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comparison ProteinQuantifier.xml @ 14:89ece0562fe0 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 21:34:51 +0000
parents d426affe977c
children
comparison
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13:d426affe977c 14:89ece0562fe0
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="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Compute peptide and protein abundances</description> 4 <description>Compute peptide and protein abundances</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 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 $protein_groups: 18 #if $protein_groups:
20 mkdir protein_groups && 19 mkdir protein_groups &&
21 ln -s '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' && 20 cp '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' &&
22 #end if 21 #end if
23 #if $design: 22 #if $design:
24 mkdir design && 23 mkdir design &&
25 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && 24 cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
26 #end if 25 #end if
27 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 26 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
28 mkdir out && 27 mkdir out &&
29 #end if 28 #end if
30 #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 29 #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
82 <configfiles> 81 <configfiles>
83 <inputs name="args_json" data_style="paths"/> 82 <inputs name="args_json" data_style="paths"/>
84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 83 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
85 </configfiles> 84 </configfiles>
86 <inputs> 85 <inputs>
87 <param argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/> 86 <param argument="-in" type="data" format="consensusxml,featurexml,idxml" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
88 <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/> 87 <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. via the ProteinInference tool).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/>
89 <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/> 88 <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
90 <param argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/> 89 <param argument="-method" type="select" label="- top - quantify based on three most abundant peptides (number can be changed in 'top')" help="- iBAQ (intensity based absolute quantification), calculate the sum of all peptide peak intensities divided by the number of theoretically observable tryptic peptides (https://rdcu.be/cND1J). Warning: only consensusXML or featureXML input is allowed!">
91 <param argument="-average" type="select" optional="true" label="Averaging method used to compute protein abundances from peptide abundances" help=""> 90 <option value="top" selected="true">top</option>
92 <option value="median" selected="true">median</option> 91 <option value="iBAQ">iBAQ</option>
93 <option value="mean">mean</option> 92 <expand macro="list_string_san" name="method"/>
94 <option value="weighted_mean">weighted_mean</option>
95 <option value="sum">sum</option>
96 <expand macro="list_string_san" name="average"/>
97 </param> 93 </param>
98 <param argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/>
99 <param argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/> 94 <param argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/>
100 <param argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/> 95 <param argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/>
101 <param argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/> 96 <param argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/>
102 <param argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/> 97 <param argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/>
98 <section name="top" title="Additional options for custom quantification using top N peptides" help="" expanded="false">
99 <param name="N" argument="-top:N" type="integer" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/>
100 <param name="aggregate" argument="-top:aggregate" type="select" label="Aggregation method used to compute protein abundances from peptide abundances" help="">
101 <option value="median" selected="true">median</option>
102 <option value="mean">mean</option>
103 <option value="weighted_mean">weighted_mean</option>
104 <option value="sum">sum</option>
105 <expand macro="list_string_san" name="aggregate"/>
106 </param>
107 <param name="include_all" argument="-top:include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'N' (no effect if 'N' is 0 or 1)" help=""/>
108 </section>
103 <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false"> 109 <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false">
104 <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/> 110 <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/>
105 <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0',all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/> 111 <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'N 0',all peptides that occur in every sample are considered.. Otherwise ('N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
106 </section> 112 </section>
107 <section name="format" title="Output formatting options" help="" expanded="false"> 113 <section name="format" title="Output formatting options" help="" expanded="false">
108 <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help=""> 114 <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="">
109 <expand macro="list_string_san" name="separator"/> 115 <expand macro="list_string_san" name="separator"/>
110 </param> 116 </param>
111 <param name="quoting" argument="-format:quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes"> 117 <param name="quoting" argument="-format:quoting" type="select" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
112 <option value="none">none</option> 118 <option value="none">none</option>
113 <option value="double" selected="true">double</option> 119 <option value="double" selected="true">double</option>
114 <option value="escape">escape</option> 120 <option value="escape">escape</option>
115 <expand macro="list_string_san" name="quoting"/> 121 <expand macro="list_string_san" name="quoting"/>
116 </param> 122 </param>
117 <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help=""> 123 <param name="replacement" argument="-format:replacement" type="text" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="">
118 <expand macro="list_string_san" name="replacement"/> 124 <expand macro="list_string_san" name="replacement"/>
119 </param> 125 </param>
120 </section> 126 </section>
121 <expand macro="adv_opts_macro"> 127 <expand macro="adv_opts_macro">
122 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 128 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
123 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 129 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
124 <expand macro="list_string_san" name="test"/> 130 <expand macro="list_string_san" name="test"/>
125 </param> 131 </param>
126 </expand> 132 </expand>
127 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 133 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
128 <option value="out_FLAG">out (Output file for protein abundances)</option> 134 <option value="out_FLAG">out (Output file for protein abundances)</option>
146 </data> 152 </data>
147 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 153 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
148 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 154 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
149 </data> 155 </data>
150 </outputs> 156 </outputs>
151 <tests><!-- TOPP_ProteinQuantifier_1 --> 157 <tests>
158 <!-- TOPP_ProteinQuantifier_1 -->
152 <test expect_num_outputs="3"> 159 <test expect_num_outputs="3">
153 <section name="adv_opts"> 160 <section name="adv_opts">
154 <param name="force" value="false"/> 161 <param name="force" value="false"/>
155 <param name="test" value="true"/> 162 <param name="test" value="true"/>
156 </section> 163 </section>
157 <param name="in" value="ProteinQuantifier_input.featureXML"/> 164 <param name="in" value="ProteinQuantifier_input.featureXML"/>
158 <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 165 <output name="out" value="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
159 <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 166 <output name="peptide_out" value="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
160 <param name="top" value="3"/> 167 <param name="method" value="top"/>
161 <param name="average" value="median"/> 168 <param name="best_charge_and_fraction" value="false"/>
162 <param name="include_all" value="false"/> 169 <param name="greedy_group_resolution" value="false"/>
163 <param name="best_charge_and_fraction" value="false"/> 170 <param name="ratios" value="false"/>
164 <param name="greedy_group_resolution" value="false"/> 171 <param name="ratiosSILAC" value="false"/>
165 <param name="ratios" value="false"/> 172 <section name="top">
166 <param name="ratiosSILAC" value="false"/> 173 <param name="N" value="3"/>
174 <param name="aggregate" value="median"/>
175 <param name="include_all" value="false"/>
176 </section>
167 <section name="consensus"> 177 <section name="consensus">
168 <param name="normalize" value="false"/> 178 <param name="normalize" value="false"/>
169 <param name="fix_peptides" value="false"/> 179 <param name="fix_peptides" value="false"/>
170 </section> 180 </section>
171 <section name="format"> 181 <section name="format">
177 <output name="ctd_out" ftype="xml"> 187 <output name="ctd_out" ftype="xml">
178 <assert_contents> 188 <assert_contents>
179 <is_valid_xml/> 189 <is_valid_xml/>
180 </assert_contents> 190 </assert_contents>
181 </output> 191 </output>
192 <assert_stdout>
193 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
194 </assert_stdout>
182 </test> 195 </test>
183 <!-- TOPP_ProteinQuantifier_2 --> 196 <!-- TOPP_ProteinQuantifier_2 -->
184 <test expect_num_outputs="3"> 197 <test expect_num_outputs="3">
185 <section name="adv_opts"> 198 <section name="adv_opts">
186 <param name="force" value="false"/> 199 <param name="force" value="false"/>
187 <param name="test" value="true"/> 200 <param name="test" value="true"/>
188 </section> 201 </section>
189 <param name="in" value="ProteinQuantifier_input.featureXML"/> 202 <param name="in" value="ProteinQuantifier_input.featureXML"/>
190 <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 203 <output name="out" value="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
191 <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 204 <output name="peptide_out" value="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
192 <param name="top" value="2"/> 205 <param name="method" value="top"/>
193 <param name="average" value="sum"/>
194 <param name="include_all" value="true"/>
195 <param name="best_charge_and_fraction" value="true"/> 206 <param name="best_charge_and_fraction" value="true"/>
196 <param name="greedy_group_resolution" value="false"/> 207 <param name="greedy_group_resolution" value="false"/>
197 <param name="ratios" value="false"/> 208 <param name="ratios" value="false"/>
198 <param name="ratiosSILAC" value="false"/> 209 <param name="ratiosSILAC" value="false"/>
210 <section name="top">
211 <param name="N" value="2"/>
212 <param name="aggregate" value="sum"/>
213 <param name="include_all" value="true"/>
214 </section>
199 <section name="consensus"> 215 <section name="consensus">
200 <param name="normalize" value="false"/> 216 <param name="normalize" value="false"/>
201 <param name="fix_peptides" value="false"/> 217 <param name="fix_peptides" value="false"/>
202 </section> 218 </section>
203 <section name="format"> 219 <section name="format">
209 <output name="ctd_out" ftype="xml"> 225 <output name="ctd_out" ftype="xml">
210 <assert_contents> 226 <assert_contents>
211 <is_valid_xml/> 227 <is_valid_xml/>
212 </assert_contents> 228 </assert_contents>
213 </output> 229 </output>
230 <assert_stdout>
231 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
232 </assert_stdout>
214 </test> 233 </test>
215 <!-- TOPP_ProteinQuantifier_3 --> 234 <!-- TOPP_ProteinQuantifier_3 -->
216 <test expect_num_outputs="3"> 235 <test expect_num_outputs="3">
217 <section name="adv_opts"> 236 <section name="adv_opts">
218 <param name="force" value="false"/> 237 <param name="force" value="false"/>
219 <param name="test" value="true"/> 238 <param name="test" value="true"/>
220 </section> 239 </section>
221 <param name="in" value="ProteinQuantifier_3_input.featureXML"/> 240 <param name="in" value="ProteinQuantifier_3_input.featureXML"/>
222 <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 241 <output name="out" value="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
223 <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 242 <output name="peptide_out" value="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
224 <param name="top" value="2"/> 243 <param name="method" value="top"/>
225 <param name="average" value="mean"/> 244 <param name="best_charge_and_fraction" value="false"/>
226 <param name="include_all" value="true"/> 245 <param name="greedy_group_resolution" value="false"/>
227 <param name="best_charge_and_fraction" value="false"/> 246 <param name="ratios" value="false"/>
228 <param name="greedy_group_resolution" value="false"/> 247 <param name="ratiosSILAC" value="false"/>
229 <param name="ratios" value="false"/> 248 <section name="top">
230 <param name="ratiosSILAC" value="false"/> 249 <param name="N" value="2"/>
250 <param name="aggregate" value="mean"/>
251 <param name="include_all" value="true"/>
252 </section>
231 <section name="consensus"> 253 <section name="consensus">
232 <param name="normalize" value="false"/> 254 <param name="normalize" value="false"/>
233 <param name="fix_peptides" value="false"/> 255 <param name="fix_peptides" value="false"/>
234 </section> 256 </section>
235 <section name="format"> 257 <section name="format">
241 <output name="ctd_out" ftype="xml"> 263 <output name="ctd_out" ftype="xml">
242 <assert_contents> 264 <assert_contents>
243 <is_valid_xml/> 265 <is_valid_xml/>
244 </assert_contents> 266 </assert_contents>
245 </output> 267 </output>
268 <assert_stdout>
269 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
270 </assert_stdout>
246 </test> 271 </test>
247 <!-- TOPP_ProteinQuantifier_4 --> 272 <!-- TOPP_ProteinQuantifier_4 -->
248 <test expect_num_outputs="2"> 273 <test expect_num_outputs="2">
249 <section name="adv_opts"> 274 <section name="adv_opts">
250 <param name="force" value="false"/> 275 <param name="force" value="false"/>
251 <param name="test" value="true"/> 276 <param name="test" value="true"/>
252 </section> 277 </section>
253 <param name="in" value="ProteinQuantifier_input.consensusXML"/> 278 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
254 <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 279 <output name="out" value="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
255 <param name="top" value="0"/> 280 <param name="method" value="top"/>
256 <param name="average" value="sum"/> 281 <param name="best_charge_and_fraction" value="false"/>
257 <param name="include_all" value="false"/> 282 <param name="greedy_group_resolution" value="false"/>
258 <param name="best_charge_and_fraction" value="false"/> 283 <param name="ratios" value="false"/>
259 <param name="greedy_group_resolution" value="false"/> 284 <param name="ratiosSILAC" value="false"/>
260 <param name="ratios" value="false"/> 285 <section name="top">
261 <param name="ratiosSILAC" value="false"/> 286 <param name="N" value="0"/>
262 <section name="consensus"> 287 <param name="aggregate" value="sum"/>
263 <param name="normalize" value="false"/> 288 <param name="include_all" value="false"/>
264 <param name="fix_peptides" value="false"/> 289 </section>
265 </section> 290 <section name="consensus">
266 <section name="format"> 291 <param name="normalize" value="false"/>
267 <param name="separator" value=""/> 292 <param name="fix_peptides" value="false"/>
268 <param name="quoting" value="double"/> 293 </section>
269 <param name="replacement" value="_"/> 294 <section name="format">
270 </section> 295 <param name="separator" value=""/>
271 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 296 <param name="quoting" value="double"/>
272 <output name="ctd_out" ftype="xml"> 297 <param name="replacement" value="_"/>
273 <assert_contents> 298 </section>
274 <is_valid_xml/> 299 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
275 </assert_contents> 300 <output name="ctd_out" ftype="xml">
276 </output> 301 <assert_contents>
302 <is_valid_xml/>
303 </assert_contents>
304 </output>
305 <assert_stdout>
306 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
307 </assert_stdout>
277 </test> 308 </test>
278 <!-- TOPP_ProteinQuantifier_5 --> 309 <!-- TOPP_ProteinQuantifier_5 -->
279 <test expect_num_outputs="2"> 310 <test expect_num_outputs="2">
280 <section name="adv_opts"> 311 <section name="adv_opts">
281 <param name="force" value="false"/> 312 <param name="force" value="false"/>
282 <param name="test" value="true"/> 313 <param name="test" value="true"/>
283 </section> 314 </section>
284 <param name="in" value="ProteinQuantifier_input.consensusXML"/> 315 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
285 <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 316 <output name="out" value="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
286 <param name="top" value="3"/> 317 <param name="method" value="top"/>
287 <param name="average" value="sum"/> 318 <param name="best_charge_and_fraction" value="false"/>
288 <param name="include_all" value="false"/> 319 <param name="greedy_group_resolution" value="false"/>
289 <param name="best_charge_and_fraction" value="false"/> 320 <param name="ratios" value="false"/>
290 <param name="greedy_group_resolution" value="false"/> 321 <param name="ratiosSILAC" value="false"/>
291 <param name="ratios" value="false"/> 322 <section name="top">
292 <param name="ratiosSILAC" value="false"/> 323 <param name="N" value="3"/>
293 <section name="consensus"> 324 <param name="aggregate" value="sum"/>
294 <param name="normalize" value="false"/> 325 <param name="include_all" value="false"/>
295 <param name="fix_peptides" value="false"/> 326 </section>
296 </section> 327 <section name="consensus">
297 <section name="format"> 328 <param name="normalize" value="false"/>
298 <param name="separator" value=""/> 329 <param name="fix_peptides" value="false"/>
299 <param name="quoting" value="double"/> 330 </section>
300 <param name="replacement" value="_"/> 331 <section name="format">
301 </section> 332 <param name="separator" value=""/>
302 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 333 <param name="quoting" value="double"/>
303 <output name="ctd_out" ftype="xml"> 334 <param name="replacement" value="_"/>
304 <assert_contents> 335 </section>
305 <is_valid_xml/> 336 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
306 </assert_contents> 337 <output name="ctd_out" ftype="xml">
307 </output> 338 <assert_contents>
339 <is_valid_xml/>
340 </assert_contents>
341 </output>
342 <assert_stdout>
343 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
344 </assert_stdout>
308 </test> 345 </test>
309 <!-- TOPP_ProteinQuantifier_6 --> 346 <!-- TOPP_ProteinQuantifier_6 -->
310 <test expect_num_outputs="2"> 347 <test expect_num_outputs="2">
311 <section name="adv_opts"> 348 <section name="adv_opts">
312 <param name="force" value="false"/> 349 <param name="force" value="false"/>
313 <param name="test" value="true"/> 350 <param name="test" value="true"/>
314 </section> 351 </section>
315 <param name="in" value="ProteinQuantifier_input.consensusXML"/> 352 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
316 <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 353 <output name="out" value="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
317 <param name="top" value="3"/> 354 <param name="method" value="top"/>
318 <param name="average" value="sum"/> 355 <param name="best_charge_and_fraction" value="false"/>
319 <param name="include_all" value="true"/> 356 <param name="greedy_group_resolution" value="false"/>
320 <param name="best_charge_and_fraction" value="false"/> 357 <param name="ratios" value="false"/>
321 <param name="greedy_group_resolution" value="false"/> 358 <param name="ratiosSILAC" value="false"/>
322 <param name="ratios" value="false"/> 359 <section name="top">
323 <param name="ratiosSILAC" value="false"/> 360 <param name="N" value="3"/>
324 <section name="consensus"> 361 <param name="aggregate" value="sum"/>
325 <param name="normalize" value="false"/> 362 <param name="include_all" value="true"/>
326 <param name="fix_peptides" value="false"/> 363 </section>
327 </section> 364 <section name="consensus">
328 <section name="format"> 365 <param name="normalize" value="false"/>
329 <param name="separator" value=""/> 366 <param name="fix_peptides" value="false"/>
330 <param name="quoting" value="double"/> 367 </section>
331 <param name="replacement" value="_"/> 368 <section name="format">
332 </section> 369 <param name="separator" value=""/>
333 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> 370 <param name="quoting" value="double"/>
334 <output name="ctd_out" ftype="xml"> 371 <param name="replacement" value="_"/>
335 <assert_contents> 372 </section>
336 <is_valid_xml/> 373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
337 </assert_contents> 374 <output name="ctd_out" ftype="xml">
338 </output> 375 <assert_contents>
376 <is_valid_xml/>
377 </assert_contents>
378 </output>
379 <assert_stdout>
380 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
381 </assert_stdout>
339 </test> 382 </test>
340 <!-- TOPP_ProteinQuantifier_7 --> 383 <!-- TOPP_ProteinQuantifier_7 -->
341 <test expect_num_outputs="2"> 384 <test expect_num_outputs="2">
342 <section name="adv_opts"> 385 <section name="adv_opts">
343 <param name="force" value="false"/> 386 <param name="force" value="false"/>
344 <param name="test" value="true"/> 387 <param name="test" value="true"/>
345 </section> 388 </section>
346 <param name="in" value="ProteinQuantifier_input.consensusXML"/> 389 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
347 <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 390 <output name="out" value="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
348 <param name="top" value="0"/> 391 <param name="method" value="top"/>
349 <param name="average" value="sum"/> 392 <param name="best_charge_and_fraction" value="false"/>
350 <param name="include_all" value="false"/> 393 <param name="greedy_group_resolution" value="false"/>
351 <param name="best_charge_and_fraction" value="false"/> 394 <param name="ratios" value="false"/>
352 <param name="greedy_group_resolution" value="false"/> 395 <param name="ratiosSILAC" value="false"/>
353 <param name="ratios" value="false"/> 396 <section name="top">
354 <param name="ratiosSILAC" value="false"/> 397 <param name="N" value="0"/>
398 <param name="aggregate" value="sum"/>
399 <param name="include_all" value="false"/>
400 </section>
355 <section name="consensus"> 401 <section name="consensus">
356 <param name="normalize" value="false"/> 402 <param name="normalize" value="false"/>
357 <param name="fix_peptides" value="true"/> 403 <param name="fix_peptides" value="true"/>
358 </section> 404 </section>
359 <section name="format"> 405 <section name="format">
365 <output name="ctd_out" ftype="xml"> 411 <output name="ctd_out" ftype="xml">
366 <assert_contents> 412 <assert_contents>
367 <is_valid_xml/> 413 <is_valid_xml/>
368 </assert_contents> 414 </assert_contents>
369 </output> 415 </output>
416 <assert_stdout>
417 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
418 </assert_stdout>
370 </test> 419 </test>
371 <!-- TOPP_ProteinQuantifier_8 --> 420 <!-- TOPP_ProteinQuantifier_8 -->
372 <test expect_num_outputs="2"> 421 <test expect_num_outputs="2">
373 <section name="adv_opts"> 422 <section name="adv_opts">
374 <param name="force" value="false"/> 423 <param name="force" value="false"/>
375 <param name="test" value="true"/> 424 <param name="test" value="true"/>
376 </section> 425 </section>
377 <param name="in" value="ProteinQuantifier_input.consensusXML"/> 426 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
378 <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 427 <output name="out" value="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
379 <param name="top" value="3"/> 428 <param name="method" value="top"/>
380 <param name="average" value="sum"/> 429 <param name="best_charge_and_fraction" value="false"/>
381 <param name="include_all" value="false"/> 430 <param name="greedy_group_resolution" value="false"/>
382 <param name="best_charge_and_fraction" value="false"/> 431 <param name="ratios" value="false"/>
383 <param name="greedy_group_resolution" value="false"/> 432 <param name="ratiosSILAC" value="false"/>
384 <param name="ratios" value="false"/> 433 <section name="top">
385 <param name="ratiosSILAC" value="false"/> 434 <param name="N" value="3"/>
435 <param name="aggregate" value="sum"/>
436 <param name="include_all" value="false"/>
437 </section>
386 <section name="consensus"> 438 <section name="consensus">
387 <param name="normalize" value="false"/> 439 <param name="normalize" value="false"/>
388 <param name="fix_peptides" value="true"/> 440 <param name="fix_peptides" value="true"/>
389 </section> 441 </section>
390 <section name="format"> 442 <section name="format">
396 <output name="ctd_out" ftype="xml"> 448 <output name="ctd_out" ftype="xml">
397 <assert_contents> 449 <assert_contents>
398 <is_valid_xml/> 450 <is_valid_xml/>
399 </assert_contents> 451 </assert_contents>
400 </output> 452 </output>
453 <assert_stdout>
454 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
455 </assert_stdout>
401 </test> 456 </test>
402 <!-- TOPP_ProteinQuantifier_9 --> 457 <!-- TOPP_ProteinQuantifier_9 -->
403 <test expect_num_outputs="3"> 458 <test expect_num_outputs="3">
404 <section name="adv_opts"> 459 <section name="adv_opts">
405 <param name="force" value="false"/> 460 <param name="force" value="false"/>
406 <param name="test" value="true"/> 461 <param name="test" value="true"/>
407 </section> 462 </section>
408 <param name="in" value="ProteinQuantifier_input.consensusXML"/> 463 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
409 <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 464 <output name="out" value="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
410 <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> 465 <output name="mztab" value="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
411 <param name="top" value="3"/> 466 <param name="method" value="top"/>
412 <param name="average" value="sum"/> 467 <param name="best_charge_and_fraction" value="false"/>
413 <param name="include_all" value="true"/> 468 <param name="greedy_group_resolution" value="false"/>
414 <param name="best_charge_and_fraction" value="false"/> 469 <param name="ratios" value="false"/>
415 <param name="greedy_group_resolution" value="false"/> 470 <param name="ratiosSILAC" value="false"/>
416 <param name="ratios" value="false"/> 471 <section name="top">
417 <param name="ratiosSILAC" value="false"/> 472 <param name="N" value="3"/>
473 <param name="aggregate" value="sum"/>
474 <param name="include_all" value="true"/>
475 </section>
418 <section name="consensus"> 476 <section name="consensus">
419 <param name="normalize" value="false"/> 477 <param name="normalize" value="false"/>
420 <param name="fix_peptides" value="true"/> 478 <param name="fix_peptides" value="true"/>
421 </section> 479 </section>
422 <section name="format"> 480 <section name="format">
428 <output name="ctd_out" ftype="xml"> 486 <output name="ctd_out" ftype="xml">
429 <assert_contents> 487 <assert_contents>
430 <is_valid_xml/> 488 <is_valid_xml/>
431 </assert_contents> 489 </assert_contents>
432 </output> 490 </output>
491 <assert_stdout>
492 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
493 </assert_stdout>
433 </test> 494 </test>
434 <!-- TOPP_ProteinQuantifier_12 --> 495 <!-- TOPP_ProteinQuantifier_12 -->
435 <test expect_num_outputs="2"> 496 <test expect_num_outputs="2">
436 <section name="adv_opts"> 497 <section name="adv_opts">
437 <param name="force" value="false"/> 498 <param name="force" value="false"/>
438 <param name="test" value="true"/> 499 <param name="test" value="true"/>
439 </section> 500 </section>
440 <param name="in" value="ProteinQuantifier_input.consensusXML"/> 501 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
441 <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 502 <output name="out" value="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
442 <param name="top" value="3"/> 503 <param name="method" value="top"/>
443 <param name="average" value="sum"/>
444 <param name="include_all" value="true"/>
445 <param name="best_charge_and_fraction" value="false"/> 504 <param name="best_charge_and_fraction" value="false"/>
446 <param name="greedy_group_resolution" value="false"/> 505 <param name="greedy_group_resolution" value="false"/>
447 <param name="ratios" value="true"/> 506 <param name="ratios" value="true"/>
448 <param name="ratiosSILAC" value="false"/> 507 <param name="ratiosSILAC" value="false"/>
508 <section name="top">
509 <param name="N" value="3"/>
510 <param name="aggregate" value="sum"/>
511 <param name="include_all" value="true"/>
512 </section>
449 <section name="consensus"> 513 <section name="consensus">
450 <param name="normalize" value="false"/> 514 <param name="normalize" value="false"/>
451 <param name="fix_peptides" value="true"/> 515 <param name="fix_peptides" value="true"/>
452 </section> 516 </section>
453 <section name="format"> 517 <section name="format">
459 <output name="ctd_out" ftype="xml"> 523 <output name="ctd_out" ftype="xml">
460 <assert_contents> 524 <assert_contents>
461 <is_valid_xml/> 525 <is_valid_xml/>
462 </assert_contents> 526 </assert_contents>
463 </output> 527 </output>
528 <assert_stdout>
529 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
530 </assert_stdout>
464 </test> 531 </test>
465 <!-- TOPP_ProteinQuantifier_13 --> 532 <!-- TOPP_ProteinQuantifier_13 -->
466 <test expect_num_outputs="2"> 533 <test expect_num_outputs="2">
467 <section name="adv_opts"> 534 <section name="adv_opts">
468 <param name="force" value="false"/> 535 <param name="force" value="false"/>
469 <param name="test" value="true"/> 536 <param name="test" value="true"/>
470 </section> 537 </section>
471 <param name="in" value="ProteinQuantifier_input.consensusXML"/> 538 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
472 <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 539 <output name="out" value="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
473 <param name="top" value="3"/> 540 <param name="method" value="top"/>
474 <param name="average" value="sum"/>
475 <param name="include_all" value="true"/>
476 <param name="best_charge_and_fraction" value="false"/> 541 <param name="best_charge_and_fraction" value="false"/>
477 <param name="greedy_group_resolution" value="false"/> 542 <param name="greedy_group_resolution" value="false"/>
478 <param name="ratios" value="false"/> 543 <param name="ratios" value="false"/>
479 <param name="ratiosSILAC" value="true"/> 544 <param name="ratiosSILAC" value="true"/>
545 <section name="top">
546 <param name="N" value="3"/>
547 <param name="aggregate" value="sum"/>
548 <param name="include_all" value="true"/>
549 </section>
480 <section name="consensus"> 550 <section name="consensus">
481 <param name="normalize" value="false"/> 551 <param name="normalize" value="false"/>
482 <param name="fix_peptides" value="true"/> 552 <param name="fix_peptides" value="true"/>
483 </section> 553 </section>
484 <section name="format"> 554 <section name="format">
490 <output name="ctd_out" ftype="xml"> 560 <output name="ctd_out" ftype="xml">
491 <assert_contents> 561 <assert_contents>
492 <is_valid_xml/> 562 <is_valid_xml/>
493 </assert_contents> 563 </assert_contents>
494 </output> 564 </output>
565 <assert_stdout>
566 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
567 </assert_stdout>
495 </test> 568 </test>
496 <!-- TOPP_ProteinQuantifier_14 --> 569 <!-- TOPP_ProteinQuantifier_14 -->
497 <test expect_num_outputs="3"> 570 <test expect_num_outputs="3">
498 <section name="adv_opts"> 571 <section name="adv_opts">
499 <param name="force" value="false"/> 572 <param name="force" value="false"/>
500 <param name="test" value="true"/> 573 <param name="test" value="true"/>
501 </section> 574 </section>
502 <param name="in" value="ProteinQuantifier_input.idXML"/> 575 <param name="in" value="ProteinQuantifier_input.idXML"/>
503 <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 576 <output name="out" value="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
504 <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> 577 <output name="peptide_out" value="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
505 <param name="top" value="0"/> 578 <param name="method" value="top"/>
506 <param name="average" value="sum"/> 579 <param name="best_charge_and_fraction" value="false"/>
507 <param name="include_all" value="false"/> 580 <param name="greedy_group_resolution" value="false"/>
508 <param name="best_charge_and_fraction" value="false"/> 581 <param name="ratios" value="false"/>
509 <param name="greedy_group_resolution" value="false"/> 582 <param name="ratiosSILAC" value="false"/>
510 <param name="ratios" value="false"/> 583 <section name="top">
511 <param name="ratiosSILAC" value="false"/> 584 <param name="N" value="0"/>
585 <param name="aggregate" value="sum"/>
586 <param name="include_all" value="false"/>
587 </section>
512 <section name="consensus"> 588 <section name="consensus">
513 <param name="normalize" value="false"/> 589 <param name="normalize" value="false"/>
514 <param name="fix_peptides" value="false"/> 590 <param name="fix_peptides" value="false"/>
515 </section> 591 </section>
516 <section name="format"> 592 <section name="format">
522 <output name="ctd_out" ftype="xml"> 598 <output name="ctd_out" ftype="xml">
523 <assert_contents> 599 <assert_contents>
524 <is_valid_xml/> 600 <is_valid_xml/>
525 </assert_contents> 601 </assert_contents>
526 </output> 602 </output>
603 <assert_stdout>
604 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
605 </assert_stdout>
606 </test>
607 <!-- TOPP_ProteinQuantifier_15 -->
608 <test expect_num_outputs="2">
609 <section name="adv_opts">
610 <param name="force" value="false"/>
611 <param name="test" value="true"/>
612 </section>
613 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
614 <output name="out" value="ProteinQuantifier_15_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
615 <param name="method" value="iBAQ"/>
616 <param name="best_charge_and_fraction" value="false"/>
617 <param name="greedy_group_resolution" value="false"/>
618 <param name="ratios" value="false"/>
619 <param name="ratiosSILAC" value="false"/>
620 <section name="top">
621 <param name="N" value="3"/>
622 <param name="aggregate" value="median"/>
623 <param name="include_all" value="false"/>
624 </section>
625 <section name="consensus">
626 <param name="normalize" value="false"/>
627 <param name="fix_peptides" value="false"/>
628 </section>
629 <section name="format">
630 <param name="separator" value=""/>
631 <param name="quoting" value="double"/>
632 <param name="replacement" value="_"/>
633 </section>
634 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
635 <output name="ctd_out" ftype="xml">
636 <assert_contents>
637 <is_valid_xml/>
638 </assert_contents>
639 </output>
640 <assert_stdout>
641 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
642 </assert_stdout>
643 </test>
644 <!-- TOPP_ProteinQuantifier_16 -->
645 <test expect_num_outputs="2">
646 <section name="adv_opts">
647 <param name="force" value="false"/>
648 <param name="test" value="true"/>
649 </section>
650 <param name="in" value="ProteinQuantifier_16_input.consensusXML"/>
651 <param name="design" value="ProteinQuantifier_16_input.tsv" ftype="tabular"/>
652 <output name="out" value="ProteinQuantifier_16_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
653 <param name="method" value="top"/>
654 <param name="best_charge_and_fraction" value="false"/>
655 <param name="greedy_group_resolution" value="false"/>
656 <param name="ratios" value="false"/>
657 <param name="ratiosSILAC" value="false"/>
658 <section name="top">
659 <param name="N" value="3"/>
660 <param name="aggregate" value="median"/>
661 <param name="include_all" value="true"/>
662 </section>
663 <section name="consensus">
664 <param name="normalize" value="false"/>
665 <param name="fix_peptides" value="false"/>
666 </section>
667 <section name="format">
668 <param name="separator" value=""/>
669 <param name="quoting" value="double"/>
670 <param name="replacement" value="_"/>
671 </section>
672 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
673 <output name="ctd_out" ftype="xml">
674 <assert_contents>
675 <is_valid_xml/>
676 </assert_contents>
677 </output>
678 <assert_stdout>
679 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
680 </assert_stdout>
527 </test> 681 </test>
528 </tests> 682 </tests>
529 <help><![CDATA[Compute peptide and protein abundances 683 <help><![CDATA[Compute peptide and protein abundances
530 684
531 685
532 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinQuantifier.html]]></help> 686 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ProteinQuantifier.html]]></help>
533 <expand macro="references"/> 687 <expand macro="references"/>
534 </tool> 688 </tool>