns which are not part of the mzTab standard" help=""> 46 <param argument="-opt_columns" type="select" multiple="true" optional="false" label="Add optional columns which are not part of the mzTab standard" help="">
48 <option value="subfeatures" selected="true">subfeatures</option> 47 <option value="subfeatures" selected="true">subfeatures</option>
49 <expand macro="list_string_san" name="opt_columns"/> 48 <expand macro="list_string_san" name="opt_columns"/>
50 </param> 49 </param>
51 <expand macro="adv_opts_macro"> 50 <expand macro="adv_opts_macro">
52 <param argument="-first_run_inference_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Does the first IdentificationRun in the file only represent (protein) inference results" help="If so, read peptide information only from second to last runs"/> 51 <param argument="-first_run_inference_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Does the first IdentificationRun in the file only represent (protein) inference results" help="If so, read peptide information only from second to last runs"/>
53 <param argument="-export_all_psms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export all PSMs instead of only the best per spectrum" help=""/> 52 <param argument="-export_all_psms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export all PSMs instead of only the best per spectrum" help=""/>
54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
55 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 54 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
56 <expand macro="list_string_san" name="test"/> 55 <expand macro="list_string_san" name="test"/>
57 </param> 56 </param>
58 </expand> 57 </expand>
59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
64 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/> 63 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
67 </data> 66 </data>
68 </outputs> 67 </outputs>
69 <tests><!-- TOPP_MzTabExporter_1 --> 68 <tests>
69 <!-- TOPP_MzTabExporter_1 -->
70 <test expect_num_outputs="2"> 70 <test expect_num_outputs="2">
71 <section name="adv_opts"> 71 <section name="adv_opts">
72 <param name="first_run_inference_only" value="false"/> 72 <param name="first_run_inference_only" value="false"/>
73 <param name="export_all_psms" value="false"/> 73 <param name="export_all_psms" value="false"/>
74 <param name="force" value="false"/> 74 <param name="force" value="false"/>
75 <param name="test" value="true"/> 75 <param name="test" value="true"/>
76 </section> 76 </section>
77 <param name="in" value="MzTabExporter_1_input.consensusXML"/> 77 <param name="in" value="MzTabExporter_1_input.consensusXML"/>
78 <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 78 <output name="out" value="MzTabExporter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
79 <param name="opt_columns" value="subfeatures"/> 79 <param name="opt_columns" value="subfeatures"/>
80 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 80 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
81 <output name="ctd_out" ftype="xml"> 81 <output name="ctd_out" ftype="xml">
82 <assert_contents> 82 <assert_contents>
83 <is_valid_xml/> 83 <is_valid_xml/>
84 </assert_contents> 84 </assert_contents>
85 </output> 85 </output>
86 <assert_stdout>
87 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
88 </assert_stdout>
86 </test> 89 </test>
87 <!-- TOPP_MzTabExporter_2 --> 90 <!-- TOPP_MzTabExporter_2 -->
88 <test expect_num_outputs="2"> 91 <test expect_num_outputs="2">
89 <section name="adv_opts"> 92 <section name="adv_opts">
90 <param name="first_run_inference_only" value="false"/> 93 <param name="first_run_inference_only" value="false"/>
91 <param name="export_all_psms" value="false"/> 94 <param name="export_all_psms" value="false"/>
92 <param name="force" value="false"/> 95 <param name="force" value="false"/>
93 <param name="test" value="true"/> 96 <param name="test" value="true"/>
94 </section> 97 </section>
95 <param name="in" value="MzTabExporter_2_input.idXML"/> 98 <param name="in" value="MzTabExporter_2_input.idXML"/>
96 <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 99 <output name="out" value="MzTabExporter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
97 <param name="opt_columns" value="subfeatures"/> 100 <param name="opt_columns" value="subfeatures"/>
98 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 101 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
99 <output name="ctd_out" ftype="xml"> 102 <output name="ctd_out" ftype="xml">
100 <assert_contents> 103 <assert_contents>
101 <is_valid_xml/> 104 <is_valid_xml/>
102 </assert_contents> 105 </assert_contents>
103 </output> 106 </output>
107 <assert_stdout>
108 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
109 </assert_stdout>
104 </test> 110 </test>
105 <!-- TOPP_MzTabExporter_3 --> 111 <!-- TOPP_MzTabExporter_3 -->
106 <test expect_num_outputs="2"> 112 <test expect_num_outputs="2">
107 <section name="adv_opts"> 113 <section name="adv_opts">
108 <param name="first_run_inference_only" value="false"/> 114 <param name="first_run_inference_only" value="false"/>
109 <param name="export_all_psms" value="false"/> 115 <param name="export_all_psms" value="false"/>
110 <param name="force" value="false"/> 116 <param name="force" value="false"/>
111 <param name="test" value="true"/> 117 <param name="test" value="true"/>
112 </section> 118 </section>
113 <param name="in" value="MzTabExporter_3_input.featureXML"/> 119 <param name="in" value="MzTabExporter_3_input.featureXML"/>
114 <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 120 <output name="out" value="MzTabExporter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
115 <param name="opt_columns" value="subfeatures"/> 121 <param name="opt_columns" value="subfeatures"/>
116 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 122 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
117 <output name="ctd_out" ftype="xml"> 123 <output name="ctd_out" ftype="xml">
118 <assert_contents> 124 <assert_contents>
119 <is_valid_xml/> 125 <is_valid_xml/>
120 </assert_contents> 126 </assert_contents>
121 </output> 127 </output>
128 <assert_stdout>
129 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
130 </assert_stdout>
122 </test> 131 </test>
123 <!-- TOPP_MzTabExporter_4 --> 132 <!-- TOPP_MzTabExporter_4 -->
124 <test expect_num_outputs="2"> 133 <test expect_num_outputs="2">
125 <section name="adv_opts"> 134 <section name="adv_opts">
126 <param name="first_run_inference_only" value="false"/> 135 <param name="first_run_inference_only" value="false"/>
127 <param name="export_all_psms" value="false"/> 136 <param name="export_all_psms" value="false"/>
128 <param name="force" value="false"/> 137 <param name="force" value="false"/>
129 <param name="test" value="true"/> 138 <param name="test" value="true"/>
130 </section> 139 </section>
131 <param name="in" value="Epifany_2_out.consensusXML"/> 140 <param name="in" value="Epifany_2_out.consensusXML"/>
132 <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 141 <output name="out" value="MzTabExporter_4_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
133 <param name="opt_columns" value="subfeatures"/> 142 <param name="opt_columns" value="subfeatures"/>
134 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 143 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
135 <output name="ctd_out" ftype="xml"> 144 <output name="ctd_out" ftype="xml">
136 <assert_contents> 145 <assert_contents>
137 <is_valid_xml/> 146 <is_valid_xml/>
138 </assert_contents> 147 </assert_contents>
139 </output> 148 </output>
149 <assert_stdout>
150 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
151 </assert_stdout>
140 </test> 152 </test>
141 <!-- TOPP_MzTabExporter_5 --> 153 <!-- TOPP_MzTabExporter_5 -->
142 <test expect_num_outputs="2"> 154 <test expect_num_outputs="2">
143 <section name="adv_opts"> 155 <section name="adv_opts">
144 <param name="first_run_inference_only" value="true"/> 156 <param name="first_run_inference_only" value="true"/>
145 <param name="export_all_psms" value="false"/> 157 <param name="export_all_psms" value="false"/>
146 <param name="force" value="false"/> 158 <param name="force" value="false"/>
147 <param name="test" value="true"/> 159 <param name="test" value="true"/>
148 </section> 160 </section>
149 <param name="in" value="MzTabExporter_5_in.consensusXML"/> 161 <param name="in" value="MzTabExporter_5_in.consensusXML"/>
150 <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 162 <output name="out" value="MzTabExporter_5_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
151 <param name="opt_columns" value="subfeatures"/> 163 <param name="opt_columns" value="subfeatures"/>
152 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 164 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
153 <output name="ctd_out" ftype="xml"> 165 <output name="ctd_out" ftype="xml">
154 <assert_contents> 166 <assert_contents>
155 <is_valid_xml/> 167 <is_valid_xml/>
156 </assert_contents> 168 </assert_contents>
157 </output> 169 </output>
170 <assert_stdout>
171 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
172 </assert_stdout>
158 </test> 173 </test>
159 <!-- TOPP_MzTabExporter_6 --> 174 <!-- TOPP_MzTabExporter_6 -->
160 <test expect_num_outputs="2"> 175 <test expect_num_outputs="2">
161 <section name="adv_opts"> 176 <section name="adv_opts">
162 <param name="first_run_inference_only" value="false"/> 177 <param name="first_run_inference_only" value="false"/>
163 <param name="export_all_psms" value="false"/> 178 <param name="export_all_psms" value="false"/>
164 <param name="force" value="false"/> 179 <param name="force" value="false"/>
165 <param name="test" value="true"/> 180 <param name="test" value="true"/>
166 </section> 181 </section>
167 <param name="in" value="MzTabExporter_6_input.idXML"/> 182 <param name="in" value="MzTabExporter_6_input.idXML"/>
168 <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 183 <output name="out" value="MzTabExporter_6_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
169 <param name="opt_columns" value="subfeatures"/> 184 <param name="opt_columns" value="subfeatures"/>
170 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 185 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
171 <output name="ctd_out" ftype="xml"> 186 <output name="ctd_out" ftype="xml">
172 <assert_contents> 187 <assert_contents>
173 <is_valid_xml/> 188 <is_valid_xml/>
174 </assert_contents> 189 </assert_contents>
175 </output> 190 </output>
191 <assert_stdout>
192 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
193 </assert_stdout>
176 </test> 194 </test>
177 <!-- TOPP_MzTabExporter_7 --> 195 <!-- TOPP_MzTabExporter_7 -->
178 <test expect_num_outputs="2"> 196 <test expect_num_outputs="2">
179 <section name="adv_opts"> 197 <section name="adv_opts">
180 <param name="first_run_inference_only" value="false"/> 198 <param name="first_run_inference_only" value="false"/>
181 <param name="export_all_psms" value="false"/> 199 <param name="export_all_psms" value="false"/>
182 <param name="force" value="false"/> 200 <param name="force" value="false"/>
183 <param name="test" value="true"/> 201 <param name="test" value="true"/>
184 </section> 202 </section>
185 <param name="in" value="MzTabExporter_7_input.consensusXML"/> 203 <param name="in" value="MzTabExporter_7_input.consensusXML"/>
186 <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 204 <output name="out" value="MzTabExporter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
187 <param name="opt_columns" value="subfeatures"/> 205 <param name="opt_columns" value="subfeatures"/>
188 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 206 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
189 <output name="ctd_out" ftype="xml"> 207 <output name="ctd_out" ftype="xml">
190 <assert_contents> 208 <assert_contents>
191 <is_valid_xml/> 209 <is_valid_xml/>
192 </assert_contents> 210 </assert_contents>
193 </output> 211 </output>
212 <assert_stdout>
213 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
214 </assert_stdout>
194 </test> 215 </test>
195 <!-- TOPP_MzTabExporter_8 --> 216 <!-- TOPP_MzTabExporter_8 -->
196 <test expect_num_outputs="2"> 217 <test expect_num_outputs="2">
197 <section name="adv_opts"> 218 <section name="adv_opts">
198 <param name="first_run_inference_only" value="false"/> 219 <param name="first_run_inference_only" value="false"/>
199 <param name="export_all_psms" value="true"/> 220 <param name="export_all_psms" value="true"/>
200 <param name="force" value="false"/> 221 <param name="force" value="false"/>
201 <param name="test" value="true"/> 222 <param name="test" value="true"/>
202 </section> 223 </section>
203 <param name="in" value="MzTabExporter_6_input.idXML"/> 224 <param name="in" value="MzTabExporter_6_input.idXML"/>
204 <output name="out" file="MzTabExporter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 225 <output name="out" value="MzTabExporter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
205 <param name="opt_columns" value="subfeatures"/> 226 <param name="opt_columns" value="subfeatures"/>
206 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 227 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
207 <output name="ctd_out" ftype="xml"> 228 <output name="ctd_out" ftype="xml">
208 <assert_contents> 229 <assert_contents>
209 <is_valid_xml/> 230 <is_valid_xml/>
210 </assert_contents> 231 </assert_contents>
211 </output> 232 </output>
233 <assert_stdout>
234 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
235 </assert_stdout>
212 </test> 236 </test>
213 </tests> 237 </tests>
214 <help><![CDATA[Exports various XML formats to an mzTab file. 238 <help><![CDATA[Exports various XML formats to an mzTab file.
215 239
216 240
217 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MzTabExporter.html]]></help> 241 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MzTabExporter.html]]></help>
218 <expand macro="references"/> 242 <expand macro="references"/>
219 </tool> 243 </tool>