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comparison FeatureLinkerUnlabeledQT.xml @ 15:aa8658367608 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:06:27 +0000
parents 91f990434dc1
children 8394bcb2b0ca
comparison
equal deleted inserted replaced
14:aa43ad3b2da6 15:aa8658367608
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Map Alignment]--> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Groups corresponding features from multiple maps.</description> 5 <description>Groups corresponding features from multiple maps.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token> 7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
19 mkdir in && 17 mkdir in_cond.in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 18 #if $in_cond.in_select == "no"
19 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])}
21 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if
21 mkdir out && 24 mkdir out &&
22 #if $design: 25 #if $design:
23 mkdir design && 26 mkdir design &&
24 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && 27 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
25 #end if 28 #end if
29 set -o pipefail && 32 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ && 33 @EXECUTABLE@ -write_ctd ./ &&
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
33 -in 36 -in
34 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 37 #if $in_cond.in_select == "no"
38 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
39 #else
40 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
41 #end if
35 -out 42 -out
36 'out/output.${gxy2omsext("consensusxml")}' 43 'out/output.${gxy2omsext("consensusxml")}'
37 #if $design: 44 #if $design:
38 -design 45 -design
39 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' 46 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
47 <configfiles> 54 <configfiles>
48 <inputs name="args_json" data_style="paths"/> 55 <inputs name="args_json" data_style="paths"/>
49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 56 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
50 </configfiles> 57 </configfiles>
51 <inputs> 58 <inputs>
52 <param name="in" argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/> 59 <conditional name="in_cond">
53 <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/> 60 <param name="in_select" type="select" label="Run tool in batch mode for -in">
54 <param name="keep_subelements" 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=""/> 61 <option value="no">No: process all datasets jointly</option>
62 <option value="yes">Yes: process each dataset in an independent job</option>
63 </param>
64 <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)"/>
66 </when>
67 <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)"/>
69 </when>
70 </conditional>
71 <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=""/>
55 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 73 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
56 <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=""/> 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=""/>
57 <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=""/> 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=""/>
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"/>
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!"/>
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)"/>
58 <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=""/> 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=""/>
59 <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=""/> 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=""/>
60 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false"> 81 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
61 <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=""/> 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=""/>
62 <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=""/> 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=""/>
63 <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=""/> 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=""/>
64 </section> 85 </section>
65 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false"> 86 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
66 <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=""/> 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=""/>
67 <param name="unit" argument="-algorithm:distance_MZ:unit" display="radio" type="select" optional="false" label="Unit of the 'max_difference' paramete" help=""> 88 <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" optional="true" label="Unit of the 'max_difference' paramete" help="">
68 <option value="Da" selected="true">Da</option> 89 <option value="Da" selected="true">Da</option>
69 <option value="ppm">ppm</option> 90 <option value="ppm">ppm</option>
70 <expand macro="list_string_san"/> 91 <expand macro="list_string_san" name="unit"/>
71 </param> 92 </param>
72 <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=""/> 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=""/>
73 <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=""/> 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=""/>
74 </section> 95 </section>
75 <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"> 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">
76 <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=""/> 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=""/>
77 <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=""/> 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=""/>
78 <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" display="radio" type="select" optional="false" 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))"> 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))">
79 <option value="enabled">enabled</option> 100 <option value="enabled">enabled</option>
80 <option value="disabled" selected="true">disabled</option> 101 <option value="disabled" selected="true">disabled</option>
81 <expand macro="list_string_san"/> 102 <expand macro="list_string_san" name="log_transform"/>
82 </param> 103 </param>
83 </section> 104 </section>
84 </section> 105 </section>
85 <expand macro="adv_opts_macro"> 106 <expand macro="adv_opts_macro">
86 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 107 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
87 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 108 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
88 <expand macro="list_string_san"/> 109 <expand macro="list_string_san" name="test"/>
89 </param> 110 </param>
90 </expand> 111 </expand>
91 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 112 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 113 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
93 </param> 114 </param>
96 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> 117 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
97 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 118 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
98 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 119 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
99 </data> 120 </data>
100 </outputs> 121 </outputs>
101 <tests> 122 <tests><!-- TOPP_FeatureLinkerUnlabeledQT_1 -->
102 <expand macro="autotest_FeatureLinkerUnlabeledQT"/> 123 <test expect_num_outputs="2">
103 <expand macro="manutest_FeatureLinkerUnlabeledQT"/> 124 <section name="adv_opts">
125 <param name="force" value="false"/>
126 <param name="test" value="true"/>
127 </section>
128 <conditional name="in_cond">
129 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
130 </conditional>
131 <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
132 <param name="keep_subelements" value="false"/>
133 <section name="algorithm">
134 <param name="use_identifications" value="false"/>
135 <param name="nr_partitions" value="100"/>
136 <param name="min_nr_diffs_per_bin" value="50"/>
137 <param name="min_IDscore_forTolCalc" value="1.0"/>
138 <param name="noID_penalty" value="0.0"/>
139 <param name="ignore_charge" value="false"/>
140 <param name="ignore_adduct" value="true"/>
141 <section name="distance_RT">
142 <param name="max_difference" value="100.0"/>
143 <param name="exponent" value="1.0"/>
144 <param name="weight" value="1.0"/>
145 </section>
146 <section name="distance_MZ">
147 <param name="max_difference" value="0.3"/>
148 <param name="unit" value="Da"/>
149 <param name="exponent" value="2.0"/>
150 <param name="weight" value="1.0"/>
151 </section>
152 <section name="distance_intensity">
153 <param name="exponent" value="1.0"/>
154 <param name="weight" value="0.0"/>
155 <param name="log_transform" value="disabled"/>
156 </section>
157 </section>
158 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
159 <output name="ctd_out" ftype="xml">
160 <assert_contents>
161 <is_valid_xml/>
162 </assert_contents>
163 </output>
164 </test>
165 <!-- TOPP_FeatureLinkerUnlabeledQT_2 -->
166 <test expect_num_outputs="2">
167 <section name="adv_opts">
168 <param name="force" value="false"/>
169 <param name="test" value="true"/>
170 </section>
171 <conditional name="in_cond">
172 <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/>
173 </conditional>
174 <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
175 <param name="keep_subelements" value="true"/>
176 <section name="algorithm">
177 <param name="use_identifications" value="false"/>
178 <param name="nr_partitions" value="100"/>
179 <param name="min_nr_diffs_per_bin" value="50"/>
180 <param name="min_IDscore_forTolCalc" value="1.0"/>
181 <param name="noID_penalty" value="0.0"/>
182 <param name="ignore_charge" value="false"/>
183 <param name="ignore_adduct" value="true"/>
184 <section name="distance_RT">
185 <param name="max_difference" value="100.0"/>
186 <param name="exponent" value="1.0"/>
187 <param name="weight" value="1.0"/>
188 </section>
189 <section name="distance_MZ">
190 <param name="max_difference" value="0.3"/>
191 <param name="unit" value="Da"/>
192 <param name="exponent" value="2.0"/>
193 <param name="weight" value="1.0"/>
194 </section>
195 <section name="distance_intensity">
196 <param name="exponent" value="1.0"/>
197 <param name="weight" value="0.0"/>
198 <param name="log_transform" value="disabled"/>
199 </section>
200 </section>
201 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
202 <output name="ctd_out" ftype="xml">
203 <assert_contents>
204 <is_valid_xml/>
205 </assert_contents>
206 </output>
207 </test>
208 <!-- TOPP_FeatureLinkerUnlabeledQT_3 -->
209 <test expect_num_outputs="2">
210 <section name="adv_opts">
211 <param name="force" value="false"/>
212 <param name="test" value="true"/>
213 </section>
214 <conditional name="in_cond">
215 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
216 </conditional>
217 <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
218 <param name="keep_subelements" value="false"/>
219 <section name="algorithm">
220 <param name="use_identifications" value="false"/>
221 <param name="nr_partitions" value="99999"/>
222 <param name="min_nr_diffs_per_bin" value="50"/>
223 <param name="min_IDscore_forTolCalc" value="1.0"/>
224 <param name="noID_penalty" value="0.0"/>
225 <param name="ignore_charge" value="false"/>
226 <param name="ignore_adduct" value="true"/>
227 <section name="distance_RT">
228 <param name="max_difference" value="100.0"/>
229 <param name="exponent" value="1.0"/>
230 <param name="weight" value="1.0"/>
231 </section>
232 <section name="distance_MZ">
233 <param name="max_difference" value="0.3"/>
234 <param name="unit" value="Da"/>
235 <param name="exponent" value="2.0"/>
236 <param name="weight" value="1.0"/>
237 </section>
238 <section name="distance_intensity">
239 <param name="exponent" value="1.0"/>
240 <param name="weight" value="0.0"/>
241 <param name="log_transform" value="disabled"/>
242 </section>
243 </section>
244 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
245 <output name="ctd_out" ftype="xml">
246 <assert_contents>
247 <is_valid_xml/>
248 </assert_contents>
249 </output>
250 </test>
251 <!-- TOPP_FeatureLinkerUnlabeledQT_4 -->
252 <test expect_num_outputs="2">
253 <section name="adv_opts">
254 <param name="force" value="false"/>
255 <param name="test" value="true"/>
256 </section>
257 <conditional name="in_cond">
258 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
259 </conditional>
260 <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
261 <param name="keep_subelements" value="false"/>
262 <section name="algorithm">
263 <param name="use_identifications" value="true"/>
264 <param name="nr_partitions" value="100"/>
265 <param name="min_nr_diffs_per_bin" value="50"/>
266 <param name="min_IDscore_forTolCalc" value="1.0"/>
267 <param name="noID_penalty" value="0.0"/>
268 <param name="ignore_charge" value="false"/>
269 <param name="ignore_adduct" value="true"/>
270 <section name="distance_RT">
271 <param name="max_difference" value="100.0"/>
272 <param name="exponent" value="1.0"/>
273 <param name="weight" value="1.0"/>
274 </section>
275 <section name="distance_MZ">
276 <param name="max_difference" value="0.3"/>
277 <param name="unit" value="Da"/>
278 <param name="exponent" value="2.0"/>
279 <param name="weight" value="1.0"/>
280 </section>
281 <section name="distance_intensity">
282 <param name="exponent" value="1.0"/>
283 <param name="weight" value="0.0"/>
284 <param name="log_transform" value="disabled"/>
285 </section>
286 </section>
287 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
288 <output name="ctd_out" ftype="xml">
289 <assert_contents>
290 <is_valid_xml/>
291 </assert_contents>
292 </output>
293 </test>
294 <!-- TOPP_FeatureLinkerUnlabeledQT_5 -->
295 <test expect_num_outputs="2">
296 <section name="adv_opts">
297 <param name="force" value="false"/>
298 <param name="test" value="true"/>
299 </section>
300 <conditional name="in_cond">
301 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
302 </conditional>
303 <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
304 <param name="keep_subelements" value="false"/>
305 <section name="algorithm">
306 <param name="use_identifications" value="false"/>
307 <param name="nr_partitions" value="100"/>
308 <param name="min_nr_diffs_per_bin" value="50"/>
309 <param name="min_IDscore_forTolCalc" value="1.0"/>
310 <param name="noID_penalty" value="0.0"/>
311 <param name="ignore_charge" value="false"/>
312 <param name="ignore_adduct" value="true"/>
313 <section name="distance_RT">
314 <param name="max_difference" value="200.0"/>
315 <param name="exponent" value="1.0"/>
316 <param name="weight" value="1.0"/>
317 </section>
318 <section name="distance_MZ">
319 <param name="max_difference" value="0.3"/>
320 <param name="unit" value="Da"/>
321 <param name="exponent" value="2.0"/>
322 <param name="weight" value="1.0"/>
323 </section>
324 <section name="distance_intensity">
325 <param name="exponent" value="1.0"/>
326 <param name="weight" value="0.0"/>
327 <param name="log_transform" value="disabled"/>
328 </section>
329 </section>
330 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
331 <output name="ctd_out" ftype="xml">
332 <assert_contents>
333 <is_valid_xml/>
334 </assert_contents>
335 </output>
336 </test>
337 <!-- TOPP_FeatureLinkerUnlabeledQT_6 -->
338 <test expect_num_outputs="2">
339 <section name="adv_opts">
340 <param name="force" value="false"/>
341 <param name="test" value="true"/>
342 </section>
343 <conditional name="in_cond">
344 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
345 </conditional>
346 <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
347 <param name="keep_subelements" value="false"/>
348 <section name="algorithm">
349 <param name="use_identifications" value="true"/>
350 <param name="nr_partitions" value="100"/>
351 <param name="min_nr_diffs_per_bin" value="50"/>
352 <param name="min_IDscore_forTolCalc" value="1.0"/>
353 <param name="noID_penalty" value="0.0"/>
354 <param name="ignore_charge" value="false"/>
355 <param name="ignore_adduct" value="true"/>
356 <section name="distance_RT">
357 <param name="max_difference" value="200.0"/>
358 <param name="exponent" value="1.0"/>
359 <param name="weight" value="1.0"/>
360 </section>
361 <section name="distance_MZ">
362 <param name="max_difference" value="0.3"/>
363 <param name="unit" value="Da"/>
364 <param name="exponent" value="2.0"/>
365 <param name="weight" value="1.0"/>
366 </section>
367 <section name="distance_intensity">
368 <param name="exponent" value="1.0"/>
369 <param name="weight" value="0.0"/>
370 <param name="log_transform" value="disabled"/>
371 </section>
372 </section>
373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
374 <output name="ctd_out" ftype="xml">
375 <assert_contents>
376 <is_valid_xml/>
377 </assert_contents>
378 </output>
379 </test>
104 </tests> 380 </tests>
105 <help><![CDATA[Groups corresponding features from multiple maps. 381 <help><![CDATA[Groups corresponding features from multiple maps.
106 382
107 383
108 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureLinkerUnlabeledQT.html]]></help> 384 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerUnlabeledQT.html]]></help>
109 <expand macro="references"/> 385 <expand macro="references"/>
110 </tool> 386 </tool>