Mercurial > repos > galaxyp > openms_psmfeatureextractor

annotate PSMFeatureExtractor.xml @ 3:2bbe01546e77 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty
author galaxyp
date Fri, 17 May 2019 10:14:42 -0400
parents 54ff34feb43d
children 8d4b175e06b5
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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="2.3.0">
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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 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
2
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13 <command detect_errors="aggressive"><![CDATA[PSMFeatureExtractor
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15 -in
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16 #for token in $param_in:
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17 $token
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18 #end for
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19 #if $param_out:
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20 -out $param_out
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21 #end if
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23 #if $rep_param_extra:
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24 -extra
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25 #for token in $rep_param_extra:
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26 #if " " in str(token):
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27 "$token.param_extra"
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28 #else
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29 $token.param_extra
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30 #end if
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31 #end for
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32 #end if
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33 #if $param_multiple_search_engines:
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34 -multiple_search_engines
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35 #end if
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36 #if $adv_opts.adv_opts_selector=='advanced':
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37 #if $adv_opts.param_skip_db_check:
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38 -skip_db_check
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39 #end if
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40 #if $adv_opts.param_concat:
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41 -concat
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42 #end if
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43 #if $adv_opts.param_impute:
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44 -impute
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45 #end if
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46 #if $adv_opts.param_limit_imputation:
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47 -limit_imputation
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48 #end if
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49 #if $adv_opts.param_force:
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50 -force
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51 #end if
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52 #end if
2
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53 ]]></command>
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54 <inputs>
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55 <param name="param_in" type="data" format="mzid,idxml" multiple="true" optional="False" size="30" label="Input file(s)" help="(-in) ">
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56 <sanitizer>
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57 <valid initial="string.printable">
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58 <remove value="'"/>
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59 <remove value="&quot;"/>
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60 </valid>
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61 </sanitizer>
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62 </param>
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63 <repeat name="rep_param_extra" min="0" title="param_extra">
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64 <param name="param_extra" type="text" size="30" label="List of the MetaData parameters to be included in a feature set for precolato" help="(-extra) ">
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65 <sanitizer>
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66 <valid initial="string.printable">
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67 <remove value="'"/>
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68 <remove value="&quot;"/>
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69 </valid>
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70 </sanitizer>
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71 </param>
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72 </repeat>
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73 <param name="param_multiple_search_engines" display="radio" type="boolean" truevalue="-multiple_search_engines" falsevalue="" checked="false" optional="True" label="Combine PSMs from different search engines by merging on scan level" help="(-multiple_search_engines) "/>
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74 <expand macro="advanced_options">
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75 <param name="param_skip_db_check" display="radio" type="boolean" truevalue="-skip_db_check" falsevalue="" checked="false" optional="True" label="Manual override to skip the check if same settings for multiple search engines were applied" help="(-skip_db_check) Only valid together with -multiple_search_engines flag"/>
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76 <param name="param_concat" display="radio" type="boolean" truevalue="-concat" falsevalue="" checked="false" optional="True" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="(-concat) Only valid together with -multiple_search_engines flag"/>
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77 <param name="param_impute" display="radio" type="boolean" truevalue="-impute" falsevalue="" checked="false" optional="True" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="(-impute) Only valid together with -multiple_search_engines flag"/>
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78 <param name="param_limit_imputation" display="radio" type="boolean" truevalue="-limit_imputation" falsevalue="" checked="false" optional="True" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="(-limit_imputation) Only valid together with -multiple_search_engines flag"/>
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79 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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80 </expand>
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81 </inputs>
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82 <outputs>
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83 <data name="param_out" metadata_source="param_in" format="input"/>
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84 </outputs>
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85 <help>Computes extra features for each input PSM.
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86
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54ff34feb43d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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88 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_PSMFeatureExtractor.html</help>
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89 </tool>