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comparison ConsensusID.xml @ 17:abffdfee3021 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"
author galaxyp
date Mon, 22 Feb 2021 10:46:10 +0000
parents feebe2054e40
children f4be248c3d47
comparison
equal deleted inserted replaced
16:01dbaf6a57e0 17:abffdfee3021
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@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy1" profile="20.05">
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> 9 <import>macros_autotest.xml</import>
15 @EXT_FOO@ 15 @EXT_FOO@
16 #import re 16 #import re
17 17
18 ## Preprocessing 18 ## Preprocessing
19 mkdir in && 19 mkdir in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 20 mkdir ${' '.join(["'in/%s'" % (i) for i, f in enumerate($in) if f])} &&
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])}
21 mkdir out && 22 mkdir out &&
22 23
23 ## Main program call 24 ## Main program call
24 25
25 set -o pipefail && 26 set -o pipefail &&
26 @EXECUTABLE@ -write_ctd ./ && 27 @EXECUTABLE@ -write_ctd ./ &&
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 28 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 29 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
29 -in 30 -in
30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 31 ${' '.join(["'in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in) if f])}
31 -out 32 -out
32 'out/output.${in[0].ext}' 33 'out/output.${in[0].ext}'
33 34
34 ## Postprocessing 35 ## Postprocessing
35 && mv 'out/output.${in[0].ext}' '$out' 36 && mv 'out/output.${in[0].ext}' '$out'
40 <inputs name="args_json" data_style="paths"/> 41 <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 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 43 </configfiles>
43 <inputs> 44 <inputs>
44 <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)"/> 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)"/>
45 <param name="rt_delta" 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=""/> 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=""/>
46 <param name="mz_delta" 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=""/> 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=""/>
47 <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=""/> 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=""/>
48 <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"> 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">
49 <option value="PEPMatrix" selected="true">PEPMatrix</option> 50 <option value="PEPMatrix" selected="true">PEPMatrix</option>
50 <option value="PEPIons">PEPIons</option> 51 <option value="PEPIons">PEPIons</option>
51 <option value="best">best</option> 52 <option value="best">best</option>
52 <option value="worst">worst</option> 53 <option value="worst">worst</option>
53 <option value="average">average</option> 54 <option value="average">average</option>
54 <option value="ranks">ranks</option> 55 <option value="ranks">ranks</option>
55 <expand macro="list_string_san"/> 56 <expand macro="list_string_san" name="algorithm"/>
56 </param> 57 </param>
57 <section name="filter" title="Options for filtering peptide hits" help="" expanded="false"> 58 <section name="filter" title="Options for filtering peptide hits" help="" expanded="false">
58 <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=""/> 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=""/>
59 <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=""/> 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=""/>
60 <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'?"/> 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'?"/>
61 <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=""/> 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=""/>
62 </section> 63 </section>
63 <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false"> 64 <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false">
64 <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=""/> 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=""/>
65 <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=""/> 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=""/>
66 </section> 67 </section>
67 <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false"> 68 <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false">
68 <param name="matrix" argument="-PEPMatrix:matrix" display="radio" type="select" optional="false" label="Substitution matrix to use for alignment-based similarity scoring" help=""> 69 <param name="matrix" argument="-PEPMatrix:matrix" display="checkboxes" type="select" optional="false" label="Substitution matrix to use for alignment-based similarity scoring" help="">
69 <option value="identity" selected="true">identity</option> 70 <option value="identity" selected="true">identity</option>
70 <option value="PAM30MS">PAM30MS</option> 71 <option value="PAM30MS">PAM30MS</option>
71 <expand macro="list_string_san"/> 72 <expand macro="list_string_san" name="matrix"/>
72 </param> 73 </param>
73 <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=""/> 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=""/>
74 </section> 75 </section>
75 <expand macro="adv_opts_macro"> 76 <expand macro="adv_opts_macro">
76 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 77 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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 <param name="test" argument="-test" type="hidden" optional="false" value="False" label="Enables the test mode (needed for internal use only)" help="">
78 <expand macro="list_string_san"/> 79 <expand macro="list_string_san" name="test"/>
79 </param> 80 </param>
80 </expand> 81 </expand>
81 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 82 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
82 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 83 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
83 </param> 84 </param>