Mercurial > repos > galaxyp > openms_precursorionselector

annotate PrecursorIonSelector.xml @ 13:1cae2aac2260 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:21:13 +0000
parents fa7a58de2977
children
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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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3 <!--Proposed Tool Section: [Targeted Experiments]-->
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1cae2aac2260 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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4 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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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>
45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 </macros>
45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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10 <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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11 <expand macro="stdio"/>
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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14 #import re
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15
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16 ## Preprocessing
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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19 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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20 mkdir out &&
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21 #end if
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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22 #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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23 mkdir next_feat &&
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45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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24 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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25 mkdir ids &&
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26 ln -s '$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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27 #if $raw_data:
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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28 mkdir raw_data &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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29 ln -s '$raw_data' 'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)' &&
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45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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30 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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31 #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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32 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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33 #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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34 #if $db_path:
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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35 mkdir db_path &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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36 ln -s '$db_path' 'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)' &&
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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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37 #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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38 #if $rt_model:
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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39 mkdir rt_model &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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40 ln -s '$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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41 #end if
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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42 #if $dt_model:
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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43 mkdir dt_model &&
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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44 ln -s '$dt_model' 'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)' &&
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45 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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46
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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47 ## Main program call
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48
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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49 set -o pipefail &&
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50 @EXECUTABLE@ -write_ctd ./ &&
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51 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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52 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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53 -in
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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54 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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55 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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56 -out
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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57 'out/output.${gxy2omsext("featurexml")}'
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58 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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59 #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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60 -next_feat
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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61 'next_feat/output.${gxy2omsext("featurexml")}'
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62 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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63 -ids
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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64 'ids/${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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65 #if $raw_data:
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66 -raw_data
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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67 'raw_data/${re.sub("[^\w\-_]", "_", $raw_data.element_identifier)}.$gxy2omsext($raw_data.ext)'
0
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68 #end if
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faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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69 #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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70 -sim_results
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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71 'sim_results/output.${gxy2omsext("txt")}'
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72 #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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73 #if $db_path:
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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74 -db_path
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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75 'db_path/${re.sub("[^\w\-_]", "_", $db_path.element_identifier)}.$gxy2omsext($db_path.ext)'
0
45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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76 #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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77 #if $rt_model:
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78 -rt_model
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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79 'rt_model/${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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80 #end if
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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81 #if $dt_model:
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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82 -dt_model
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83 'dt_model/${re.sub("[^\w\-_]", "_", $dt_model.element_identifier)}.$gxy2omsext($dt_model.ext)'
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84 #end if
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85 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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86 | tee '$stdout'
0
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87 #end if
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88
9
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89 ## Postprocessing
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90 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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91 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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92 #end if
9
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93 #if "next_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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94 && mv 'next_feat/output.${gxy2omsext("featurexml")}' '$next_feat'
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95 #end if
9
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96 #if "sim_results_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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97 && mv 'sim_results/output.${gxy2omsext("txt")}' '$sim_results'
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98 #end if
9
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99 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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100 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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101 #end if]]></command>
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102 <configfiles>
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103 <inputs name="args_json" data_style="paths"/>
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104 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "algorithm": {"Preprocessing": {"tmp_dir": "\$TMP_DIR"}}}]]></configfile>
9
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105 </configfiles>
0
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106 <inputs>
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107 <param argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/>
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108 <param argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/>
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109 <param argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/>
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110 <param argument="-raw_data" type="data" format="mzml" optional="true" label="Input profile data" help=" select mzml data sets(s)"/>
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111 <param 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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112 <param argument="-store_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is stored" help=""/>
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113 <param argument="-simulation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Simulate the whole LC-MS/MS run" help=""/>
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114 <param argument="-db_path" type="data" format="fasta" optional="true" label="db file" help=" select fasta data sets(s)"/>
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115 <param argument="-rt_model" type="data" format="txt" optional="true" label="SVM Model for RTPredict" help=" select txt data sets(s)"/>
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116 <param argument="-dt_model" type="data" format="txt" optional="true" label="SVM Model for PTPredict" help=" select txt data sets(s)"/>
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117 <param 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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118 <expand macro="list_string_val" name="fixed_modifications"/>
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119 <expand macro="list_string_san" name="fixed_modifications"/>
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120 </param>
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121 <section name="algorithm" title="Settings for the compound list creation and rescoring" help="" expanded="false">
13
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122 <param name="type" argument="-algorithm:type" type="select" optional="true" label="Strategy for precursor ion selection" help="">
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123 <option value="ILP_IPS">ILP_IPS</option>
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124 <option value="IPS" selected="true">IPS</option>
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125 <option value="SPS">SPS</option>
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126 <option value="Upshift">Upshift</option>
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127 <option value="Downshift">Downshift</option>
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128 <option value="DEX">DEX</option>
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129 <expand macro="list_string_san" name="type"/>
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130 </param>
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131 <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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132 <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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133 <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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134 <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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135 <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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136 <section name="MIPFormulation" title="" help="" expanded="false">
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137 <section name="thresholds" title="" help="" expanded="false">
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138 <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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139 <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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140 <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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141 <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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142 <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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143 <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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144 <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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145 <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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146 <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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147 <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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148 </section>
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149 <section name="combined_ilp" title="" help="" expanded="false">
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150 <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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151 <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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152 <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=""/>
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153 <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=""/>
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154 </section>
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155 <section name="feature_based" title="" help="" expanded="false">
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156 <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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157 <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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158 </section>
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159 </section>
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160 <section name="Preprocessing" title="" help="" expanded="false">
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161 <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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162 <param name="precursor_mass_tolerance_unit" argument="-algorithm:Preprocessing:precursor_mass_tolerance_unit" type="select" optional="true" label="Precursor mass tolerance unit" help="">
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163 <option value="ppm" selected="true">ppm</option>
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164 <option value="Da">Da</option>
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165 <expand macro="list_string_san" name="precursor_mass_tolerance_unit"/>
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166 </param>
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167 <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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168 <expand macro="list_string_san" name="preprocessed_db_path"/>
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169 </param>
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170 <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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171 <expand macro="list_string_san" name="preprocessed_db_pred_rt_path"/>
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172 </param>
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173 <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="">
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174 <expand macro="list_string_san" name="preprocessed_db_pred_dt_path"/>
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175 </param>
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176 <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 parallelly predicted" help=""/>
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177 <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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178 <param name="taxonomy" argument="-algorithm:Preprocessing:taxonomy" type="text" optional="true" value="" label="Taxonomy" help="">
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179 <expand macro="list_string_san" name="taxonomy"/>
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180 </param>
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181 <param name="store_peptide_sequences" argument="-algorithm:Preprocessing:store_peptide_sequences" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if peptide sequences should be stored" help=""/>
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182 <section name="rt_settings" title="" help="" expanded="false">
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183 <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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184 <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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185 <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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186 <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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187 <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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188 </section>
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189 </section>
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190 </section>
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191 <expand macro="adv_opts_macro">
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192 <param argument="-solver" type="select" optional="true" label="LP solver type" help="">
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193 <option value="GLPK" selected="true">GLPK</option>
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194 <option value="COINOR">COINOR</option>
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195 <expand macro="list_string_san" name="solver"/>
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196 </param>
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197 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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198 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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199 <expand macro="list_string_san" name="test"/>
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200 </param>
0
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201 </expand>
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202 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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203 <option value="out_FLAG">out (modified feature map)</option>
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204 <option value="next_feat_FLAG">next_feat (feature map (featureXML) file with the selected precursors)</option>
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205 <option value="sim_results_FLAG">sim_results (File containing the results of the simulation run)</option>
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206 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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207 </param>
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208 </inputs>
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209 <outputs>
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210 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
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211 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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212 </data>
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213 <data name="next_feat" label="${tool.name} on ${on_string}: next_feat" format="featurexml">
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214 <filter>OPTIONAL_OUTPUTS is not None and "next_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
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215 </data>
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216 <data name="sim_results" label="${tool.name} on ${on_string}: sim_results" format="txt">
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217 <filter>OPTIONAL_OUTPUTS is not None and "sim_results_FLAG" in OPTIONAL_OUTPUTS</filter>
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218 </data>
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219 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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220 <filter>OPTIONAL_OUTPUTS is None</filter>
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221 </data>
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222 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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223 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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224 </data>
0
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225 </outputs>
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226 <tests><!-- TOPP_PrecursorIonSelector_1 -->
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227 <test expect_num_outputs="2">
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228 <section name="adv_opts">
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229 <param name="solver" value="GLPK"/>
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230 <param name="force" value="false"/>
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231 <param name="test" value="true"/>
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232 </section>
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233 <param name="in" value="PrecursorIonSelector_features.featureXML"/>
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234 <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
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235 <param name="num_precursors" value="1"/>
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236 <param name="load_preprocessing" value="false"/>
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237 <param name="store_preprocessing" value="false"/>
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238 <param name="simulation" value="true"/>
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239 <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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240 <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
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241 <param name="fixed_modifications" value=""/>
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242 <section name="algorithm">
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243 <param name="type" value="IPS"/>
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244 <param name="max_iteration" value="10"/>
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245 <param name="rt_bin_capacity" value="10"/>
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246 <param name="step_size" value="1"/>
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247 <param name="peptide_min_prob" value="0.2"/>
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248 <param name="sequential_spectrum_order" value="false"/>
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249 <section name="MIPFormulation">
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250 <section name="thresholds">
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251 <param name="min_protein_probability" value="0.2"/>
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252 <param name="min_protein_id_probability" value="0.95"/>
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253 <param name="min_pt_weight" value="0.5"/>
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254 <param name="min_mz" value="500.0"/>
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255 <param name="max_mz" value="5000.0"/>
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256 <param name="min_pred_pep_prob" value="0.5"/>
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257 <param name="min_rt_weight" value="0.5"/>
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258 <param name="use_peptide_rule" value="true"/>
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259 <param name="min_peptide_ids" value="2"/>
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260 <param name="min_peptide_probability" value="0.95"/>
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261 </section>
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262 <section name="combined_ilp">
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263 <param name="k1" value="0.2"/>
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264 <param name="k2" value="0.2"/>
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265 <param name="k3" value="0.4"/>
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266 <param name="scale_matching_probs" value="true"/>
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267 </section>
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268 <section name="feature_based">
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269 <param name="no_intensity_normalization" value="false"/>
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270 <param name="max_number_precursors_per_feature" value="1"/>
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271 </section>
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272 </section>
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273 <section name="Preprocessing">
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274 <param name="precursor_mass_tolerance" value="0.9"/>
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275 <param name="precursor_mass_tolerance_unit" value="Da"/>
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276 <param name="preprocessed_db_path" value=""/>
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277 <param name="preprocessed_db_pred_rt_path" value=""/>
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278 <param name="preprocessed_db_pred_dt_path" value=""/>
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279 <param name="max_peptides_per_run" value="100000"/>
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280 <param name="missed_cleavages" value="1"/>
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281 <param name="taxonomy" value=""/>
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282 <param name="store_peptide_sequences" value="false"/>
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283 <section name="rt_settings">
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284 <param name="min_rt" value="960.0"/>
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285 <param name="max_rt" value="3840.0"/>
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286 <param name="rt_step_size" value="30.0"/>
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287 <param name="gauss_mean" value="-1.0"/>
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288 <param name="gauss_sigma" value="3.0"/>
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289 </section>
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290 </section>
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291 </section>
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292 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/>
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293 <output name="ctd_out" ftype="xml">
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294 <assert_contents>
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295 <is_valid_xml/>
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296 </assert_contents>
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297 </output>
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298 </test>
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299 <!-- TOPP_PrecursorIonSelector_2 -->
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300 <test expect_num_outputs="2">
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301 <section name="adv_opts">
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302 <param name="solver" value="GLPK"/>
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303 <param name="force" value="false"/>
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304 <param name="test" value="true"/>
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305 </section>
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306 <param name="in" value="PrecursorIonSelector_features.featureXML"/>
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307 <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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308 <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
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309 <param name="num_precursors" value="1"/>
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310 <param name="load_preprocessing" value="false"/>
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311 <param name="store_preprocessing" value="false"/>
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312 <param name="simulation" value="false"/>
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313 <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
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314 <param name="fixed_modifications" value=""/>
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315 <section name="algorithm">
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316 <param name="type" value="IPS"/>
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317 <param name="max_iteration" value="10"/>
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318 <param name="rt_bin_capacity" value="10"/>
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319 <param name="step_size" value="1"/>
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320 <param name="peptide_min_prob" value="0.2"/>
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321 <param name="sequential_spectrum_order" value="false"/>
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322 <section name="MIPFormulation">
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323 <section name="thresholds">
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324 <param name="min_protein_probability" value="0.2"/>
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325 <param name="min_protein_id_probability" value="0.95"/>
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326 <param name="min_pt_weight" value="0.5"/>
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327 <param name="min_mz" value="500.0"/>
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328 <param name="max_mz" value="5000.0"/>
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329 <param name="min_pred_pep_prob" value="0.5"/>
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330 <param name="min_rt_weight" value="0.5"/>
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331 <param name="use_peptide_rule" value="true"/>
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332 <param name="min_peptide_ids" value="2"/>
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333 <param name="min_peptide_probability" value="0.95"/>
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334 </section>
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335 <section name="combined_ilp">
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336 <param name="k1" value="0.2"/>
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337 <param name="k2" value="0.2"/>
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338 <param name="k3" value="0.4"/>
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339 <param name="scale_matching_probs" value="true"/>
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340 </section>
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341 <section name="feature_based">
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342 <param name="no_intensity_normalization" value="false"/>
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343 <param name="max_number_precursors_per_feature" value="1"/>
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344 </section>
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345 </section>
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346 <section name="Preprocessing">
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347 <param name="precursor_mass_tolerance" value="0.9"/>
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348 <param name="precursor_mass_tolerance_unit" value="Da"/>
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349 <param name="preprocessed_db_path" value=""/>
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350 <param name="preprocessed_db_pred_rt_path" value=""/>
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351 <param name="preprocessed_db_pred_dt_path" value=""/>
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352 <param name="max_peptides_per_run" value="100000"/>
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353 <param name="missed_cleavages" value="1"/>
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354 <param name="taxonomy" value=""/>
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355 <param name="store_peptide_sequences" value="false"/>
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356 <section name="rt_settings">
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357 <param name="min_rt" value="960.0"/>
1cae2aac2260 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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358 <param name="max_rt" value="3840.0"/>
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359 <param name="rt_step_size" value="30.0"/>
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360 <param name="gauss_mean" value="-1.0"/>
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361 <param name="gauss_sigma" value="3.0"/>
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362 </section>
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363 </section>
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364 </section>
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365 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
1cae2aac2260 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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366 <output name="ctd_out" ftype="xml">
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367 <assert_contents>
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368 <is_valid_xml/>
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369 </assert_contents>
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370 </output>
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371 </test>
9
faac17171cc2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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372 </tests>
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373 <help><![CDATA[PrecursorIonSelector
0
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374
45a9649b4891 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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375
13
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376 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PrecursorIonSelector.html]]></help>
9
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377 <expand macro="references"/>
0
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378 </tool>