Mercurial > repos > galaxyp > openms_consensusid

annotate ConsensusID.xml @ 16:01dbaf6a57e0 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author galaxyp
date Fri, 06 Nov 2020 19:49:28 +0000
parents feebe2054e40
children abffdfee3021
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Computes a consensus of peptide identifications of several identification engines.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ConsensusID</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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18 ## Preprocessing
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19 mkdir in &&
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20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
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21 mkdir out &&
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23 ## Main program call
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24
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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31 -out
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32 'out/output.${in[0].ext}'
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34 ## Postprocessing
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35 && mv 'out/output.${in[0].ext}' '$out'
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36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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38 #end if]]></command>
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39 <configfiles>
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40 <inputs name="args_json" data_style="paths"/>
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41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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42 </configfiles>
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43 <inputs>
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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)"/>
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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=""/>
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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=""/>
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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=""/>
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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">
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49 <option value="PEPMatrix" selected="true">PEPMatrix</option>
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50 <option value="PEPIons">PEPIons</option>
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51 <option value="best">best</option>
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52 <option value="worst">worst</option>
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53 <option value="average">average</option>
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54 <option value="ranks">ranks</option>
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55 <expand macro="list_string_san"/>
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56 </param>
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57 <section name="filter" title="Options for filtering peptide hits" help="" expanded="false">
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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=""/>
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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=""/>
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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'?"/>
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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=""/>
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62 </section>
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63 <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false">
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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=""/>
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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=""/>
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66 </section>
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67 <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false">
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68 <param name="matrix" argument="-PEPMatrix:matrix" display="radio" type="select" optional="false" label="Substitution matrix to use for alignment-based similarity scoring" help="">
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69 <option value="identity" selected="true">identity</option>
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70 <option value="PAM30MS">PAM30MS</option>
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71 <expand macro="list_string_san"/>
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72 </param>
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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=""/>
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74 </section>
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75 <expand macro="adv_opts_macro">
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76 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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77 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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78 <expand macro="list_string_san"/>
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79 </param>
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80 </expand>
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81 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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82 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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83 </param>
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84 </inputs>
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85 <outputs>
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86 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
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87 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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88 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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89 </data>
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90 </outputs>
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91 <tests>
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92 <expand macro="autotest_ConsensusID"/>
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93 <expand macro="manutest_ConsensusID"/>
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94 </tests>
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95 <help><![CDATA[Computes a consensus of peptide identifications of several identification engines.
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96
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97
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98 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_ConsensusID.html]]></help>
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99 <expand macro="references"/>
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100 </tool>