Mercurial > repos > galaxyp > openms_psmfeatureextractor

annotate PSMFeatureExtractor.xml @ 8:59736982ab7b draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"
author galaxyp
date Mon, 14 Dec 2020 16:54:21 +0000
parents 151e4b119c70
children 047020d9012f
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16a3498124d1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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: [Utilities]-->
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4 <tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy1" profile="20.05">
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5 <description>Computes extra features for each input PSM.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PSMFeatureExtractor</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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17
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18 ## Preprocessing
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19 mkdir in &&
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20 #if $in
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21 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
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22 #else if $in_single
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23 ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' &&
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24 #end if
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25 mkdir out &&
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27 ## Main program call
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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33 -in
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34 #if $in
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35 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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36 #else if $in_single
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37 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' &&
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38 #end if
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39 -out
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40 'out/output.${out_type}'
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41
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42 ## Postprocessing
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43 && mv 'out/output.${out_type}' '$out'
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44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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45 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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46 #end if]]></command>
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47 <configfiles>
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48 <inputs name="args_json" data_style="paths"/>
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49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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50 </configfiles>
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51 <inputs>
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52 <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of -in or -in_list is required)"/>
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53 <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s) for joint processing" help="(exactly one of -in or -in_list is required)"/>
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54 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
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55 <option value="idXML">idxml</option>
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56 <option value="mzid">mzid</option>
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57 <expand macro="list_string_san"/>
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58 </param>
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59 <param name="extra" argument="-extra" type="text" optional="true" value="" label="List of the MetaData parameters to be included in a feature set for precolato" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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60 <expand macro="list_string_val"/>
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61 <expand macro="list_string_san"/>
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62 </param>
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63 <param name="multiple_search_engines" argument="-multiple_search_engines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Combine PSMs from different search engines by merging on scan level" help=""/>
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64 <expand macro="adv_opts_macro">
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65 <param name="skip_db_check" argument="-skip_db_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Manual override to skip the check if same settings for multiple search engines were applied" help="Only valid together with -multiple_search_engines flag"/>
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66 <param name="concat" argument="-concat" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="Only valid together with -multiple_search_engines flag"/>
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67 <param name="impute" argument="-impute" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="Only valid together with -multiple_search_engines flag"/>
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68 <param name="limit_imputation" argument="-limit_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="Only valid together with -multiple_search_engines flag"/>
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69 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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70 <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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71 <expand macro="list_string_san"/>
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72 </param>
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73 </expand>
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74 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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75 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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76 </param>
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77 </inputs>
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78 <outputs>
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79 <data name="out" label="${tool.name} on ${on_string}: out">
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80 <change_format>
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81 <when input="out_type" value="idXML" format="idxml"/>
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82 <when input="out_type" value="mzid" format="mzid"/>
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83 </change_format>
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84 </data>
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85 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
8d4b175e06b5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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86 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
8d4b175e06b5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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87 </data>
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88 </outputs>
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89 <tests>
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90 <expand macro="autotest_PSMFeatureExtractor"/>
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91 <expand macro="manutest_PSMFeatureExtractor"/>
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92 </tests>
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93 <help><![CDATA[Computes extra features for each input PSM.
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94
16a3498124d1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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95
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96 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_PSMFeatureExtractor.html]]></help>
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97 <expand macro="references"/>
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98 </tool>