Mercurial > repos > galaxyp > openms_precursorionselector

annotate PrecursorIonSelector.xml @ 9:faac17171cc2 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 16:17:23 +0000
parents de49246e559a
children fa7a58de2977
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45a9649b4891 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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59e80620e2df planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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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45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 <!--Proposed Tool Section: [Targeted Experiments]-->
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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4 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 <description>PrecursorIonSelector</description>
45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros>
45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 <token name="@EXECUTABLE@">PrecursorIonSelector</token>
45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 <import>macros.xml</import>
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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9 <import>macros_autotest.xml</import>
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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10 <import>macros_test.xml</import>
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45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 </macros>
45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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12 <expand macro="requirements"/>
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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13 <expand macro="stdio"/>
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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15 @EXT_FOO@
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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16 #import re
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17
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18 ## Preprocessing
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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19 mkdir in &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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22 mkdir out &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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23 #end if
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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24 #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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25 mkdir next_feat &&
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45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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26 #end if
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27 mkdir ids &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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28 ln -s '$ids' 'ids/${re.sub("[^\w\-_]", "_", $ids.element_identifier)}.$gxy2omsext($ids.ext)' &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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29 #if $raw_data:
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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30 mkdir raw_data &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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31 ln -s '$raw_data' 'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)' &&
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32 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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33 #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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34 mkdir sim_results &&
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45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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35 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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36 #if $db_path:
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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37 mkdir db_path &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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38 ln -s '$db_path' 'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)' &&
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39 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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40 #if $rt_model:
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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41 mkdir rt_model &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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42 ln -s '$rt_model' 'rt_model/${re.sub("[^\w\-_]", "_", $rt_model.element_identifier)}.$gxy2omsext($rt_model.ext)' &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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43 #end if
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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44 #if $dt_model:
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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45 mkdir dt_model &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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46 ln -s '$dt_model' 'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)' &&
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47 #end if
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48
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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49 ## Main program call
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50
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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51 set -o pipefail &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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52 @EXECUTABLE@ -write_ctd ./ &&
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53 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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54 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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55 -in
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56 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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57 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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58 -out
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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59 'out/output.${gxy2omsext("featurexml")}'
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60 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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61 #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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62 -next_feat
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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63 'next_feat/output.${gxy2omsext("featurexml")}'
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64 #end if
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65 -ids
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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66 'ids/${re.sub("[^\w\-_]", "_", $ids.element_identifier)}.$gxy2omsext($ids.ext)'
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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67 #if $raw_data:
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68 -raw_data
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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69 'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)'
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70 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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71 #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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72 -sim_results
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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73 'sim_results/output.${gxy2omsext("txt")}'
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74 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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75 #if $db_path:
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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76 -db_path
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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77 'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)'
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78 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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79 #if $rt_model:
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80 -rt_model
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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81 'rt_model/${re.sub("[^\w\-_]", "_", $rt_model.element_identifier)}.$gxy2omsext($rt_model.ext)'
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82 #end if
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83 #if $dt_model:
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84 -dt_model
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85 'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)'
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86 #end if
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87 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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88 | tee '$stdout'
0
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89 #end if
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90
9
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91 ## Postprocessing
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92 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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93 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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94 #end if
9
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95 #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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96 && mv 'next_feat/output.${gxy2omsext("featurexml")}' '$next_feat'
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97 #end if
9
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98 #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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99 && mv 'sim_results/output.${gxy2omsext("txt")}' '$sim_results'
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100 #end if
9
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101 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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102 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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103 #end if]]></command>
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104 <configfiles>
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105 <inputs name="args_json" data_style="paths"/>
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106 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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107 </configfiles>
0
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108 <inputs>
9
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109 <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/>
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110 <param name="ids" argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/>
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111 <param name="num_precursors" argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/>
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112 <param name="raw_data" argument="-raw_data" type="data" format="mzml" optional="true" label="Input profile data" help=" select mzml data sets(s)"/>
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113 <param name="load_preprocessing" argument="-load_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is loaded from file, not calculated" help=""/>
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114 <param name="store_preprocessing" argument="-store_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is stored" help=""/>
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115 <param name="simulation" argument="-simulation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Simulate the whole LC-MS/MS run" help=""/>
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116 <param name="db_path" argument="-db_path" type="data" format="fasta" optional="true" label="db file" help=" select fasta data sets(s)"/>
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117 <param name="rt_model" argument="-rt_model" type="data" format="txt" optional="true" label="SVM Model for RTPredict" help=" select txt data sets(s)"/>
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118 <param name="dt_model" argument="-dt_model" type="data" format="txt" optional="true" label="SVM Model for PTPredict" help=" select txt data sets(s)"/>
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119 <param name="fixed_modifications" argument="-fixed_modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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120 <expand macro="list_string_val"/>
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121 <expand macro="list_string_san"/>
0
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122 </param>
9
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123 <section name="algorithm" title="Settings for the compound list creation and rescoring" help="" expanded="false">
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124 <param name="type" argument="-algorithm:type" type="select" optional="false" label="Strategy for precursor ion selection" help="">
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125 <option value="ILP_IPS">ILP_IPS</option>
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126 <option value="IPS" selected="true">IPS</option>
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127 <option value="SPS">SPS</option>
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128 <option value="Upshift">Upshift</option>
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129 <option value="Downshift">Downshift</option>
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130 <option value="DEX">DEX</option>
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131 <expand macro="list_string_san"/>
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132 </param>
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133 <param name="max_iteration" argument="-algorithm:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximal number of iterations" help=""/>
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134 <param name="rt_bin_capacity" argument="-algorithm:rt_bin_capacity" type="integer" optional="true" min="1" value="10" label="Maximal number of precursors per rt bin" help=""/>
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135 <param name="step_size" argument="-algorithm:step_size" type="integer" optional="true" min="1" value="1" label="Maximal number of precursors per iteration" help=""/>
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136 <param name="peptide_min_prob" argument="-algorithm:peptide_min_prob" type="float" optional="true" value="0.2" label="Minimal peptide probability" help=""/>
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137 <param name="sequential_spectrum_order" argument="-algorithm:sequential_spectrum_order" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, precursors are selected sequentially with respect to their RT" help=""/>
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138 <section name="MIPFormulation" title="" help="" expanded="false">
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139 <section name="thresholds" title="" help="" expanded="false">
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140 <param name="min_protein_probability" argument="-algorithm:MIPFormulation:thresholds:min_protein_probability" type="float" optional="true" min="0.0" max="1.0" value="0.2" label="Minimal protein probability for a protein to be considered in the ILP" help=""/>
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141 <param name="min_protein_id_probability" argument="-algorithm:MIPFormulation:thresholds:min_protein_id_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Minimal protein probability for a protein to be considered identified" help=""/>
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142 <param name="min_pt_weight" argument="-algorithm:MIPFormulation:thresholds:min_pt_weight" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal pt weight of a precurso" help=""/>
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143 <param name="min_mz" argument="-algorithm:MIPFormulation:thresholds:min_mz" type="float" optional="true" min="0.0" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
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144 <param name="max_mz" argument="-algorithm:MIPFormulation:thresholds:max_mz" type="float" optional="true" min="0.0" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help=""/>
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145 <param name="min_pred_pep_prob" argument="-algorithm:MIPFormulation:thresholds:min_pred_pep_prob" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal predicted peptide probability of a precurso" help=""/>
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146 <param name="min_rt_weight" argument="-algorithm:MIPFormulation:thresholds:min_rt_weight" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Minimal rt weight of a precurso" help=""/>
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147 <param name="use_peptide_rule" argument="-algorithm:MIPFormulation:thresholds:use_peptide_rule" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use peptide rule instead of minimal protein id probability" help=""/>
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148 <param name="min_peptide_ids" argument="-algorithm:MIPFormulation:thresholds:min_peptide_ids" type="integer" optional="true" min="1" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help=""/>
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149 <param name="min_peptide_probability" argument="-algorithm:MIPFormulation:thresholds:min_peptide_probability" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help=""/>
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150 </section>
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151 <section name="combined_ilp" title="" help="" expanded="false">
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152 <param name="k1" argument="-algorithm:MIPFormulation:combined_ilp:k1" type="float" optional="true" min="0.0" value="0.2" label="combined ilp: weight for z_i" help=""/>
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153 <param name="k2" argument="-algorithm:MIPFormulation:combined_ilp:k2" type="float" optional="true" min="0.0" value="0.2" label="combined ilp: weight for x_j,s*int_j,s" help=""/>
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154 <param name="k3" argument="-algorithm:MIPFormulation:combined_ilp:k3" type="float" optional="true" min="0.0" value="0.4" label="combined ilp: weight for -x_j,s*w_j,s" help=""/>
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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155 <param name="scale_matching_probs" argument="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help=""/>
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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156 </section>
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157 <section name="feature_based" title="" help="" expanded="false">
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158 <param name="no_intensity_normalization" argument="-algorithm:MIPFormulation:feature_based:no_intensity_normalization" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag indicating if intensities shall be scaled to be in [0,1]" help="This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1"/>
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159 <param name="max_number_precursors_per_feature" argument="-algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature" type="integer" optional="true" min="1" value="1" label="The maximal number of precursors per feature" help=""/>
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160 </section>
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161 </section>
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162 <section name="Preprocessing" title="" help="" expanded="false">
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163 <param name="precursor_mass_tolerance" argument="-algorithm:Preprocessing:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help=""/>
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164 <param name="precursor_mass_tolerance_unit" argument="-algorithm:Preprocessing:precursor_mass_tolerance_unit" display="radio" type="select" optional="false" label="Precursor mass tolerance unit" help="">
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165 <option value="ppm" selected="true">ppm</option>
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166 <option value="Da">Da</option>
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167 <expand macro="list_string_san"/>
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168 </param>
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169 <param name="preprocessed_db_path" argument="-algorithm:Preprocessing:preprocessed_db_path" type="text" optional="true" value="" label="Path where the preprocessed database should be stored" help="">
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170 <expand macro="list_string_san"/>
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171 </param>
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172 <param name="preprocessed_db_pred_rt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_rt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
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173 <expand macro="list_string_san"/>
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174 </param>
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175 <param name="preprocessed_db_pred_dt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_dt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help="">
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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176 <expand macro="list_string_san"/>
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177 </param>
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178 <param name="max_peptides_per_run" argument="-algorithm:Preprocessing:max_peptides_per_run" type="integer" optional="true" min="1" value="100000" label="Number of peptides for that the pt and rt are parallely predicted" help=""/>
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179 <param name="missed_cleavages" argument="-algorithm:Preprocessing:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Number of allowed missed cleavages" help=""/>
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180 <param name="taxonomy" argument="-algorithm:Preprocessing:taxonomy" type="text" optional="true" value="" label="Taxonomy" help="">
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181 <expand macro="list_string_san"/>
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182 </param>
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183 <param name="store_peptide_sequences" argument="-algorithm:Preprocessing:store_peptide_sequences" type="text" optional="true" value="false" label="Flag if peptide sequences should be stored" help="">
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184 <expand macro="list_string_san"/>
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185 </param>
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186 <section name="rt_settings" title="" help="" expanded="false">
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187 <param name="min_rt" argument="-algorithm:Preprocessing:rt_settings:min_rt" type="float" optional="true" min="1.0" value="960.0" label="Minimal RT in the experiment (in seconds)" help=""/>
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188 <param name="max_rt" argument="-algorithm:Preprocessing:rt_settings:max_rt" type="float" optional="true" value="3840.0" label="Maximal RT in the experiment (in seconds)" help=""/>
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189 <param name="rt_step_size" argument="-algorithm:Preprocessing:rt_settings:rt_step_size" type="float" optional="true" value="30.0" label="Time between two consecutive spectra (in seconds)" help=""/>
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190 <param name="gauss_mean" argument="-algorithm:Preprocessing:rt_settings:gauss_mean" type="float" optional="true" value="-1.0" label="mean of the gauss curve" help=""/>
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191 <param name="gauss_sigma" argument="-algorithm:Preprocessing:rt_settings:gauss_sigma" type="float" optional="true" value="3.0" label="std of the gauss curve" help=""/>
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192 </section>
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193 </section>
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194 </section>
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195 <expand macro="adv_opts_macro">
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196 <param name="solver" argument="-solver" display="radio" type="select" optional="false" label="LP solver type" help="">
0
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197 <option value="GLPK" selected="true">GLPK</option>
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198 <option value="COINOR">COINOR</option>
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199 <expand macro="list_string_san"/>
0
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200 </param>
9
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201 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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202 <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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203 <expand macro="list_string_san"/>
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204 </param>
0
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205 </expand>
9
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206 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
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207 <option value="out_FLAG">out (std of the gauss curve)</option>
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208 <option value="next_feat_FLAG">next_feat (std of the gauss curve)</option>
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209 <option value="sim_results_FLAG">sim_results (std of the gauss curve)</option>
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210 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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211 </param>
0
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212 </inputs>
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213 <outputs>
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214 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
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215 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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216 </data>
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217 <data name="next_feat" label="${tool.name} on ${on_string}: next_feat" format="featurexml">
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218 <filter>OPTIONAL_OUTPUTS is not None and "next_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
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219 </data>
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220 <data name="sim_results" label="${tool.name} on ${on_string}: sim_results" format="txt">
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221 <filter>OPTIONAL_OUTPUTS is not None and "sim_results_FLAG" in OPTIONAL_OUTPUTS</filter>
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222 </data>
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223 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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224 <filter>OPTIONAL_OUTPUTS is None</filter>
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225 </data>
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226 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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227 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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228 </data>
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229 </outputs>
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230 <tests>
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231 <expand macro="autotest_PrecursorIonSelector"/>
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232 <expand macro="manutest_PrecursorIonSelector"/>
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233 </tests>
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234 <help><![CDATA[PrecursorIonSelector
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235
45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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236
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237 For more information, visit http://www.openms.de/documentation/TOPP_PrecursorIonSelector.html]]></help>
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238 <expand macro="references"/>
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239 </tool>