Mercurial > repos > galaxyp > openms_multiplexresolver

comparison MultiplexResolver.xml @ 13:021fdb80f204 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:14:58 +0000
parents b3dcd2098472
children 53b202a738c3
comparison
equal deleted inserted replaced
12:d0304fb829c0 13:021fdb80f204
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Completes peptide multiplets and resolves conflicts within them.</description> 5 <description>Completes peptide multiplets and resolves conflicts within them.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MultiplexResolver</token> 7 <token name="@EXECUTABLE@">MultiplexResolver</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@
60 <configfiles> 58 <configfiles>
61 <inputs name="args_json" data_style="paths"/> 59 <inputs name="args_json" data_style="paths"/>
62 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
63 </configfiles> 61 </configfiles>
64 <inputs> 62 <inputs>
65 <param name="in" argument="-in" type="data" format="consensusxml" optional="false" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/> 63 <param argument="-in" type="data" format="consensusxml" optional="false" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/>
66 <param name="in_blacklist" argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/> 64 <param argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/>
67 <section name="algorithm" title="Parameters for the algorithm" help="" expanded="false"> 65 <section name="algorithm" title="Parameters for the algorithm" help="" expanded="false">
68 <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example. . [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL"> 66 <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example. [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
69 <expand macro="list_string_san"/> 67 <expand macro="list_string_san" name="labels"/>
70 </param> 68 </param>
71 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/> 69 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
72 <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" optional="true" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/> 70 <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" optional="true" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/>
73 <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" optional="true" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/> 71 <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" optional="true" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/>
74 <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" optional="true" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/> 72 <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" optional="true" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/>
88 <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/> 86 <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/>
89 <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/> 87 <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/>
90 <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/> 88 <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/>
91 </section> 89 </section>
92 <expand macro="adv_opts_macro"> 90 <expand macro="adv_opts_macro">
93 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 91 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
94 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 92 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
95 <expand macro="list_string_san"/> 93 <expand macro="list_string_san" name="test"/>
96 </param> 94 </param>
97 </expand> 95 </expand>
98 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 96 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
99 <option value="out_conflicts_FLAG">out_conflicts (Optional output containing peptide multiplets without ID annotation or with conflicting quant/ID information)</option> 97 <option value="out_conflicts_FLAG">out_conflicts (Optional output containing peptide multiplets without ID annotation or with conflicting quant/ID information)</option>
100 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 98 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
107 </data> 105 </data>
108 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 106 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
109 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 107 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
110 </data> 108 </data>
111 </outputs> 109 </outputs>
112 <tests> 110 <tests><!-- UTILS_MultiplexResolver_1 -->
113 <expand macro="autotest_MultiplexResolver"/> 111 <test expect_num_outputs="3">
114 <expand macro="manutest_MultiplexResolver"/> 112 <section name="adv_opts">
113 <param name="force" value="false"/>
114 <param name="test" value="true"/>
115 </section>
116 <param name="in" value="MultiplexResolver_1_input.consensusXML"/>
117 <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
118 <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
119 <section name="algorithm">
120 <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/>
121 <param name="missed_cleavages" value="1"/>
122 <param name="mass_tolerance" value="0.1"/>
123 <param name="mz_tolerance" value="10"/>
124 <param name="rt_tolerance" value="5"/>
125 </section>
126 <section name="labels">
127 <param name="Arg6" value="6.0201290268"/>
128 <param name="Arg10" value="10.0082686"/>
129 <param name="Lys4" value="4.0251069836"/>
130 <param name="Lys6" value="6.0201290268"/>
131 <param name="Lys8" value="8.0141988132"/>
132 <param name="Leu3" value="3.01883"/>
133 <param name="Dimethyl0" value="28.0313"/>
134 <param name="Dimethyl4" value="32.056407"/>
135 <param name="Dimethyl6" value="34.063117"/>
136 <param name="Dimethyl8" value="36.07567"/>
137 <param name="ICPL0" value="105.021464"/>
138 <param name="ICPL4" value="109.046571"/>
139 <param name="ICPL6" value="111.041593"/>
140 <param name="ICPL10" value="115.0667"/>
141 </section>
142 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
143 <output name="ctd_out" ftype="xml">
144 <assert_contents>
145 <is_valid_xml/>
146 </assert_contents>
147 </output>
148 </test>
149 <!-- UTILS_MultiplexResolver_2 -->
150 <test expect_num_outputs="3">
151 <section name="adv_opts">
152 <param name="force" value="false"/>
153 <param name="test" value="true"/>
154 </section>
155 <param name="in" value="MultiplexResolver_2_input.consensusXML"/>
156 <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
157 <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
158 <section name="algorithm">
159 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
160 <param name="missed_cleavages" value="4"/>
161 <param name="mass_tolerance" value="0.1"/>
162 <param name="mz_tolerance" value="10"/>
163 <param name="rt_tolerance" value="5"/>
164 </section>
165 <section name="labels">
166 <param name="Arg6" value="6.0201290268"/>
167 <param name="Arg10" value="10.0082686"/>
168 <param name="Lys4" value="4.0251069836"/>
169 <param name="Lys6" value="6.0201290268"/>
170 <param name="Lys8" value="8.0141988132"/>
171 <param name="Leu3" value="3.01883"/>
172 <param name="Dimethyl0" value="28.0313"/>
173 <param name="Dimethyl4" value="32.056407"/>
174 <param name="Dimethyl6" value="34.063117"/>
175 <param name="Dimethyl8" value="36.07567"/>
176 <param name="ICPL0" value="105.021464"/>
177 <param name="ICPL4" value="109.046571"/>
178 <param name="ICPL6" value="111.041593"/>
179 <param name="ICPL10" value="115.0667"/>
180 </section>
181 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
182 <output name="ctd_out" ftype="xml">
183 <assert_contents>
184 <is_valid_xml/>
185 </assert_contents>
186 </output>
187 </test>
188 <!-- UTILS_MultiplexResolver_3 -->
189 <test expect_num_outputs="3">
190 <section name="adv_opts">
191 <param name="force" value="false"/>
192 <param name="test" value="true"/>
193 </section>
194 <param name="in" value="MultiplexResolver_3_input.consensusXML"/>
195 <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
196 <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
197 <section name="algorithm">
198 <param name="labels" value="[][Leu3]"/>
199 <param name="missed_cleavages" value="2"/>
200 <param name="mass_tolerance" value="0.1"/>
201 <param name="mz_tolerance" value="10"/>
202 <param name="rt_tolerance" value="5"/>
203 </section>
204 <section name="labels">
205 <param name="Arg6" value="6.0201290268"/>
206 <param name="Arg10" value="10.0082686"/>
207 <param name="Lys4" value="4.0251069836"/>
208 <param name="Lys6" value="6.0201290268"/>
209 <param name="Lys8" value="8.0141988132"/>
210 <param name="Leu3" value="3.01883"/>
211 <param name="Dimethyl0" value="28.0313"/>
212 <param name="Dimethyl4" value="32.056407"/>
213 <param name="Dimethyl6" value="34.063117"/>
214 <param name="Dimethyl8" value="36.07567"/>
215 <param name="ICPL0" value="105.021464"/>
216 <param name="ICPL4" value="109.046571"/>
217 <param name="ICPL6" value="111.041593"/>
218 <param name="ICPL10" value="115.0667"/>
219 </section>
220 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
221 <output name="ctd_out" ftype="xml">
222 <assert_contents>
223 <is_valid_xml/>
224 </assert_contents>
225 </output>
226 </test>
227 <!-- UTILS_MultiplexResolver_4 -->
228 <test expect_num_outputs="3">
229 <section name="adv_opts">
230 <param name="force" value="false"/>
231 <param name="test" value="true"/>
232 </section>
233 <param name="in" value="MultiplexResolver_4_input.consensusXML"/>
234 <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/>
235 <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
236 <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
237 <section name="algorithm">
238 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
239 <param name="missed_cleavages" value="3"/>
240 <param name="mass_tolerance" value="0.1"/>
241 <param name="mz_tolerance" value="10"/>
242 <param name="rt_tolerance" value="10"/>
243 </section>
244 <section name="labels">
245 <param name="Arg6" value="6.0201290268"/>
246 <param name="Arg10" value="10.0082686"/>
247 <param name="Lys4" value="4.0251069836"/>
248 <param name="Lys6" value="6.0201290268"/>
249 <param name="Lys8" value="8.0141988132"/>
250 <param name="Leu3" value="3.01883"/>
251 <param name="Dimethyl0" value="28.0313"/>
252 <param name="Dimethyl4" value="32.056407"/>
253 <param name="Dimethyl6" value="34.063117"/>
254 <param name="Dimethyl8" value="36.07567"/>
255 <param name="ICPL0" value="105.021464"/>
256 <param name="ICPL4" value="109.046571"/>
257 <param name="ICPL6" value="111.041593"/>
258 <param name="ICPL10" value="115.0667"/>
259 </section>
260 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
261 <output name="ctd_out" ftype="xml">
262 <assert_contents>
263 <is_valid_xml/>
264 </assert_contents>
265 </output>
266 </test>
115 </tests> 267 </tests>
116 <help><![CDATA[Completes peptide multiplets and resolves conflicts within them. 268 <help><![CDATA[Completes peptide multiplets and resolves conflicts within them.
117 269
118 270
119 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MultiplexResolver.html]]></help> 271 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MultiplexResolver.html]]></help>
120 <expand macro="references"/> 272 <expand macro="references"/>
121 </tool> 273 </tool>