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comparison MzTabExporter.xml @ 13:2735db4dd8d9 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:23:13 +0000
parents 9bf4fbcf20c8
children 748dfbdf2201
comparison
equal deleted inserted replaced
12:ee860980edc6 13:2735db4dd8d9
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: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="MzTabExporter" name="MzTabExporter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <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> 5 <description>Exports various XML formats to an mzTab file.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MzTabExporter</token> 7 <token name="@EXECUTABLE@">MzTabExporter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
43 <configfiles> 41 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 44 </configfiles>
47 <inputs> 45 <inputs>
48 <param name="in" 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)"/> 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)"/>
49 <param name="opt_columns" argument="-opt_columns" multiple="true" type="select" optional="true" label="Add optional columns which are not part of the mzTab standard" help=""> 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="">
50 <option value="subfeatures" selected="true">subfeatures</option> 48 <option value="subfeatures" selected="true">subfeatures</option>
51 <expand macro="list_string_san"/> 49 <expand macro="list_string_san" name="opt_columns"/>
52 </param> 50 </param>
53 <expand macro="adv_opts_macro"> 51 <expand macro="adv_opts_macro">
54 <param name="first_run_inference_only" 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"/> 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"/>
55 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 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=""/>
56 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
57 <expand macro="list_string_san"/> 55 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
56 <expand macro="list_string_san" name="test"/>
58 </param> 57 </param>
59 </expand> 58 </expand>
60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
62 </param> 61 </param>
65 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/> 64 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
68 </data> 67 </data>
69 </outputs> 68 </outputs>
70 <tests> 69 <tests><!-- TOPP_MzTabExporter_1 -->
71 <expand macro="autotest_MzTabExporter"/> 70 <test expect_num_outputs="2">
72 <expand macro="manutest_MzTabExporter"/> 71 <section name="adv_opts">
72 <param name="first_run_inference_only" value="false"/>
73 <param name="export_all_psms" value="false"/>
74 <param name="force" value="false"/>
75 <param name="test" value="true"/>
76 </section>
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"/>
79 <param name="opt_columns" value="subfeatures"/>
80 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
81 <output name="ctd_out" ftype="xml">
82 <assert_contents>
83 <is_valid_xml/>
84 </assert_contents>
85 </output>
86 </test>
87 <!-- TOPP_MzTabExporter_2 -->
88 <test expect_num_outputs="2">
89 <section name="adv_opts">
90 <param name="first_run_inference_only" value="false"/>
91 <param name="export_all_psms" value="false"/>
92 <param name="force" value="false"/>
93 <param name="test" value="true"/>
94 </section>
95 <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"/>
97 <param name="opt_columns" value="subfeatures"/>
98 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
99 <output name="ctd_out" ftype="xml">
100 <assert_contents>
101 <is_valid_xml/>
102 </assert_contents>
103 </output>
104 </test>
105 <!-- TOPP_MzTabExporter_3 -->
106 <test expect_num_outputs="2">
107 <section name="adv_opts">
108 <param name="first_run_inference_only" value="false"/>
109 <param name="export_all_psms" value="false"/>
110 <param name="force" value="false"/>
111 <param name="test" value="true"/>
112 </section>
113 <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"/>
115 <param name="opt_columns" value="subfeatures"/>
116 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
117 <output name="ctd_out" ftype="xml">
118 <assert_contents>
119 <is_valid_xml/>
120 </assert_contents>
121 </output>
122 </test>
123 <!-- TOPP_MzTabExporter_4 -->
124 <test expect_num_outputs="2">
125 <section name="adv_opts">
126 <param name="first_run_inference_only" value="false"/>
127 <param name="export_all_psms" value="false"/>
128 <param name="force" value="false"/>
129 <param name="test" value="true"/>
130 </section>
131 <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"/>
133 <param name="opt_columns" value="subfeatures"/>
134 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
135 <output name="ctd_out" ftype="xml">
136 <assert_contents>
137 <is_valid_xml/>
138 </assert_contents>
139 </output>
140 </test>
141 <!-- TOPP_MzTabExporter_5 -->
142 <test expect_num_outputs="2">
143 <section name="adv_opts">
144 <param name="first_run_inference_only" value="true"/>
145 <param name="export_all_psms" value="false"/>
146 <param name="force" value="false"/>
147 <param name="test" value="true"/>
148 </section>
149 <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"/>
151 <param name="opt_columns" value="subfeatures"/>
152 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
153 <output name="ctd_out" ftype="xml">
154 <assert_contents>
155 <is_valid_xml/>
156 </assert_contents>
157 </output>
158 </test>
159 <!-- TOPP_MzTabExporter_6 -->
160 <test expect_num_outputs="2">
161 <section name="adv_opts">
162 <param name="first_run_inference_only" value="false"/>
163 <param name="export_all_psms" value="false"/>
164 <param name="force" value="false"/>
165 <param name="test" value="true"/>
166 </section>
167 <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"/>
169 <param name="opt_columns" value="subfeatures"/>
170 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
171 <output name="ctd_out" ftype="xml">
172 <assert_contents>
173 <is_valid_xml/>
174 </assert_contents>
175 </output>
176 </test>
177 <!-- TOPP_MzTabExporter_7 -->
178 <test expect_num_outputs="2">
179 <section name="adv_opts">
180 <param name="first_run_inference_only" value="false"/>
181 <param name="export_all_psms" value="false"/>
182 <param name="force" value="false"/>
183 <param name="test" value="true"/>
184 </section>
185 <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"/>
187 <param name="opt_columns" value="subfeatures"/>
188 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
189 <output name="ctd_out" ftype="xml">
190 <assert_contents>
191 <is_valid_xml/>
192 </assert_contents>
193 </output>
194 </test>
195 <!-- TOPP_MzTabExporter_8 -->
196 <test expect_num_outputs="2">
197 <section name="adv_opts">
198 <param name="first_run_inference_only" value="false"/>
199 <param name="export_all_psms" value="true"/>
200 <param name="force" value="false"/>
201 <param name="test" value="true"/>
202 </section>
203 <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"/>
205 <param name="opt_columns" value="subfeatures"/>
206 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
207 <output name="ctd_out" ftype="xml">
208 <assert_contents>
209 <is_valid_xml/>
210 </assert_contents>
211 </output>
212 </test>
73 </tests> 213 </tests>
74 <help><![CDATA[Exports various XML formats to an mzTab file. 214 <help><![CDATA[Exports various XML formats to an mzTab file.
75 215
76 216
77 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MzTabExporter.html]]></help> 217 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MzTabExporter.html]]></help>
78 <expand macro="references"/> 218 <expand macro="references"/>
79 </tool> 219 </tool>