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comparison MultiplexResolver.xml @ 14:53b202a738c3 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 21:32:24 +0000
parents 021fdb80f204
children
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13:021fdb80f204 14:53b202a738c3
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: [Utilities]--> 2 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Completes peptide multiplets and resolves conflicts within them.</description> 4 <description>Completes peptide multiplets and resolves conflicts within them</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MultiplexResolver</token> 6 <token name="@EXECUTABLE@">MultiplexResolver</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
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 #if $in_blacklist: 18 #if $in_blacklist:
20 mkdir in_blacklist && 19 mkdir in_blacklist &&
21 ln -s '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' && 20 cp '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' &&
22 #end if 21 #end if
23 mkdir out && 22 mkdir out &&
24 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 23 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir out_conflicts && 24 mkdir out_conflicts &&
26 #end if 25 #end if
58 <configfiles> 57 <configfiles>
59 <inputs name="args_json" data_style="paths"/> 58 <inputs name="args_json" data_style="paths"/>
60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 59 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
61 </configfiles> 60 </configfiles>
62 <inputs> 61 <inputs>
63 <param argument="-in" type="data" format="consensusxml" optional="false" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/> 62 <param argument="-in" type="data" format="consensusxml" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/>
64 <param argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/> 63 <param argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/>
65 <section name="algorithm" title="Parameters for the algorithm" help="" expanded="false"> 64 <section name="algorithm" title="Parameters for the algorithm" help="" expanded="false">
66 <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example. [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL"> 65 <param name="labels" argument="-algorithm:labels" type="text" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example. [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
67 <expand macro="list_string_san" name="labels"/> 66 <expand macro="list_string_san" name="labels"/>
68 </param> 67 </param>
69 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/> 68 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
70 <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" optional="true" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/> 69 <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/>
71 <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" optional="true" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/> 70 <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/>
72 <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" optional="true" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/> 71 <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/>
73 </section> 72 </section>
74 <section name="labels" title="Isotopic labels that can be specified in section 'algorithm:labels'" help="" expanded="false"> 73 <section name="labels" title="Isotopic labels that can be specified in section 'algorithm:labels'" help="" expanded="false">
75 <param name="Arg6" argument="-labels:Arg6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> 74 <param name="Arg6" argument="-labels:Arg6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
76 <param name="Arg10" argument="-labels:Arg10" type="float" optional="true" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/> 75 <param name="Arg10" argument="-labels:Arg10" type="float" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/>
77 <param name="Lys4" argument="-labels:Lys4" type="float" optional="true" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/> 76 <param name="Lys4" argument="-labels:Lys4" type="float" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/>
78 <param name="Lys6" argument="-labels:Lys6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> 77 <param name="Lys6" argument="-labels:Lys6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
79 <param name="Lys8" argument="-labels:Lys8" type="float" optional="true" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/> 78 <param name="Lys8" argument="-labels:Lys8" type="float" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/>
80 <param name="Leu3" argument="-labels:Leu3" type="float" optional="true" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/> 79 <param name="Leu3" argument="-labels:Leu3" type="float" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/>
81 <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" optional="true" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/> 80 <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/>
82 <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" optional="true" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/> 81 <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/>
83 <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" optional="true" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/> 82 <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/>
84 <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" optional="true" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/> 83 <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/>
85 <param name="ICPL0" argument="-labels:ICPL0" type="float" optional="true" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/> 84 <param name="ICPL0" argument="-labels:ICPL0" type="float" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/>
86 <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/> 85 <param name="ICPL4" argument="-labels:ICPL4" type="float" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/>
87 <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/> 86 <param name="ICPL6" argument="-labels:ICPL6" type="float" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/>
88 <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/> 87 <param name="ICPL10" argument="-labels:ICPL10" type="float" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/>
89 </section> 88 </section>
90 <expand macro="adv_opts_macro"> 89 <expand macro="adv_opts_macro">
91 <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=""/>
92 <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">
93 <expand macro="list_string_san" name="test"/> 92 <expand macro="list_string_san" name="test"/>
94 </param> 93 </param>
95 </expand> 94 </expand>
96 <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">
97 <option value="out_conflicts_FLAG">out_conflicts (Optional output containing peptide multiplets without ID annotation or with conflicting quant/ID information)</option> 96 <option value="out_conflicts_FLAG">out_conflicts (Optional output containing peptide multiplets without ID annotation or with conflicting quant/ID information)</option>
105 </data> 104 </data>
106 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 105 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
107 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 106 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
108 </data> 107 </data>
109 </outputs> 108 </outputs>
110 <tests><!-- UTILS_MultiplexResolver_1 --> 109 <tests>
110 <!-- TOPP_MultiplexResolver_1 -->
111 <test expect_num_outputs="3"> 111 <test expect_num_outputs="3">
112 <section name="adv_opts"> 112 <section name="adv_opts">
113 <param name="force" value="false"/> 113 <param name="force" value="false"/>
114 <param name="test" value="true"/> 114 <param name="test" value="true"/>
115 </section> 115 </section>
116 <param name="in" value="MultiplexResolver_1_input.consensusXML"/> 116 <param name="in" value="MultiplexResolver_1_input.consensusXML"/>
117 <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 117 <output name="out" value="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
118 <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 118 <output name="out_conflicts" value="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
119 <section name="algorithm"> 119 <section name="algorithm">
120 <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/> 120 <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/>
121 <param name="missed_cleavages" value="1"/> 121 <param name="missed_cleavages" value="1"/>
122 <param name="mass_tolerance" value="0.1"/> 122 <param name="mass_tolerance" value="0.1"/>
123 <param name="mz_tolerance" value="10"/> 123 <param name="mz_tolerance" value="10"/>
143 <output name="ctd_out" ftype="xml"> 143 <output name="ctd_out" ftype="xml">
144 <assert_contents> 144 <assert_contents>
145 <is_valid_xml/> 145 <is_valid_xml/>
146 </assert_contents> 146 </assert_contents>
147 </output> 147 </output>
148 </test> 148 <assert_stdout>
149 <!-- UTILS_MultiplexResolver_2 --> 149 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
150 </assert_stdout>
151 </test>
152 <!-- TOPP_MultiplexResolver_2 -->
150 <test expect_num_outputs="3"> 153 <test expect_num_outputs="3">
151 <section name="adv_opts"> 154 <section name="adv_opts">
152 <param name="force" value="false"/> 155 <param name="force" value="false"/>
153 <param name="test" value="true"/> 156 <param name="test" value="true"/>
154 </section> 157 </section>
155 <param name="in" value="MultiplexResolver_2_input.consensusXML"/> 158 <param name="in" value="MultiplexResolver_2_input.consensusXML"/>
156 <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 159 <output name="out" value="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
157 <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 160 <output name="out_conflicts" value="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
158 <section name="algorithm"> 161 <section name="algorithm">
159 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> 162 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
160 <param name="missed_cleavages" value="4"/> 163 <param name="missed_cleavages" value="4"/>
161 <param name="mass_tolerance" value="0.1"/> 164 <param name="mass_tolerance" value="0.1"/>
162 <param name="mz_tolerance" value="10"/> 165 <param name="mz_tolerance" value="10"/>
182 <output name="ctd_out" ftype="xml"> 185 <output name="ctd_out" ftype="xml">
183 <assert_contents> 186 <assert_contents>
184 <is_valid_xml/> 187 <is_valid_xml/>
185 </assert_contents> 188 </assert_contents>
186 </output> 189 </output>
187 </test> 190 <assert_stdout>
188 <!-- UTILS_MultiplexResolver_3 --> 191 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
192 </assert_stdout>
193 </test>
194 <!-- TOPP_MultiplexResolver_3 -->
189 <test expect_num_outputs="3"> 195 <test expect_num_outputs="3">
190 <section name="adv_opts"> 196 <section name="adv_opts">
191 <param name="force" value="false"/> 197 <param name="force" value="false"/>
192 <param name="test" value="true"/> 198 <param name="test" value="true"/>
193 </section> 199 </section>
194 <param name="in" value="MultiplexResolver_3_input.consensusXML"/> 200 <param name="in" value="MultiplexResolver_3_input.consensusXML"/>
195 <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 201 <output name="out" value="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
196 <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 202 <output name="out_conflicts" value="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
197 <section name="algorithm"> 203 <section name="algorithm">
198 <param name="labels" value="[][Leu3]"/> 204 <param name="labels" value="[][Leu3]"/>
199 <param name="missed_cleavages" value="2"/> 205 <param name="missed_cleavages" value="2"/>
200 <param name="mass_tolerance" value="0.1"/> 206 <param name="mass_tolerance" value="0.1"/>
201 <param name="mz_tolerance" value="10"/> 207 <param name="mz_tolerance" value="10"/>
221 <output name="ctd_out" ftype="xml"> 227 <output name="ctd_out" ftype="xml">
222 <assert_contents> 228 <assert_contents>
223 <is_valid_xml/> 229 <is_valid_xml/>
224 </assert_contents> 230 </assert_contents>
225 </output> 231 </output>
226 </test> 232 <assert_stdout>
227 <!-- UTILS_MultiplexResolver_4 --> 233 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
234 </assert_stdout>
235 </test>
236 <!-- TOPP_MultiplexResolver_4 -->
228 <test expect_num_outputs="3"> 237 <test expect_num_outputs="3">
229 <section name="adv_opts"> 238 <section name="adv_opts">
230 <param name="force" value="false"/> 239 <param name="force" value="false"/>
231 <param name="test" value="true"/> 240 <param name="test" value="true"/>
232 </section> 241 </section>
233 <param name="in" value="MultiplexResolver_4_input.consensusXML"/> 242 <param name="in" value="MultiplexResolver_4_input.consensusXML"/>
234 <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/> 243 <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/>
235 <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 244 <output name="out" value="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
236 <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 245 <output name="out_conflicts" value="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
237 <section name="algorithm"> 246 <section name="algorithm">
238 <param name="labels" value="[Dimethyl0][Dimethyl6]"/> 247 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
239 <param name="missed_cleavages" value="3"/> 248 <param name="missed_cleavages" value="3"/>
240 <param name="mass_tolerance" value="0.1"/> 249 <param name="mass_tolerance" value="0.1"/>
241 <param name="mz_tolerance" value="10"/> 250 <param name="mz_tolerance" value="10"/>
261 <output name="ctd_out" ftype="xml"> 270 <output name="ctd_out" ftype="xml">
262 <assert_contents> 271 <assert_contents>
263 <is_valid_xml/> 272 <is_valid_xml/>
264 </assert_contents> 273 </assert_contents>
265 </output> 274 </output>
275 <assert_stdout>
276 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
277 </assert_stdout>
266 </test> 278 </test>
267 </tests> 279 </tests>
268 <help><![CDATA[Completes peptide multiplets and resolves conflicts within them. 280 <help><![CDATA[Completes peptide multiplets and resolves conflicts within them.
269 281
270 282
271 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MultiplexResolver.html]]></help> 283 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MultiplexResolver.html]]></help>
272 <expand macro="references"/> 284 <expand macro="references"/>
273 </tool> 285 </tool>