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comparison ConsensusID.xml @ 15:feebe2054e40 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:16:41 +0000
parents fdc984e79f40
children abffdfee3021
comparison
equal deleted inserted replaced
14:205508001e9a 15:feebe2054e40
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 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
21 mkdir out && 21 mkdir out &&
22 22
23 ## Main program call 23 ## Main program call
24 24
25 set -o pipefail && 25 set -o pipefail &&
26 @EXECUTABLE@ -write_ctd ./ && 26 @EXECUTABLE@ -write_ctd ./ &&
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
29 -in 29 -in
30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
31 -out 31 -out
32 'out/output.${in.ext}' 32 'out/output.${in[0].ext}'
33 33
34 ## Postprocessing 34 ## Postprocessing
35 && mv 'out/output.${in.ext}' '$out' 35 && mv 'out/output.${in[0].ext}' '$out'
36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
37 && mv '@EXECUTABLE@.ctd' '$ctd_out' 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
38 #end if]]></command> 38 #end if]]></command>
39 <configfiles> 39 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 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> 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 42 </configfiles>
43 <inputs> 43 <inputs>
44 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/> 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="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=""/> 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="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=""/> 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="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=""/>
47 <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"> 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">
48 <option value="PEPMatrix" selected="true">PEPMatrix</option> 49 <option value="PEPMatrix" selected="true">PEPMatrix</option>
49 <option value="PEPIons">PEPIons</option> 50 <option value="PEPIons">PEPIons</option>
50 <option value="best">best</option> 51 <option value="best">best</option>
51 <option value="worst">worst</option> 52 <option value="worst">worst</option>
55 </param> 56 </param>
56 <section name="filter" title="Options for filtering peptide hits" help="" expanded="false"> 57 <section name="filter" title="Options for filtering peptide hits" help="" expanded="false">
57 <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=""/> 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=""/>
58 <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=""/> 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=""/>
59 <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'?"/> 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="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=""/>
60 </section> 62 </section>
61 <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false"> 63 <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false">
62 <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=""/> 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=""/>
63 <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=""/> 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=""/>
64 </section> 66 </section>
69 <expand macro="list_string_san"/> 71 <expand macro="list_string_san"/>
70 </param> 72 </param>
71 <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=""/> 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=""/>
72 </section> 74 </section>
73 <expand macro="adv_opts_macro"> 75 <expand macro="adv_opts_macro">
74 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 76 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
75 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 77 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
76 <expand macro="list_string_san"/> 78 <expand macro="list_string_san"/>
77 </param> 79 </param>
78 </expand> 80 </expand>
79 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 81 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
80 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 82 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
81 </param> 83 </param>
82 </inputs> 84 </inputs>
83 <outputs> 85 <outputs>
84 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/> 86 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
91 <expand macro="manutest_ConsensusID"/> 93 <expand macro="manutest_ConsensusID"/>
92 </tests> 94 </tests>
93 <help><![CDATA[Computes a consensus of peptide identifications of several identification engines. 95 <help><![CDATA[Computes a consensus of peptide identifications of several identification engines.
94 96
95 97
96 For more information, visit http://www.openms.de/documentation/TOPP_ConsensusID.html]]></help> 98 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_ConsensusID.html]]></help>
97 <expand macro="references"/> 99 <expand macro="references"/>
98 </tool> 100 </tool>