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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 21:41:12 +0000
parents de7a553552a6
children
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13:de7a553552a6 14:74d39f98b0c4
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: [Targeted Experiments]--> 2 <!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
4 <tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Generates assays according to different models for a specific TraML</description> 4 <description>Generates assays according to different models for a specific TraML</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">OpenSwathAssayGenerator</token> 6 <token name="@EXECUTABLE@">OpenSwathAssayGenerator</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if $swath_windows_file: 19 #if $swath_windows_file:
21 mkdir swath_windows_file && 20 mkdir swath_windows_file &&
22 ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' && 21 cp '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
23 #end if 22 #end if
24 #if $unimod_file: 23 #if $unimod_file:
25 mkdir unimod_file && 24 mkdir unimod_file &&
26 ln -s '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)' && 25 cp '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)' &&
27 #end if 26 #end if
28 27
29 ## Main program call 28 ## Main program call
30 29
31 set -o pipefail && 30 set -o pipefail &&
53 <configfiles> 52 <configfiles>
54 <inputs name="args_json" data_style="paths"/> 53 <inputs name="args_json" data_style="paths"/>
55 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
56 </configfiles> 55 </configfiles>
57 <inputs> 56 <inputs>
58 <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/> 57 <param argument="-in" type="data" format="mrm,pqp,tabular,traml" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
59 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help=""> 58 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
60 <option value="TraML">traml</option> 59 <option value="TraML">traml</option>
61 <option value="pqp">pqp</option> 60 <option value="pqp">pqp</option>
62 <option value="tsv">tabular (tsv)</option> 61 <option value="tsv">tabular (tsv)</option>
62 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
63 <expand macro="list_string_san" name="out_type"/> 63 <expand macro="list_string_san" name="out_type"/>
64 </param> 64 </param>
65 <param argument="-min_transitions" type="integer" optional="true" value="6" label="minimal number of transitions" help=""/> 65 <param argument="-min_transitions" type="integer" value="6" label="minimal number of transitions" help=""/>
66 <param argument="-max_transitions" type="integer" optional="true" value="6" label="maximal number of transitions" help=""/> 66 <param argument="-max_transitions" type="integer" value="6" label="maximal number of transitions" help=""/>
67 <param argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help=""> 67 <param argument="-allowed_fragment_types" type="text" value="b,y" label="allowed fragment types" help="">
68 <expand macro="list_string_san" name="allowed_fragment_types"/> 68 <expand macro="list_string_san" name="allowed_fragment_types"/>
69 </param> 69 </param>
70 <param argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help=""> 70 <param argument="-allowed_fragment_charges" type="text" value="1,2,3,4" label="allowed fragment charge states" help="">
71 <expand macro="list_string_san" name="allowed_fragment_charges"/> 71 <expand macro="list_string_san" name="allowed_fragment_charges"/>
72 </param> 72 </param>
73 <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/> 73 <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
74 <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/> 74 <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
75 <param argument="-precursor_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/> 75 <param argument="-precursor_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/>
76 <param argument="-precursor_lower_mz_limit" type="float" optional="true" value="400.0" label="lower MZ limit for precursor ions" help=""/> 76 <param argument="-precursor_lower_mz_limit" type="float" value="400.0" label="lower MZ limit for precursor ions" help=""/>
77 <param argument="-precursor_upper_mz_limit" type="float" optional="true" value="1200.0" label="upper MZ limit for precursor ions" help=""/> 77 <param argument="-precursor_upper_mz_limit" type="float" value="1200.0" label="upper MZ limit for precursor ions" help=""/>
78 <param argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/> 78 <param argument="-product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
79 <param argument="-product_lower_mz_limit" type="float" optional="true" value="350.0" label="lower MZ limit for fragment ions" help=""/> 79 <param argument="-product_lower_mz_limit" type="float" value="350.0" label="lower MZ limit for fragment ions" help=""/>
80 <param argument="-product_upper_mz_limit" type="float" optional="true" value="2000.0" label="upper MZ limit for fragment ions" help=""/> 80 <param argument="-product_upper_mz_limit" type="float" value="2000.0" label="upper MZ limit for fragment ions" help=""/>
81 <param argument="-swath_windows_file" type="data" format="txt" optional="true" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline" help="Note that the first line is a header and will be skipped select txt data sets(s)"/> 81 <param argument="-swath_windows_file" type="data" format="txt" optional="true" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
82 <param argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/> 82 <param argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/>
83 <param argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/> 83 <param argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/>
84 <expand macro="adv_opts_macro"> 84 <expand macro="adv_opts_macro">
85 <param argument="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/> 85 <param argument="-max_num_alternative_localizations" type="integer" value="10000" label="IPF: maximum number of site-localization permutations" help=""/>
86 <param argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/> 86 <param argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/>
87 <param argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/> 87 <param argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/>
88 <param argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/> 88 <param argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/>
89 <param argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/> 89 <param argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/>
90 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 90 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
91 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 91 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
92 <expand macro="list_string_san" name="test"/> 92 <expand macro="list_string_san" name="test"/>
93 </param> 93 </param>
94 </expand> 94 </expand>
95 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 95 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
96 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 96 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
105 </data> 105 </data>
106 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 106 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
107 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 107 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
108 </data> 108 </data>
109 </outputs> 109 </outputs>
110 <tests><!-- TOPP_OpenSwathAssayGenerator_test_1 --> 110 <tests>
111 <!-- TOPP_OpenSwathAssayGenerator_test_1 -->
111 <test expect_num_outputs="2"> 112 <test expect_num_outputs="2">
112 <section name="adv_opts"> 113 <section name="adv_opts">
113 <param name="max_num_alternative_localizations" value="10000"/> 114 <param name="max_num_alternative_localizations" value="10000"/>
114 <param name="disable_identification_ms2_precursors" value="false"/> 115 <param name="disable_identification_ms2_precursors" value="false"/>
115 <param name="disable_identification_specific_losses" value="false"/> 116 <param name="disable_identification_specific_losses" value="false"/>
117 <param name="enable_swath_specifity" value="false"/> 118 <param name="enable_swath_specifity" value="false"/>
118 <param name="force" value="false"/> 119 <param name="force" value="false"/>
119 <param name="test" value="true"/> 120 <param name="test" value="true"/>
120 </section> 121 </section>
121 <param name="in" value="OpenSwathAssayGenerator_input.TraML"/> 122 <param name="in" value="OpenSwathAssayGenerator_input.TraML"/>
122 <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 123 <output name="out" value="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
123 <param name="out_type" value="TraML"/> 124 <param name="out_type" value="TraML"/>
124 <param name="min_transitions" value="6"/> 125 <param name="min_transitions" value="6"/>
125 <param name="max_transitions" value="6"/> 126 <param name="max_transitions" value="6"/>
126 <param name="allowed_fragment_types" value="b,y"/> 127 <param name="allowed_fragment_types" value="b,y"/>
127 <param name="allowed_fragment_charges" value="2,3"/> 128 <param name="allowed_fragment_charges" value="2,3"/>
138 <output name="ctd_out" ftype="xml"> 139 <output name="ctd_out" ftype="xml">
139 <assert_contents> 140 <assert_contents>
140 <is_valid_xml/> 141 <is_valid_xml/>
141 </assert_contents> 142 </assert_contents>
142 </output> 143 </output>
144 <assert_stdout>
145 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
146 </assert_stdout>
143 </test> 147 </test>
144 <!-- TOPP_OpenSwathAssayGenerator_test_2 --> 148 <!-- TOPP_OpenSwathAssayGenerator_test_2 -->
145 <test expect_num_outputs="2"> 149 <test expect_num_outputs="2">
146 <section name="adv_opts"> 150 <section name="adv_opts">
147 <param name="max_num_alternative_localizations" value="10000"/> 151 <param name="max_num_alternative_localizations" value="10000"/>
151 <param name="enable_swath_specifity" value="false"/> 155 <param name="enable_swath_specifity" value="false"/>
152 <param name="force" value="false"/> 156 <param name="force" value="false"/>
153 <param name="test" value="true"/> 157 <param name="test" value="true"/>
154 </section> 158 </section>
155 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> 159 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
156 <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 160 <output name="out" value="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
157 <param name="out_type" value="TraML"/> 161 <param name="out_type" value="TraML"/>
158 <param name="min_transitions" value="6"/> 162 <param name="min_transitions" value="6"/>
159 <param name="max_transitions" value="6"/> 163 <param name="max_transitions" value="6"/>
160 <param name="allowed_fragment_types" value="b,y"/> 164 <param name="allowed_fragment_types" value="b,y"/>
161 <param name="allowed_fragment_charges" value="1,2,3,4"/> 165 <param name="allowed_fragment_charges" value="1,2,3,4"/>
173 <output name="ctd_out" ftype="xml"> 177 <output name="ctd_out" ftype="xml">
174 <assert_contents> 178 <assert_contents>
175 <is_valid_xml/> 179 <is_valid_xml/>
176 </assert_contents> 180 </assert_contents>
177 </output> 181 </output>
182 <assert_stdout>
183 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
184 </assert_stdout>
178 </test> 185 </test>
179 <!-- TOPP_OpenSwathAssayGenerator_test_3 --> 186 <!-- TOPP_OpenSwathAssayGenerator_test_3 -->
180 <test expect_num_outputs="2"> 187 <test expect_num_outputs="2">
181 <section name="adv_opts"> 188 <section name="adv_opts">
182 <param name="max_num_alternative_localizations" value="10000"/> 189 <param name="max_num_alternative_localizations" value="10000"/>
186 <param name="enable_swath_specifity" value="false"/> 193 <param name="enable_swath_specifity" value="false"/>
187 <param name="force" value="false"/> 194 <param name="force" value="false"/>
188 <param name="test" value="true"/> 195 <param name="test" value="true"/>
189 </section> 196 </section>
190 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> 197 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
191 <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/> 198 <output name="out" value="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
192 <param name="out_type" value="TraML"/> 199 <param name="out_type" value="TraML"/>
193 <param name="min_transitions" value="6"/> 200 <param name="min_transitions" value="6"/>
194 <param name="max_transitions" value="6"/> 201 <param name="max_transitions" value="6"/>
195 <param name="allowed_fragment_types" value="b,y"/> 202 <param name="allowed_fragment_types" value="b,y"/>
196 <param name="allowed_fragment_charges" value="1,2,3,4"/> 203 <param name="allowed_fragment_charges" value="1,2,3,4"/>
208 <output name="ctd_out" ftype="xml"> 215 <output name="ctd_out" ftype="xml">
209 <assert_contents> 216 <assert_contents>
210 <is_valid_xml/> 217 <is_valid_xml/>
211 </assert_contents> 218 </assert_contents>
212 </output> 219 </output>
220 <assert_stdout>
221 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
222 </assert_stdout>
213 </test> 223 </test>
214 </tests> 224 </tests>
215 <help><![CDATA[Generates assays according to different models for a specific TraML 225 <help><![CDATA[Generates assays according to different models for a specific TraML
216 226
217 227
218 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathAssayGenerator.html]]></help> 228 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathAssayGenerator.html]]></help>
219 <expand macro="references"/> 229 <expand macro="references"/>
220 </tool> 230 </tool>