Mercurial > repos > galaxyp > openms_consensusid
comparison ConsensusID.xml @ 18:f4be248c3d47 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 19:03:29 +0000 |
parents | abffdfee3021 |
children | 91da6dd00bbc |
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17:abffdfee3021 | 18:f4be248c3d47 |
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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: [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> |