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comparison ProteinInference.xml @ 13:98adda3af74a 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 19:00:46 +0000
parents 7951e3db2efd
children e278a1abeebe
comparison
equal deleted inserted replaced
12:5db940d296d7 13:98adda3af74a
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: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="ProteinInference" name="ProteinInference" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="ProteinInference" name="ProteinInference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Protein inference based on an aggregation of the scores of the identified peptides.</description> 5 <description>Protein inference based on an aggregation of the scores of the identified peptides.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ProteinInference</token> 7 <token name="@EXECUTABLE@">ProteinInference</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($in_cond.in.ext)' &&
23 #end if
21 mkdir out && 24 mkdir out &&
22 25
23 ## Main program call 26 ## Main program call
24 27
25 set -o pipefail && 28 set -o pipefail &&
26 @EXECUTABLE@ -write_ctd ./ && 29 @EXECUTABLE@ -write_ctd ./ &&
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
29 -in 32 -in
30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 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($in_cond.in.ext)'
37 #end if
31 -out 38 -out
32 'out/output.${gxy2omsext("idxml")}' 39 'out/output.${out_type}'
33 40
34 ## Postprocessing 41 ## Postprocessing
35 && mv 'out/output.${gxy2omsext("idxml")}' '$out' 42 && mv 'out/output.${out_type}' '$out'
36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 43 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
37 && mv '@EXECUTABLE@.ctd' '$ctd_out' 44 && mv '@EXECUTABLE@.ctd' '$ctd_out'
38 #end if]]></command> 45 #end if]]></command>
39 <configfiles> 46 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 47 <inputs name="args_json" data_style="paths"/>
41 <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>
42 </configfiles> 49 </configfiles>
43 <inputs> 50 <inputs>
44 <param name="in" argument="-in" type="data" format="idxml" multiple="true" optional="false" label="input file(s)" help=" select idxml data sets(s)"/> 51 <conditional name="in_cond">
45 <param name="merge_runs" argument="-merge_runs" display="radio" type="select" optional="false" label="If your idXML contains multiple runs, merge them beforehand?" help=""> 52 <param name="in_select" type="select" label="Run tool in batch mode for -in">
46 <option value="no" selected="true">no</option> 53 <option value="no">No: process all datasets jointly</option>
47 <option value="all">all</option> 54 <option value="yes">Yes: process each dataset in an independent job</option>
48 <expand macro="list_string_san"/> 55 </param>
56 <when value="no">
57 <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="false" label="input file(s)" help=" select consensusxml,idxml data sets(s)"/>
58 </when>
59 <when value="yes">
60 <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="false" label="input file(s)" help=" select consensusxml,idxml data sets(s)"/>
61 </when>
62 </conditional>
63 <param argument="-out_type" display="radio" type="select" optional="false" label="output file type" help="">
64 <option value="consensusXML">consensusxml</option>
65 <option value="idXML">idxml</option>
66 <expand macro="list_string_san" name="out_type"/>
49 </param> 67 </param>
50 <param name="annotate_indist_groups" argument="-annotate_indist_groups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If you want to annotate indistinguishable protein groups, either for reporting or for group based quant" help="later. Only works with a single ID run in the file"/> 68 <param argument="-merge_runs" type="select" optional="true" label="If your idXML contains multiple runs, merge them beforehand" help="Otherwise performs inference separately per run">
69 <option value="no">no</option>
70 <option value="all" selected="true">all</option>
71 <expand macro="list_string_san" name="merge_runs"/>
72 </param>
73 <param argument="-protein_fdr" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Additionally calculate the target-decoy FDR on protein-level after inference" help=""/>
51 <section name="Merging" title="" help="" expanded="false"> 74 <section name="Merging" title="" help="" expanded="false">
52 <param name="annotate_origin" argument="-Merging:annotate_origin" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If true, adds a map_index MetaValue to the PeptideIDs to annotate the IDRun they came from" help=""/> 75 <param name="annotate_origin" argument="-Merging:annotate_origin" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If true, adds a map_index MetaValue to the PeptideIDs to annotate the IDRun they came from" help=""/>
53 <param name="allow_disagreeing_settings" argument="-Merging:allow_disagreeing_settings" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force merging of disagreeing runs" help="Use at your own risk"/> 76 <param name="allow_disagreeing_settings" argument="-Merging:allow_disagreeing_settings" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force merging of disagreeing runs" help="Use at your own risk"/>
54 </section> 77 </section>
55 <section name="Algorithm" title="" help="" expanded="false"> 78 <section name="Algorithm" title="" help="" expanded="false">
56 <param name="min_peptides_per_protein" argument="-Algorithm:min_peptides_per_protein" type="integer" optional="true" min="0" value="1" label="Minimal number of peptides needed for a protein identification" help="If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept"/> 79 <param name="min_peptides_per_protein" argument="-Algorithm:min_peptides_per_protein" type="integer" optional="true" min="0" value="1" label="Minimal number of peptides needed for a protein identification" help="If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept"/>
57 <param name="score_aggregation_method" argument="-Algorithm:score_aggregation_method" display="radio" type="select" optional="false" label="How to aggregate scores of peptides matching to the same protein?" help=""> 80 <param name="score_aggregation_method" argument="-Algorithm:score_aggregation_method" type="select" optional="true" label="How to aggregate scores of peptides matching to the same protein?" help="">
58 <option value="maximum" selected="true">maximum</option> 81 <option value="best" selected="true">best</option>
59 <option value="product">product</option> 82 <option value="product">product</option>
60 <option value="sum">sum</option> 83 <option value="sum">sum</option>
61 <expand macro="list_string_san"/> 84 <option value="maximum">maximum</option>
62 </param> 85 <expand macro="list_string_san" name="score_aggregation_method"/>
63 <param name="treat_charge_variants_separately" argument="-Algorithm:treat_charge_variants_separately" type="text" optional="true" value="true" label="If this is set, different charge variants of the same peptide sequence count as individual evidences" help=""> 86 </param>
64 <expand macro="list_string_san"/> 87 <param name="treat_charge_variants_separately" argument="-Algorithm:treat_charge_variants_separately" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If this is true, different charge variants of the same peptide sequence count as individual evidences" help=""/>
65 </param> 88 <param name="treat_modification_variants_separately" argument="-Algorithm:treat_modification_variants_separately" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If this is true, different modification variants of the same peptide sequence count as individual evidences" help=""/>
66 <param name="treat_modification_variants_separately" argument="-Algorithm:treat_modification_variants_separately" type="text" optional="true" value="true" label="If this is set, different modification variants of the same peptide sequence count as individual evidences" help=""> 89 <param name="use_shared_peptides" argument="-Algorithm:use_shared_peptides" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If this is true, shared peptides are used as evidences" help="Note: shared_peptides are not deleted and potentially resolved in postprocessing as well"/>
67 <expand macro="list_string_san"/> 90 <param name="skip_count_annotation" argument="-Algorithm:skip_count_annotation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this is set, peptide counts won't be annotated at the proteins" help=""/>
68 </param> 91 <param name="annotate_indistinguishable_groups" argument="-Algorithm:annotate_indistinguishable_groups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If this is true, calculates and annotates indistinguishable protein groups" help=""/>
69 <param name="use_shared_peptides" argument="-Algorithm:use_shared_peptides" type="text" optional="true" value="true" label="If this is set, shared peptides are used as evidences" help=""> 92 <param name="greedy_group_resolution" argument="-Algorithm:greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this is true, shared peptides will be associated to best proteins only" help="(i.e. become potentially quantifiable razor peptides)"/>
70 <expand macro="list_string_san"/>
71 </param>
72 <param name="skip_count_annotation" argument="-Algorithm:skip_count_annotation" type="text" optional="true" value="false" label="If this is true, peptide counts won't be annotated at the proteins" help="">
73 <expand macro="list_string_san"/>
74 </param>
75 </section> 93 </section>
76 <expand macro="adv_opts_macro"> 94 <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=""/> 95 <param argument="-conservative_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use (D+1)/(T) instead of (D+1)/(T+D) for reporting protein FDRs" help=""/>
78 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 96 <param argument="-picked_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use picked protein FDRs" help=""/>
79 <expand macro="list_string_san"/> 97 <param argument="-picked_decoy_string" type="text" optional="true" value="" label="If using picked protein FDRs, which decoy string was used" help="Leave blank for auto-detection">
98 <expand macro="list_string_san" name="picked_decoy_string"/>
99 </param>
100 <param argument="-picked_decoy_prefix" type="select" optional="true" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
101 <option value="prefix" selected="true">prefix</option>
102 <option value="suffix">suffix</option>
103 <expand macro="list_string_san" name="picked_decoy_prefix"/>
104 </param>
105 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
106 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
107 <expand macro="list_string_san" name="test"/>
80 </param> 108 </param>
81 </expand> 109 </expand>
82 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 110 <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> 111 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
84 </param> 112 </param>
85 </inputs> 113 </inputs>
86 <outputs> 114 <outputs>
87 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 115 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml">
116 <change_format>
117 <when input="out_type" value="idXML" format="idxml"/>
118 </change_format>
119 </data>
88 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 120 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
89 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 121 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
90 </data> 122 </data>
91 </outputs> 123 </outputs>
92 <tests> 124 <tests><!-- TOPP_ProteinInference_1 -->
93 <expand macro="autotest_ProteinInference"/> 125 <test expect_num_outputs="2">
94 <expand macro="manutest_ProteinInference"/> 126 <section name="adv_opts">
127 <param name="conservative_fdr" value="true"/>
128 <param name="picked_fdr" value="true"/>
129 <param name="picked_decoy_string" value=""/>
130 <param name="picked_decoy_prefix" value="prefix"/>
131 <param name="force" value="false"/>
132 <param name="test" value="true"/>
133 </section>
134 <conditional name="in_cond">
135 <param name="in" value="ProteinInference_1_input.idXML"/>
136 </conditional>
137 <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
138 <param name="out_type" value="idXML"/>
139 <param name="merge_runs" value="all"/>
140 <param name="protein_fdr" value="false"/>
141 <section name="Merging">
142 <param name="annotate_origin" value="false"/>
143 <param name="allow_disagreeing_settings" value="false"/>
144 </section>
145 <section name="Algorithm">
146 <param name="min_peptides_per_protein" value="1"/>
147 <param name="score_aggregation_method" value="best"/>
148 <param name="treat_charge_variants_separately" value="true"/>
149 <param name="treat_modification_variants_separately" value="true"/>
150 <param name="use_shared_peptides" value="false"/>
151 <param name="skip_count_annotation" value="false"/>
152 <param name="annotate_indistinguishable_groups" value="true"/>
153 <param name="greedy_group_resolution" value="false"/>
154 </section>
155 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
156 <output name="ctd_out" ftype="xml">
157 <assert_contents>
158 <is_valid_xml/>
159 </assert_contents>
160 </output>
161 </test>
162 <!-- TOPP_ProteinInference_2 -->
163 <test expect_num_outputs="2">
164 <section name="adv_opts">
165 <param name="conservative_fdr" value="true"/>
166 <param name="picked_fdr" value="true"/>
167 <param name="picked_decoy_string" value=""/>
168 <param name="picked_decoy_prefix" value="prefix"/>
169 <param name="force" value="false"/>
170 <param name="test" value="true"/>
171 </section>
172 <conditional name="in_cond">
173 <param name="in" value="Epifany_2_input.consensusXML"/>
174 </conditional>
175 <output name="out" file="ProteinInference_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
176 <param name="out_type" value="consensusXML"/>
177 <param name="merge_runs" value="all"/>
178 <param name="protein_fdr" value="false"/>
179 <section name="Merging">
180 <param name="annotate_origin" value="true"/>
181 <param name="allow_disagreeing_settings" value="false"/>
182 </section>
183 <section name="Algorithm">
184 <param name="min_peptides_per_protein" value="1"/>
185 <param name="score_aggregation_method" value="best"/>
186 <param name="treat_charge_variants_separately" value="true"/>
187 <param name="treat_modification_variants_separately" value="true"/>
188 <param name="use_shared_peptides" value="false"/>
189 <param name="skip_count_annotation" value="false"/>
190 <param name="annotate_indistinguishable_groups" value="true"/>
191 <param name="greedy_group_resolution" value="false"/>
192 </section>
193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
194 <output name="ctd_out" ftype="xml">
195 <assert_contents>
196 <is_valid_xml/>
197 </assert_contents>
198 </output>
199 </test>
200 <!-- TOPP_ProteinInference_3 -->
201 <test expect_num_outputs="2">
202 <section name="adv_opts">
203 <param name="conservative_fdr" value="true"/>
204 <param name="picked_fdr" value="true"/>
205 <param name="picked_decoy_string" value="_rev"/>
206 <param name="picked_decoy_prefix" value="suffix"/>
207 <param name="force" value="false"/>
208 <param name="test" value="true"/>
209 </section>
210 <conditional name="in_cond">
211 <param name="in" value="MSstatsConverter_3_in.consensusXML"/>
212 </conditional>
213 <output name="out" file="ProteinInference_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
214 <param name="out_type" value="consensusXML"/>
215 <param name="merge_runs" value="all"/>
216 <param name="protein_fdr" value="true"/>
217 <section name="Merging">
218 <param name="annotate_origin" value="true"/>
219 <param name="allow_disagreeing_settings" value="false"/>
220 </section>
221 <section name="Algorithm">
222 <param name="min_peptides_per_protein" value="1"/>
223 <param name="score_aggregation_method" value="best"/>
224 <param name="treat_charge_variants_separately" value="true"/>
225 <param name="treat_modification_variants_separately" value="true"/>
226 <param name="use_shared_peptides" value="true"/>
227 <param name="skip_count_annotation" value="false"/>
228 <param name="annotate_indistinguishable_groups" value="true"/>
229 <param name="greedy_group_resolution" value="false"/>
230 </section>
231 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
232 <output name="ctd_out" ftype="xml">
233 <assert_contents>
234 <is_valid_xml/>
235 </assert_contents>
236 </output>
237 </test>
95 </tests> 238 </tests>
96 <help><![CDATA[Protein inference based on an aggregation of the scores of the identified peptides. 239 <help><![CDATA[Protein inference based on an aggregation of the scores of the identified peptides.
97 240
98 241
99 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_ProteinInference.html]]></help> 242 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinInference.html]]></help>
100 <expand macro="references"/> 243 <expand macro="references"/>
101 </tool> 244 </tool>