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comparison ConsensusID.xml @ 18:f4be248c3d47 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 19:03:29 +0000
parents abffdfee3021
children 91da6dd00bbc
comparison
equal deleted inserted replaced
17:abffdfee3021 18:f4be248c3d47
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: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy1" profile="20.05"> 4 <tool id="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Computes a consensus of peptide identifications of several identification engines.</description> 5 <description>Computes a consensus of peptide identifications of several identification engines.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ConsensusID</token> 7 <token name="@EXECUTABLE@">ConsensusID</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 mkdir ${' '.join(["'in/%s'" % (i) for i, f in enumerate($in) if f])} && 18 #if $in_cond.in_select == "no"
21 ${' '.join(["ln -s '%s' 'in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in) if f])} 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($in_cond.in.ext)' &&
23 #end if
22 mkdir out && 24 mkdir out &&
23 25
24 ## Main program call 26 ## Main program call
25 27
26 set -o pipefail && 28 set -o pipefail &&
27 @EXECUTABLE@ -write_ctd ./ && 29 @EXECUTABLE@ -write_ctd ./ &&
28 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
29 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
30 -in 32 -in
31 ${' '.join(["'in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in) if f])} 33 #if $in_cond.in_select == "no"
34 ${' '.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])}
35 #else
36 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
37 #end if
32 -out 38 -out
33 'out/output.${in[0].ext}' 39 'out/output.${in_cond.in[0].ext}'
34 40
35 ## Postprocessing 41 ## Postprocessing
36 && mv 'out/output.${in[0].ext}' '$out' 42 && mv 'out/output.${in_cond.in[0].ext}' '$out'
37 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 43 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
38 && mv '@EXECUTABLE@.ctd' '$ctd_out' 44 && mv '@EXECUTABLE@.ctd' '$ctd_out'
39 #end if]]></command> 45 #end if]]></command>
40 <configfiles> 46 <configfiles>
41 <inputs name="args_json" data_style="paths"/> 47 <inputs name="args_json" data_style="paths"/>
42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 48 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
43 </configfiles> 49 </configfiles>
44 <inputs> 50 <inputs>
45 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/> 51 <conditional name="in_cond">
46 <param name="rt_delta" argument="-rt_delta" type="float" optional="false" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/> 52 <param name="in_select" type="select" label="Run tool in batch mode for -in">
47 <param name="mz_delta" argument="-mz_delta" type="float" optional="false" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/> 53 <option value="no">No: process all datasets jointly</option>
48 <param name="per_spectrum" argument="-per_spectrum" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(only idXML) if set, mapping will be done based on exact matching of originating mzml file and spectrum_ref" help=""/> 54 <option value="yes">Yes: process each dataset in an independent job</option>
49 <param name="algorithm" argument="-algorithm" type="select" optional="false" label="Algorithm used for consensus scoring" help="* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.. * PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores.. * best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.. * worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs.. * average: For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.. * ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types"> 55 </param>
56 <when value="no">
57 <param argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="true" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
58 </when>
59 <when value="yes">
60 <param argument="-in" type="data" format="consensusxml,featurexml,idxml" multiple="false" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
61 </when>
62 </conditional>
63 <param argument="-rt_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/>
64 <param argument="-mz_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/>
65 <param argument="-per_spectrum" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(only idXML) if set, mapping will be done based on exact matching of originating mzml file and spectrum_ref" help=""/>
66 <param argument="-algorithm" type="select" optional="true" label="Algorithm used for consensus scoring" help="* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.. * PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores.. * best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.. * worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs.. * average: For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.. * ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types">
50 <option value="PEPMatrix" selected="true">PEPMatrix</option> 67 <option value="PEPMatrix" selected="true">PEPMatrix</option>
51 <option value="PEPIons">PEPIons</option> 68 <option value="PEPIons">PEPIons</option>
52 <option value="best">best</option> 69 <option value="best">best</option>
53 <option value="worst">worst</option> 70 <option value="worst">worst</option>
54 <option value="average">average</option> 71 <option value="average">average</option>
55 <option value="ranks">ranks</option> 72 <option value="ranks">ranks</option>
56 <expand macro="list_string_san" name="algorithm"/> 73 <expand macro="list_string_san" name="algorithm"/>
57 </param> 74 </param>
58 <section name="filter" title="Options for filtering peptide hits" help="" expanded="false"> 75 <section name="filter" title="Options for filtering peptide hits" help="" expanded="false">
59 <param name="considered_hits" argument="-filter:considered_hits" type="integer" optional="false" min="0" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help=""/> 76 <param name="considered_hits" argument="-filter:considered_hits" type="integer" optional="true" min="0" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help=""/>
60 <param name="min_support" argument="-filter:min_support" type="float" optional="false" min="0.0" max="1.0" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help=""/> 77 <param name="min_support" argument="-filter:min_support" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help=""/>
61 <param name="count_empty" argument="-filter:count_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Count empty ID runs" help="(i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?"/> 78 <param name="count_empty" argument="-filter:count_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Count empty ID runs" help="(i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?"/>
62 <param name="keep_old_scores" argument="-filter:keep_old_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set, keeps the original scores as user params" help=""/> 79 <param name="keep_old_scores" argument="-filter:keep_old_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set, keeps the original scores as user params" help=""/>
63 </section> 80 </section>
64 <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false"> 81 <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false">
65 <param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" optional="false" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help=""/> 82 <param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" optional="true" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help=""/>
66 <param name="min_shared" argument="-PEPIons:min_shared" type="integer" optional="false" min="1" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/> 83 <param name="min_shared" argument="-PEPIons:min_shared" type="integer" optional="true" min="1" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/>
67 </section> 84 </section>
68 <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false"> 85 <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false">
69 <param name="matrix" argument="-PEPMatrix:matrix" display="checkboxes" type="select" optional="false" label="Substitution matrix to use for alignment-based similarity scoring" help=""> 86 <param name="matrix" argument="-PEPMatrix:matrix" type="select" optional="true" label="Substitution matrix to use for alignment-based similarity scoring" help="">
70 <option value="identity" selected="true">identity</option> 87 <option value="identity">identity</option>
71 <option value="PAM30MS">PAM30MS</option> 88 <option value="PAM30MS" selected="true">PAM30MS</option>
72 <expand macro="list_string_san" name="matrix"/> 89 <expand macro="list_string_san" name="matrix"/>
73 </param> 90 </param>
74 <param name="penalty" argument="-PEPMatrix:penalty" type="integer" optional="false" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/> 91 <param name="penalty" argument="-PEPMatrix:penalty" type="integer" optional="true" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/>
75 </section> 92 </section>
76 <expand macro="adv_opts_macro"> 93 <expand macro="adv_opts_macro">
77 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 94 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
78 <param name="test" argument="-test" type="hidden" optional="false" value="False" label="Enables the test mode (needed for internal use only)" help=""> 95 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
79 <expand macro="list_string_san" name="test"/> 96 <expand macro="list_string_san" name="test"/>
80 </param> 97 </param>
81 </expand> 98 </expand>
82 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 99 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
83 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 100 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
87 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/> 104 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
88 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 105 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
89 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 106 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
90 </data> 107 </data>
91 </outputs> 108 </outputs>
92 <tests> 109 <tests><!-- TOPP_ConsensusID_1 -->
93 <expand macro="autotest_ConsensusID"/> 110 <test expect_num_outputs="2">
94 <expand macro="manutest_ConsensusID"/> 111 <section name="adv_opts">
112 <param name="force" value="false"/>
113 <param name="test" value="true"/>
114 </section>
115 <conditional name="in_cond">
116 <param name="in" value="ConsensusID_1_input.idXML"/>
117 </conditional>
118 <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
119 <param name="rt_delta" value="0.1"/>
120 <param name="mz_delta" value="0.1"/>
121 <param name="per_spectrum" value="false"/>
122 <param name="algorithm" value="PEPMatrix"/>
123 <section name="filter">
124 <param name="considered_hits" value="0"/>
125 <param name="min_support" value="0.0"/>
126 <param name="count_empty" value="false"/>
127 <param name="keep_old_scores" value="false"/>
128 </section>
129 <section name="PEPIons">
130 <param name="mass_tolerance" value="0.5"/>
131 <param name="min_shared" value="2"/>
132 </section>
133 <section name="PEPMatrix">
134 <param name="matrix" value="PAM30MS"/>
135 <param name="penalty" value="5"/>
136 </section>
137 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
138 <output name="ctd_out" ftype="xml">
139 <assert_contents>
140 <is_valid_xml/>
141 </assert_contents>
142 </output>
143 </test>
144 <!-- TOPP_ConsensusID_2 -->
145 <test expect_num_outputs="2">
146 <section name="adv_opts">
147 <param name="force" value="false"/>
148 <param name="test" value="true"/>
149 </section>
150 <conditional name="in_cond">
151 <param name="in" value="ConsensusID_2_input.featureXML"/>
152 </conditional>
153 <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
154 <param name="rt_delta" value="0.1"/>
155 <param name="mz_delta" value="0.1"/>
156 <param name="per_spectrum" value="false"/>
157 <param name="algorithm" value="average"/>
158 <section name="filter">
159 <param name="considered_hits" value="0"/>
160 <param name="min_support" value="0.0"/>
161 <param name="count_empty" value="false"/>
162 <param name="keep_old_scores" value="false"/>
163 </section>
164 <section name="PEPIons">
165 <param name="mass_tolerance" value="0.5"/>
166 <param name="min_shared" value="2"/>
167 </section>
168 <section name="PEPMatrix">
169 <param name="matrix" value="PAM30MS"/>
170 <param name="penalty" value="5"/>
171 </section>
172 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
173 <output name="ctd_out" ftype="xml">
174 <assert_contents>
175 <is_valid_xml/>
176 </assert_contents>
177 </output>
178 </test>
179 <!-- TOPP_ConsensusID_3 -->
180 <test expect_num_outputs="2">
181 <section name="adv_opts">
182 <param name="force" value="false"/>
183 <param name="test" value="true"/>
184 </section>
185 <conditional name="in_cond">
186 <param name="in" value="ConsensusID_3_input.consensusXML"/>
187 </conditional>
188 <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
189 <param name="rt_delta" value="0.1"/>
190 <param name="mz_delta" value="0.1"/>
191 <param name="per_spectrum" value="false"/>
192 <param name="algorithm" value="best"/>
193 <section name="filter">
194 <param name="considered_hits" value="0"/>
195 <param name="min_support" value="0.0"/>
196 <param name="count_empty" value="false"/>
197 <param name="keep_old_scores" value="false"/>
198 </section>
199 <section name="PEPIons">
200 <param name="mass_tolerance" value="0.5"/>
201 <param name="min_shared" value="2"/>
202 </section>
203 <section name="PEPMatrix">
204 <param name="matrix" value="PAM30MS"/>
205 <param name="penalty" value="5"/>
206 </section>
207 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
208 <output name="ctd_out" ftype="xml">
209 <assert_contents>
210 <is_valid_xml/>
211 </assert_contents>
212 </output>
213 </test>
214 <!-- TOPP_ConsensusID_4 -->
215 <test expect_num_outputs="2">
216 <section name="adv_opts">
217 <param name="force" value="false"/>
218 <param name="test" value="true"/>
219 </section>
220 <conditional name="in_cond">
221 <param name="in" value="ConsensusID_1_input.idXML"/>
222 </conditional>
223 <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
224 <param name="rt_delta" value="0.1"/>
225 <param name="mz_delta" value="0.1"/>
226 <param name="per_spectrum" value="false"/>
227 <param name="algorithm" value="PEPMatrix"/>
228 <section name="filter">
229 <param name="considered_hits" value="6"/>
230 <param name="min_support" value="0.0"/>
231 <param name="count_empty" value="false"/>
232 <param name="keep_old_scores" value="false"/>
233 </section>
234 <section name="PEPIons">
235 <param name="mass_tolerance" value="0.5"/>
236 <param name="min_shared" value="2"/>
237 </section>
238 <section name="PEPMatrix">
239 <param name="matrix" value="identity"/>
240 <param name="penalty" value="5"/>
241 </section>
242 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
243 <output name="ctd_out" ftype="xml">
244 <assert_contents>
245 <is_valid_xml/>
246 </assert_contents>
247 </output>
248 </test>
249 <!-- TOPP_ConsensusID_5 -->
250 <test expect_num_outputs="2">
251 <section name="adv_opts">
252 <param name="force" value="false"/>
253 <param name="test" value="true"/>
254 </section>
255 <conditional name="in_cond">
256 <param name="in" value="ConsensusID_1_input.idXML"/>
257 </conditional>
258 <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
259 <param name="rt_delta" value="0.1"/>
260 <param name="mz_delta" value="0.1"/>
261 <param name="per_spectrum" value="false"/>
262 <param name="algorithm" value="PEPIons"/>
263 <section name="filter">
264 <param name="considered_hits" value="0"/>
265 <param name="min_support" value="0.0"/>
266 <param name="count_empty" value="false"/>
267 <param name="keep_old_scores" value="false"/>
268 </section>
269 <section name="PEPIons">
270 <param name="mass_tolerance" value="0.5"/>
271 <param name="min_shared" value="2"/>
272 </section>
273 <section name="PEPMatrix">
274 <param name="matrix" value="PAM30MS"/>
275 <param name="penalty" value="5"/>
276 </section>
277 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
278 <output name="ctd_out" ftype="xml">
279 <assert_contents>
280 <is_valid_xml/>
281 </assert_contents>
282 </output>
283 </test>
284 <!-- TOPP_ConsensusID_6 -->
285 <test expect_num_outputs="2">
286 <section name="adv_opts">
287 <param name="force" value="false"/>
288 <param name="test" value="true"/>
289 </section>
290 <conditional name="in_cond">
291 <param name="in" value="ConsensusID_1_input.idXML"/>
292 </conditional>
293 <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
294 <param name="rt_delta" value="0.1"/>
295 <param name="mz_delta" value="0.1"/>
296 <param name="per_spectrum" value="false"/>
297 <param name="algorithm" value="best"/>
298 <section name="filter">
299 <param name="considered_hits" value="0"/>
300 <param name="min_support" value="0.5"/>
301 <param name="count_empty" value="false"/>
302 <param name="keep_old_scores" value="false"/>
303 </section>
304 <section name="PEPIons">
305 <param name="mass_tolerance" value="0.5"/>
306 <param name="min_shared" value="2"/>
307 </section>
308 <section name="PEPMatrix">
309 <param name="matrix" value="PAM30MS"/>
310 <param name="penalty" value="5"/>
311 </section>
312 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
313 <output name="ctd_out" ftype="xml">
314 <assert_contents>
315 <is_valid_xml/>
316 </assert_contents>
317 </output>
318 </test>
319 <!-- TOPP_ConsensusID_7 -->
320 <test expect_num_outputs="2">
321 <section name="adv_opts">
322 <param name="force" value="false"/>
323 <param name="test" value="true"/>
324 </section>
325 <conditional name="in_cond">
326 <param name="in" value="ConsensusID_6_input.idXML"/>
327 </conditional>
328 <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
329 <param name="rt_delta" value="0.1"/>
330 <param name="mz_delta" value="0.1"/>
331 <param name="per_spectrum" value="true"/>
332 <param name="algorithm" value="best"/>
333 <section name="filter">
334 <param name="considered_hits" value="0"/>
335 <param name="min_support" value="0.0"/>
336 <param name="count_empty" value="false"/>
337 <param name="keep_old_scores" value="true"/>
338 </section>
339 <section name="PEPIons">
340 <param name="mass_tolerance" value="0.5"/>
341 <param name="min_shared" value="2"/>
342 </section>
343 <section name="PEPMatrix">
344 <param name="matrix" value="PAM30MS"/>
345 <param name="penalty" value="5"/>
346 </section>
347 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
348 <output name="ctd_out" ftype="xml">
349 <assert_contents>
350 <is_valid_xml/>
351 </assert_contents>
352 </output>
353 </test>
354 <!-- TOPP_ConsensusID_8 -->
355 <test expect_num_outputs="2">
356 <section name="adv_opts">
357 <param name="force" value="false"/>
358 <param name="test" value="true"/>
359 </section>
360 <conditional name="in_cond">
361 <param name="in" value="ConsensusID_8_input.idXML"/>
362 </conditional>
363 <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
364 <param name="rt_delta" value="0.1"/>
365 <param name="mz_delta" value="0.1"/>
366 <param name="per_spectrum" value="true"/>
367 <param name="algorithm" value="best"/>
368 <section name="filter">
369 <param name="considered_hits" value="0"/>
370 <param name="min_support" value="0.0"/>
371 <param name="count_empty" value="false"/>
372 <param name="keep_old_scores" value="true"/>
373 </section>
374 <section name="PEPIons">
375 <param name="mass_tolerance" value="0.5"/>
376 <param name="min_shared" value="2"/>
377 </section>
378 <section name="PEPMatrix">
379 <param name="matrix" value="PAM30MS"/>
380 <param name="penalty" value="5"/>
381 </section>
382 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
383 <output name="ctd_out" ftype="xml">
384 <assert_contents>
385 <is_valid_xml/>
386 </assert_contents>
387 </output>
388 </test>
95 </tests> 389 </tests>
96 <help><![CDATA[Computes a consensus of peptide identifications of several identification engines. 390 <help><![CDATA[Computes a consensus of peptide identifications of several identification engines.
97 391
98 392
99 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_ConsensusID.html]]></help> 393 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ConsensusID.html]]></help>
100 <expand macro="references"/> 394 <expand macro="references"/>
101 </tool> 395 </tool>