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comparison ProteinInference.xml @ 9:e18096659b38 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:19:26 +0000
parents 4a39dd3bbe69
children 7951e3db2efd
comparison
equal deleted inserted replaced
8:66d8e5a850f1 9:e18096659b38
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="2.3.0"> 4 <tool id="ProteinInference" name="ProteinInference" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Protein inference based on the number of 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>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[ProteinInference 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
18 #if $param_out: 21 mkdir out &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $param_min_peptides_per_protein: 24
22 -min_peptides_per_protein $param_min_peptides_per_protein 25 set -o pipefail &&
23 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if $param_treat_charge_variants_separately: 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 -treat_charge_variants_separately 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 #end if 29 -in
27 #if $param_treat_modification_variants_separately: 30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
28 -treat_modification_variants_separately 31 -out
29 #end if 32 'out/output.${gxy2omsext("idxml")}'
30 #if $adv_opts.adv_opts_selector=='advanced': 33
31 #if $adv_opts.param_force: 34 ## Postprocessing
32 -force 35 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
33 #end if 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 #end if 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 ]]></command> 38 #end if]]></command>
39 <configfiles>
40 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles>
36 <inputs> 43 <inputs>
37 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="idxml" multiple="true" optional="false" label="input file(s)" help=" select idxml data sets(s)"/>
38 <param name="param_min_peptides_per_protein" type="integer" min="1" optional="True" value="2" label="Minimal number of peptides needed for a protein identification" help="(-min_peptides_per_protein) "/> 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="">
39 <param name="param_treat_charge_variants_separately" display="radio" type="boolean" truevalue="-treat_charge_variants_separately" falsevalue="" checked="false" optional="True" label="If this flag is set, different charge variants of the same peptide sequence count as inidividual evidences" help="(-treat_charge_variants_separately) "/> 46 <option value="no" selected="true">no</option>
40 <param name="param_treat_modification_variants_separately" display="radio" type="boolean" truevalue="-treat_modification_variants_separately" falsevalue="" checked="false" optional="True" label="If this flag is set, different modification variants of the same peptide sequence count as individual evidences" help="(-treat_modification_variants_separately) "/> 47 <option value="all">all</option>
41 <expand macro="advanced_options"> 48 <expand macro="list_string_san"/>
42 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 49 </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"/>
51 <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=""/>
53 </section>
54 <section name="Algorithm" title="" help="" expanded="false">
55 <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"/>
56 <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="">
57 <option value="maximum" selected="true">maximum</option>
58 <option value="product">product</option>
59 <option value="sum">sum</option>
60 <expand macro="list_string_san"/>
61 </param>
62 <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="">
63 <expand macro="list_string_san"/>
64 </param>
65 <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="">
66 <expand macro="list_string_san"/>
67 </param>
68 <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="">
69 <expand macro="list_string_san"/>
70 </param>
71 <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="">
72 <expand macro="list_string_san"/>
73 </param>
74 </section>
75 <expand macro="adv_opts_macro">
76 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
77 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
78 <expand macro="list_string_san"/>
79 </param>
43 </expand> 80 </expand>
81 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
82 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
83 </param>
44 </inputs> 84 </inputs>
45 <outputs> 85 <outputs>
46 <data name="param_out" format="idxml"/> 86 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
87 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
88 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
89 </data>
47 </outputs> 90 </outputs>
48 <help>Protein inference based on the number of identified peptides. 91 <tests>
92 <expand macro="autotest_ProteinInference"/>
93 <expand macro="manutest_ProteinInference"/>
94 </tests>
95 <help><![CDATA[Protein inference based on an aggregation of the scores of the identified peptides.
49 96
50 97
51 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ProteinInference.html</help> 98 For more information, visit http://www.openms.de/documentation/TOPP_ProteinInference.html]]></help>
99 <expand macro="references"/>
52 </tool> 100 </tool>