Mercurial > repos > galaxyp > openms_featurelinkerunlabeledqt
comparison FeatureLinkerUnlabeledQT.xml @ 15:aa8658367608 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:06:27 +0000 |
parents | 91f990434dc1 |
children | 8394bcb2b0ca |
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14:aa43ad3b2da6 | 15:aa8658367608 |
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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> |