Mercurial > repos > galaxyp > openms_rtevaluation

annotate RTEvaluation.xml @ 9:0cf2a9047a17 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:24:40 +0000
parents 07dfbd60b100
children b08e0ac606a4
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d5b15b21844b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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="RTEvaluation" name="RTEvaluation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">RTEvaluation</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 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 #if $sequences_file:
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22 mkdir sequences_file &&
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23 ln -s '$sequences_file' 'sequences_file/${re.sub("[^\w\-_]", "_", $sequences_file.element_identifier)}.$gxy2omsext($sequences_file.ext)' &&
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24 #end if
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25 mkdir out &&
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27 ## Main program call
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__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 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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35 #if $sequences_file:
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36 -sequences_file
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37 'sequences_file/${re.sub("[^\w\-_]", "_", $sequences_file.element_identifier)}.$gxy2omsext($sequences_file.ext)'
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38 #end if
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39 -out
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40 'out/output.${gxy2omsext("csv")}'
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42 ## Postprocessing
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43 && mv 'out/output.${gxy2omsext("csv")}' '$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" argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/>
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53 <param name="sequences_file" argument="-sequences_file" type="data" format="fasta" optional="true" label="Fasta File" help=" select fasta data sets(s)"/>
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54 <param name="latex" argument="-latex" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Indicates whether the output file format of the table should be LaTeX or CSV (default)" help=""/>
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55 <param name="p_value_dim_1" argument="-p_value_dim_1" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Significance level of first dimension RT filte" help=""/>
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56 <param name="p_value_dim_2" argument="-p_value_dim_2" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Significance level of second dimension RT filte" help=""/>
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57 <expand macro="adv_opts_macro">
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58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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59 <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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60 <expand macro="list_string_san"/>
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61 </param>
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62 </expand>
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63 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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65 </param>
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66 </inputs>
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67 <outputs>
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68 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
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69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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71 </data>
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72 </outputs>
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73 <tests>
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74 <expand macro="autotest_RTEvaluation"/>
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75 <expand macro="manutest_RTEvaluation"/>
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76 </tests>
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77 <help><![CDATA[Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
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78
d5b15b21844b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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0cf2a9047a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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80 For more information, visit http://www.openms.de/documentation/UTILS_RTEvaluation.html]]></help>
0cf2a9047a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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81 <expand macro="references"/>
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d5b15b21844b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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82 </tool>