Mercurial > repos > galaxyp > openms_featurelinkerunlabeledqt

comparison FeatureLinkerUnlabeledQT.xml @ 16:8394bcb2b0ca 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 21:36:52 +0000
parents aa8658367608
children
comparison
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15:aa8658367608 16:8394bcb2b0ca
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: [Map Alignment]--> 2 <!--Proposed Tool Section: [Feature Linking]-->
4 <tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Groups corresponding features from multiple maps.</description> 4 <description>Groups corresponding features from multiple maps</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token> 6 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in_cond.in && 16 mkdir in_cond.in &&
18 #if $in_cond.in_select == "no" 17 #if $in_cond.in_select == "no"
19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} 19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
21 #else 20 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && 21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if 22 #end if
24 mkdir out && 23 mkdir out &&
25 #if $design: 24 #if $design:
26 mkdir design && 25 mkdir design &&
27 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && 26 cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
28 #end if 27 #end if
29 28
30 ## Main program call 29 ## Main program call
31 30
32 set -o pipefail && 31 set -o pipefail &&
60 <param name="in_select" type="select" label="Run tool in batch mode for -in"> 59 <param name="in_select" type="select" label="Run tool in batch mode for -in">
61 <option value="no">No: process all datasets jointly</option> 60 <option value="no">No: process all datasets jointly</option>
62 <option value="yes">Yes: process each dataset in an independent job</option> 61 <option value="yes">Yes: process each dataset in an independent job</option>
63 </param> 62 </param>
64 <when value="no"> 63 <when value="no">
65 <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/> 64 <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
66 </when> 65 </when>
67 <when value="yes"> 66 <when value="yes">
68 <param argument="-in" type="data" format="consensusxml,featurexml" multiple="false" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/> 67 <param argument="-in" type="data" format="consensusxml,featurexml" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
69 </when> 68 </when>
70 </conditional> 69 </conditional>
71 <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/> 70 <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
72 <param argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/> 71 <param argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
73 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 72 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
74 <param name="use_identifications" argument="-algorithm:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" help=""/> 73 <param name="use_identifications" argument="-algorithm:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" help=""/>
75 <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" optional="true" min="1" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution)" help=""/> 74 <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" min="1" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution)" help=""/>
76 <param name="min_nr_diffs_per_bin" argument="-algorithm:min_nr_diffs_per_bin" type="integer" optional="true" min="5" value="50" label="If IDs are used: How many differences from matching IDs should be used to calculate a linking tolerance for unIDed features in an RT region" help="RT regions will be extended until that number is reached"/> 75 <param name="min_nr_diffs_per_bin" argument="-algorithm:min_nr_diffs_per_bin" type="integer" min="5" value="50" label="If IDs are used: How many differences from matching IDs should be used to calculate a linking tolerance for unIDed features in an RT region" help="RT regions will be extended until that number is reached"/>
77 <param name="min_IDscore_forTolCalc" argument="-algorithm:min_IDscore_forTolCalc" type="float" optional="true" value="1.0" label="If IDs are used: What is the minimum score of an ID to assume a reliable match for tolerance calculation" help="Check your current score type!"/> 76 <param name="min_IDscore_forTolCalc" argument="-algorithm:min_IDscore_forTolCalc" type="float" value="1.0" label="If IDs are used: What is the minimum score of an ID to assume a reliable match for tolerance calculation" help="Check your current score type!"/>
78 <param name="noID_penalty" argument="-algorithm:noID_penalty" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="If IDs are used: For the normalized distances, how high should the penalty for missing IDs be" help="0 = no bias, 1 = IDs inside the max tolerances always preferred (even if much further away)"/> 77 <param name="noID_penalty" argument="-algorithm:noID_penalty" type="float" min="0.0" max="1.0" value="0.0" label="If IDs are used: For the normalized distances, how high should the penalty for missing IDs be" help="0 = no bias, 1 = IDs inside the max tolerances always preferred (even if much further away)"/>
79 <param name="ignore_charge" argument="-algorithm:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/> 78 <param name="ignore_charge" argument="-algorithm:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/>
80 <param name="ignore_adduct" argument="-algorithm:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/> 79 <param name="ignore_adduct" argument="-algorithm:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/>
81 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false"> 80 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
82 <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/> 81 <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
83 <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> 82 <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
84 <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/> 83 <param name="weight" argument="-algorithm:distance_RT:weight" type="float" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
85 </section> 84 </section>
86 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false"> 85 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
87 <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/> 86 <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
88 <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" optional="true" label="Unit of the 'max_difference' paramete" help=""> 87 <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" label="Unit of the 'max_difference' paramete" help="">
89 <option value="Da" selected="true">Da</option> 88 <option value="Da" selected="true">Da</option>
90 <option value="ppm">ppm</option> 89 <option value="ppm">ppm</option>
91 <expand macro="list_string_san" name="unit"/> 90 <expand macro="list_string_san" name="unit"/>
92 </param> 91 </param>
93 <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> 92 <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
94 <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/> 93 <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
95 </section> 94 </section>
96 <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false"> 95 <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
97 <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> 96 <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
98 <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/> 97 <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
99 <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="true" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))"> 98 <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
100 <option value="enabled">enabled</option> 99 <option value="enabled">enabled</option>
101 <option value="disabled" selected="true">disabled</option> 100 <option value="disabled" selected="true">disabled</option>
102 <expand macro="list_string_san" name="log_transform"/> 101 <expand macro="list_string_san" name="log_transform"/>
103 </param> 102 </param>
104 </section> 103 </section>
105 </section> 104 </section>
106 <expand macro="adv_opts_macro"> 105 <expand macro="adv_opts_macro">
107 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 106 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
108 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 107 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
109 <expand macro="list_string_san" name="test"/> 108 <expand macro="list_string_san" name="test"/>
110 </param> 109 </param>
111 </expand> 110 </expand>
112 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 111 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
113 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 112 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
117 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> 116 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
118 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 117 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
119 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 118 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
120 </data> 119 </data>
121 </outputs> 120 </outputs>
122 <tests><!-- TOPP_FeatureLinkerUnlabeledQT_1 --> 121 <tests>
122 <!-- TOPP_FeatureLinkerUnlabeledQT_1 -->
123 <test expect_num_outputs="2"> 123 <test expect_num_outputs="2">
124 <section name="adv_opts"> 124 <section name="adv_opts">
125 <param name="force" value="false"/> 125 <param name="force" value="false"/>
126 <param name="test" value="true"/> 126 <param name="test" value="true"/>
127 </section> 127 </section>
128 <conditional name="in_cond"> 128 <conditional name="in_cond">
129 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> 129 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
130 </conditional> 130 </conditional>
131 <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 131 <output name="out" value="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
132 <param name="keep_subelements" value="false"/> 132 <param name="keep_subelements" value="false"/>
133 <section name="algorithm"> 133 <section name="algorithm">
134 <param name="use_identifications" value="false"/> 134 <param name="use_identifications" value="false"/>
135 <param name="nr_partitions" value="100"/> 135 <param name="nr_partitions" value="100"/>
136 <param name="min_nr_diffs_per_bin" value="50"/> 136 <param name="min_nr_diffs_per_bin" value="50"/>
159 <output name="ctd_out" ftype="xml"> 159 <output name="ctd_out" ftype="xml">
160 <assert_contents> 160 <assert_contents>
161 <is_valid_xml/> 161 <is_valid_xml/>
162 </assert_contents> 162 </assert_contents>
163 </output> 163 </output>
164 <assert_stdout>
165 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
166 </assert_stdout>
164 </test> 167 </test>
165 <!-- TOPP_FeatureLinkerUnlabeledQT_2 --> 168 <!-- TOPP_FeatureLinkerUnlabeledQT_2 -->
166 <test expect_num_outputs="2"> 169 <test expect_num_outputs="2">
167 <section name="adv_opts"> 170 <section name="adv_opts">
168 <param name="force" value="false"/> 171 <param name="force" value="false"/>
169 <param name="test" value="true"/> 172 <param name="test" value="true"/>
170 </section> 173 </section>
171 <conditional name="in_cond"> 174 <conditional name="in_cond">
172 <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/> 175 <param name="in" value="FeatureLinkerUnlabeledQT_1_output_0.consensusXML,FeatureLinkerUnlabeledQT_1_output_1.consensusXML"/>
173 </conditional> 176 </conditional>
174 <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 177 <output name="out" value="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
175 <param name="keep_subelements" value="true"/> 178 <param name="keep_subelements" value="true"/>
176 <section name="algorithm"> 179 <section name="algorithm">
177 <param name="use_identifications" value="false"/> 180 <param name="use_identifications" value="false"/>
178 <param name="nr_partitions" value="100"/> 181 <param name="nr_partitions" value="100"/>
179 <param name="min_nr_diffs_per_bin" value="50"/> 182 <param name="min_nr_diffs_per_bin" value="50"/>
202 <output name="ctd_out" ftype="xml"> 205 <output name="ctd_out" ftype="xml">
203 <assert_contents> 206 <assert_contents>
204 <is_valid_xml/> 207 <is_valid_xml/>
205 </assert_contents> 208 </assert_contents>
206 </output> 209 </output>
210 <assert_stdout>
211 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
212 </assert_stdout>
207 </test> 213 </test>
208 <!-- TOPP_FeatureLinkerUnlabeledQT_3 --> 214 <!-- TOPP_FeatureLinkerUnlabeledQT_3 -->
209 <test expect_num_outputs="2"> 215 <test expect_num_outputs="2">
210 <section name="adv_opts"> 216 <section name="adv_opts">
211 <param name="force" value="false"/> 217 <param name="force" value="false"/>
212 <param name="test" value="true"/> 218 <param name="test" value="true"/>
213 </section> 219 </section>
214 <conditional name="in_cond"> 220 <conditional name="in_cond">
215 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/> 221 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
216 </conditional> 222 </conditional>
217 <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 223 <output name="out" value="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
218 <param name="keep_subelements" value="false"/> 224 <param name="keep_subelements" value="false"/>
219 <section name="algorithm"> 225 <section name="algorithm">
220 <param name="use_identifications" value="false"/> 226 <param name="use_identifications" value="false"/>
221 <param name="nr_partitions" value="99999"/> 227 <param name="nr_partitions" value="99999"/>
222 <param name="min_nr_diffs_per_bin" value="50"/> 228 <param name="min_nr_diffs_per_bin" value="50"/>
245 <output name="ctd_out" ftype="xml"> 251 <output name="ctd_out" ftype="xml">
246 <assert_contents> 252 <assert_contents>
247 <is_valid_xml/> 253 <is_valid_xml/>
248 </assert_contents> 254 </assert_contents>
249 </output> 255 </output>
256 <assert_stdout>
257 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
258 </assert_stdout>
250 </test> 259 </test>
251 <!-- TOPP_FeatureLinkerUnlabeledQT_4 --> 260 <!-- TOPP_FeatureLinkerUnlabeledQT_4 -->
252 <test expect_num_outputs="2"> 261 <test expect_num_outputs="2">
253 <section name="adv_opts"> 262 <section name="adv_opts">
254 <param name="force" value="false"/> 263 <param name="force" value="false"/>
255 <param name="test" value="true"/> 264 <param name="test" value="true"/>
256 </section> 265 </section>
257 <conditional name="in_cond"> 266 <conditional name="in_cond">
258 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> 267 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
259 </conditional> 268 </conditional>
260 <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 269 <output name="out" value="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
261 <param name="keep_subelements" value="false"/> 270 <param name="keep_subelements" value="false"/>
262 <section name="algorithm"> 271 <section name="algorithm">
263 <param name="use_identifications" value="true"/> 272 <param name="use_identifications" value="true"/>
264 <param name="nr_partitions" value="100"/> 273 <param name="nr_partitions" value="100"/>
265 <param name="min_nr_diffs_per_bin" value="50"/> 274 <param name="min_nr_diffs_per_bin" value="50"/>
288 <output name="ctd_out" ftype="xml"> 297 <output name="ctd_out" ftype="xml">
289 <assert_contents> 298 <assert_contents>
290 <is_valid_xml/> 299 <is_valid_xml/>
291 </assert_contents> 300 </assert_contents>
292 </output> 301 </output>
302 <assert_stdout>
303 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
304 </assert_stdout>
293 </test> 305 </test>
294 <!-- TOPP_FeatureLinkerUnlabeledQT_5 --> 306 <!-- TOPP_FeatureLinkerUnlabeledQT_5 -->
295 <test expect_num_outputs="2"> 307 <test expect_num_outputs="2">
296 <section name="adv_opts"> 308 <section name="adv_opts">
297 <param name="force" value="false"/> 309 <param name="force" value="false"/>
298 <param name="test" value="true"/> 310 <param name="test" value="true"/>
299 </section> 311 </section>
300 <conditional name="in_cond"> 312 <conditional name="in_cond">
301 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> 313 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
302 </conditional> 314 </conditional>
303 <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 315 <output name="out" value="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
304 <param name="keep_subelements" value="false"/> 316 <param name="keep_subelements" value="false"/>
305 <section name="algorithm"> 317 <section name="algorithm">
306 <param name="use_identifications" value="false"/> 318 <param name="use_identifications" value="false"/>
307 <param name="nr_partitions" value="100"/> 319 <param name="nr_partitions" value="100"/>
308 <param name="min_nr_diffs_per_bin" value="50"/> 320 <param name="min_nr_diffs_per_bin" value="50"/>
331 <output name="ctd_out" ftype="xml"> 343 <output name="ctd_out" ftype="xml">
332 <assert_contents> 344 <assert_contents>
333 <is_valid_xml/> 345 <is_valid_xml/>
334 </assert_contents> 346 </assert_contents>
335 </output> 347 </output>
348 <assert_stdout>
349 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
350 </assert_stdout>
336 </test> 351 </test>
337 <!-- TOPP_FeatureLinkerUnlabeledQT_6 --> 352 <!-- TOPP_FeatureLinkerUnlabeledQT_6 -->
338 <test expect_num_outputs="2"> 353 <test expect_num_outputs="2">
339 <section name="adv_opts"> 354 <section name="adv_opts">
340 <param name="force" value="false"/> 355 <param name="force" value="false"/>
341 <param name="test" value="true"/> 356 <param name="test" value="true"/>
342 </section> 357 </section>
343 <conditional name="in_cond"> 358 <conditional name="in_cond">
344 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> 359 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
345 </conditional> 360 </conditional>
346 <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> 361 <output name="out" value="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
347 <param name="keep_subelements" value="false"/> 362 <param name="keep_subelements" value="false"/>
348 <section name="algorithm"> 363 <section name="algorithm">
349 <param name="use_identifications" value="true"/> 364 <param name="use_identifications" value="true"/>
350 <param name="nr_partitions" value="100"/> 365 <param name="nr_partitions" value="100"/>
351 <param name="min_nr_diffs_per_bin" value="50"/> 366 <param name="min_nr_diffs_per_bin" value="50"/>
374 <output name="ctd_out" ftype="xml"> 389 <output name="ctd_out" ftype="xml">
375 <assert_contents> 390 <assert_contents>
376 <is_valid_xml/> 391 <is_valid_xml/>
377 </assert_contents> 392 </assert_contents>
378 </output> 393 </output>
394 <assert_stdout>
395 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
396 </assert_stdout>
379 </test> 397 </test>
380 </tests> 398 </tests>
381 <help><![CDATA[Groups corresponding features from multiple maps. 399 <help><![CDATA[Groups corresponding features from multiple maps.
382 400
383 401
384 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerUnlabeledQT.html]]></help> 402 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureLinkerUnlabeledQT.html]]></help>
385 <expand macro="references"/> 403 <expand macro="references"/>
386 </tool> 404 </tool>