Mercurial > repos > galaxyp > openms_openswathanalyzer

annotate OpenSwathAnalyzer.xml @ 14:9cdf469a3241 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:38:17 +0000
parents 08488066d588
children
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1 <!--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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2 <!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
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3 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Picks peaks and finds features in an SWATH-MS or SRM experiment</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir tr &&
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19 cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
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20 #if $rt_norm:
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21 mkdir rt_norm &&
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22 cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
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23 #end if
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24 mkdir out &&
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25 #if $swath_files_cond.swath_files:
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26 mkdir swath_files_cond.swath_files &&
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27 #if $swath_files_cond.swath_files_select == "no"
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28 mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} &&
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29 ${' '.join(["cp '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
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30 #else
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31 cp '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' &&
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32 #end if
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33 #end if
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35 ## Main program call
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37 set -o pipefail &&
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38 @EXECUTABLE@ -write_ctd ./ &&
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39 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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40 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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41 -in
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42 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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43 -tr
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44 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
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45 #if $rt_norm:
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46 -rt_norm
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47 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)'
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48 #end if
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49 -out
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50 'out/output.${gxy2omsext("featurexml")}'
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51 #if $swath_files_cond.swath_files:
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52 -swath_files
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53 #if $swath_files_cond.swath_files_select == "no"
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54 ${' '.join(["'swath_files_cond.swath_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
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55 #else
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56 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)'
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57 #end if
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58 #end if
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60 ## Postprocessing
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61 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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62 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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63 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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64 #end if]]></command>
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65 <configfiles>
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66 <inputs name="args_json" data_style="paths"/>
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67 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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68 </configfiles>
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69 <inputs>
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70 <param argument="-in" type="data" format="mzml" label="input file containing the chromatograms" help=" select mzml data sets(s)"/>
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71 <param argument="-tr" type="data" format="traml" label="transition file" help=" select traml data sets(s)"/>
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72 <param argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
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73 <param argument="-no-strict" type="boolean" truevalue="true" falsevalue="false" checked="false" label="run in non-strict mode and allow some chromatograms to not be mapped" help=""/>
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74 <conditional name="swath_files_cond">
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75 <param name="swath_files_select" type="select" label="Run tool in batch mode for -swath_files">
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76 <option value="no">No: process all datasets jointly</option>
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77 <option value="yes">Yes: process each dataset in an independent job</option>
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78 </param>
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79 <when value="no">
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80 <param argument="-swath_files" type="data" format="mzml" multiple="true" optional="true" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be used select mzml data sets(s)"/>
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81 </when>
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82 <when value="yes">
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83 <param argument="-swath_files" type="data" format="mzml" optional="true" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be used select mzml data sets(s)"/>
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84 </when>
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85 </conditional>
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86 <param argument="-min_upper_edge_dist" type="float" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/>
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87 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
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88 <param name="type" argument="-model:type" type="select" label="Type of model" help="">
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89 <option value="linear" selected="true">linear</option>
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90 <option value="b_spline">b_spline</option>
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91 <option value="interpolated">interpolated</option>
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92 <option value="lowess">lowess</option>
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93 <expand macro="list_string_san" name="type"/>
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94 </param>
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95 <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
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96 </section>
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97 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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98 <param name="stop_report_after_feature" argument="-algorithm:stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help=""/>
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99 <param name="rt_extraction_window" argument="-algorithm:rt_extraction_window" type="float" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" help="For this to work, the TraML input file needs to contain normalized RT values"/>
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100 <param name="rt_normalization_factor" argument="-algorithm:rt_normalization_factor" type="float" value="1.0" label="The normalized RT is expected to be between 0 and 1" help="If your normalized RT has a different range, pass this here (e.g. it goes from 0 to 100, set this value to 100)"/>
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101 <param name="quantification_cutoff" argument="-algorithm:quantification_cutoff" type="float" min="0.0" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help=""/>
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102 <param name="write_convex_hull" argument="-algorithm:write_convex_hull" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write out all points of all features into the featureXML" help=""/>
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103 <param name="spectrum_addition_method" argument="-algorithm:spectrum_addition_method" type="select" label="For spectrum addition, either use simple concatenation or use peak resampling" help="">
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104 <option value="simple" selected="true">simple</option>
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105 <option value="resample">resample</option>
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106 <expand macro="list_string_san" name="spectrum_addition_method"/>
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107 </param>
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108 <param name="add_up_spectra" argument="-algorithm:add_up_spectra" type="integer" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
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109 <param name="spacing_for_spectra_resampling" argument="-algorithm:spacing_for_spectra_resampling" type="float" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
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110 <param name="uis_threshold_sn" argument="-algorithm:uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
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111 <param name="uis_threshold_peak_area" argument="-algorithm:uis_threshold_peak_area" type="integer" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
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112 <param name="scoring_model" argument="-algorithm:scoring_model" type="select" label="Scoring model to use" help="">
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113 <option value="default" selected="true">default</option>
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114 <option value="single_transition">single_transition</option>
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115 <expand macro="list_string_san" name="scoring_model"/>
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116 </param>
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117 <param name="im_extra_drift" argument="-algorithm:im_extra_drift" type="float" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
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118 <param name="strict" argument="-algorithm:strict" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help=""/>
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119 <section name="TransitionGroupPicker" title="" help="" expanded="false">
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120 <param name="stop_after_feature" argument="-algorithm:TransitionGroupPicker:stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
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121 <param name="stop_after_intensity_ratio" argument="-algorithm:TransitionGroupPicker:stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help=""/>
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122 <param name="min_peak_width" argument="-algorithm:TransitionGroupPicker:min_peak_width" type="float" value="0.001" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
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123 <param name="peak_integration" argument="-algorithm:TransitionGroupPicker:peak_integration" type="select" label="Calculate the peak area and height either the smoothed or the raw chromatogram data" help="">
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124 <option value="original" selected="true">original</option>
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125 <option value="smoothed">smoothed</option>
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126 <expand macro="list_string_san" name="peak_integration"/>
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127 </param>
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128 <param name="background_subtraction" argument="-algorithm:TransitionGroupPicker:background_subtraction" type="select" label="Remove background from peak signal using estimated noise levels" help="The 'original' method is only provided for historical purposes, please use the 'exact' method and set parameters using the PeakIntegrator: settings. The same original or smoothed chromatogram specified by peak_integration will be used for background estimation">
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129 <option value="none" selected="true">none</option>
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130 <option value="original">original</option>
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131 <option value="exact">exact</option>
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132 <expand macro="list_string_san" name="background_subtraction"/>
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133 </param>
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134 <param name="recalculate_peaks" argument="-algorithm:TransitionGroupPicker:recalculate_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="Tries to use the consensus (median) peak border if the variation within the picked peaks is too large"/>
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135 <param name="use_precursors" argument="-algorithm:TransitionGroupPicker:use_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use precursor chromatogram for peak picking (note that this may lead to precursor signal driving the peak picking)" help=""/>
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136 <param name="use_consensus" argument="-algorithm:TransitionGroupPicker:use_consensus" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use consensus peak boundaries when computing transition group picking (if false, compute independent peak boundaries for each transition)" help=""/>
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137 <param name="recalculate_peaks_max_z" argument="-algorithm:TransitionGroupPicker:recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
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138 <param name="minimal_quality" argument="-algorithm:TransitionGroupPicker:minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
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139 <param name="resample_boundary" argument="-algorithm:TransitionGroupPicker:resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
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140 <param name="compute_peak_quality" argument="-algorithm:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
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141 <param name="compute_peak_shape_metrics" argument="-algorithm:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
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142 <param name="compute_total_mi" argument="-algorithm:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
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143 <param name="boundary_selection_method" argument="-algorithm:TransitionGroupPicker:boundary_selection_method" type="select" label="Method to use when selecting the best boundaries for peaks" help="">
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144 <option value="largest" selected="true">largest</option>
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145 <option value="widest">widest</option>
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146 <expand macro="list_string_san" name="boundary_selection_method"/>
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147 </param>
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148 <section name="PeakPickerMRM" title="" help="" expanded="false">
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149 <param name="sgolay_frame_length" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
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150 <param name="sgolay_polynomial_order" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help=""/>
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151 <param name="gauss_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help=""/>
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152 <param name="use_gauss" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help=""/>
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153 <param name="peak_width" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data" help="(e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
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154 <param name="signal_to_noise" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="float" min="0.0" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more" help="Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
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155 <param name="sn_win_len" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help=""/>
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156 <param name="sn_bin_count" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help=""/>
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157 <param name="write_sn_log_messages" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help=""/>
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158 <param name="remove_overlapping_peaks" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to remove overlapping peaks during peak picking" help=""/>
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159 <param name="method" argument="-algorithm:TransitionGroupPicker:PeakPickerMRM:method" type="select" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="">
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160 <option value="legacy">legacy</option>
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161 <option value="corrected" selected="true">corrected</option>
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162 <option value="crawdad">crawdad</option>
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163 <expand macro="list_string_san" name="method"/>
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164 </param>
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165 </section>
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166 <section name="PeakIntegrator" title="" help="" expanded="false">
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167 <param name="integration_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:integration_type" type="select" label="The integration technique to use in integratePeak() and estimateBackground() which uses either the summed intensity, integration by Simpson's rule or trapezoidal integration" help="">
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168 <option value="intensity_sum" selected="true">intensity_sum</option>
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169 <option value="simpson">simpson</option>
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170 <option value="trapezoid">trapezoid</option>
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171 <expand macro="list_string_san" name="integration_type"/>
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172 </param>
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173 <param name="baseline_type" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type" type="select" label="The baseline type to use in estimateBackground() based on the peak boundaries" help="A rectangular baseline shape is computed based either on the minimal intensity of the peak boundaries, the maximum intensity or the average intensity (base_to_base)">
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174 <option value="base_to_base" selected="true">base_to_base</option>
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175 <option value="vertical_division">vertical_division</option>
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176 <option value="vertical_division_min">vertical_division_min</option>
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177 <option value="vertical_division_max">vertical_division_max</option>
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178 <expand macro="list_string_san" name="baseline_type"/>
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179 </param>
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180 <param name="fit_EMG" argument="-algorithm:TransitionGroupPicker:PeakIntegrator:fit_EMG" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit the chromatogram/spectrum to the EMG peak model" help=""/>
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181 </section>
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182 </section>
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183 <section name="DIAScoring" title="" help="" expanded="false">
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184 <param name="dia_extraction_window" argument="-algorithm:DIAScoring:dia_extraction_window" type="float" min="0.0" value="0.05" label="DIA extraction window in Th or ppm" help=""/>
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185 <param name="dia_extraction_unit" argument="-algorithm:DIAScoring:dia_extraction_unit" type="select" label="DIA extraction window unit" help="">
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186 <option value="Th" selected="true">Th</option>
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187 <option value="ppm">ppm</option>
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188 <expand macro="list_string_san" name="dia_extraction_unit"/>
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189 </param>
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190 <param name="dia_centroided" argument="-algorithm:DIAScoring:dia_centroided" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use centroided DIA data" help=""/>
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191 <param name="dia_byseries_intensity_min" argument="-algorithm:DIAScoring:dia_byseries_intensity_min" type="float" min="0.0" value="300.0" label="DIA b/y series minimum intensity to conside" help=""/>
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192 <param name="dia_byseries_ppm_diff" argument="-algorithm:DIAScoring:dia_byseries_ppm_diff" type="float" min="0.0" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help=""/>
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193 <param name="dia_nr_isotopes" argument="-algorithm:DIAScoring:dia_nr_isotopes" type="integer" min="0" value="4" label="DIA number of isotopes to conside" help=""/>
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194 <param name="dia_nr_charges" argument="-algorithm:DIAScoring:dia_nr_charges" type="integer" min="0" value="4" label="DIA number of charges to conside" help=""/>
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195 <param name="peak_before_mono_max_ppm_diff" argument="-algorithm:DIAScoring:peak_before_mono_max_ppm_diff" type="float" min="0.0" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help=""/>
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196 </section>
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197 <section name="EMGScoring" title="" help="" expanded="false">
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198 <param name="interpolation_step" argument="-algorithm:EMGScoring:interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help=""/>
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199 <param name="tolerance_stdev_bounding_box" argument="-algorithm:EMGScoring:tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help=""/>
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200 <param name="max_iteration" argument="-algorithm:EMGScoring:max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help=""/>
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201 <param name="init_mom" argument="-algorithm:EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Initialize parameters using method of moments estimators" help=""/>
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202 <section name="statistics" title="" help="" expanded="false">
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203 <param name="mean" argument="-algorithm:EMGScoring:statistics:mean" type="float" value="1.0" label="Centroid position of the model" help=""/>
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204 <param name="variance" argument="-algorithm:EMGScoring:statistics:variance" type="float" value="1.0" label="Variance of the model" help=""/>
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205 </section>
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206 </section>
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207 <section name="Scores" title="" help="" expanded="false">
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208 <param name="use_shape_score" argument="-algorithm:Scores:use_shape_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help=""/>
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209 <param name="use_coelution_score" argument="-algorithm:Scores:use_coelution_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help=""/>
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210 <param name="use_rt_score" argument="-algorithm:Scores:use_rt_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the retention time score (this score measure the difference in retention time)" help=""/>
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211 <param name="use_library_score" argument="-algorithm:Scores:use_library_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the library score" help=""/>
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212 <param name="use_elution_model_score" argument="-algorithm:Scores:use_elution_model_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help=""/>
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213 <param name="use_intensity_score" argument="-algorithm:Scores:use_intensity_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the intensity score" help=""/>
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214 <param name="use_nr_peaks_score" argument="-algorithm:Scores:use_nr_peaks_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the number of peaks score" help=""/>
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215 <param name="use_total_xic_score" argument="-algorithm:Scores:use_total_xic_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the total XIC score" help=""/>
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216 <param name="use_total_mi_score" argument="-algorithm:Scores:use_total_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the total MI score" help=""/>
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217 <param name="use_sn_score" argument="-algorithm:Scores:use_sn_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the SN (signal to noise) score" help=""/>
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218 <param name="use_mi_score" argument="-algorithm:Scores:use_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MI (mutual information) score" help=""/>
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219 <param name="use_dia_scores" argument="-algorithm:Scores:use_dia_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the DIA (SWATH) scores" help="If turned off, will not use fragment ion spectra for scoring"/>
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220 <param name="use_ms1_correlation" argument="-algorithm:Scores:use_ms1_correlation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the correlation scores with the MS1 elution profiles" help=""/>
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221 <param name="use_sonar_scores" argument="-algorithm:Scores:use_sonar_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for SONAR scans (scanning swath)" help=""/>
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222 <param name="use_ion_mobility_scores" argument="-algorithm:Scores:use_ion_mobility_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for Ion Mobility scans" help=""/>
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223 <param name="use_ms1_fullscan" argument="-algorithm:Scores:use_ms1_fullscan" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help=""/>
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224 <param name="use_ms1_mi" argument="-algorithm:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MS1 MI score" help=""/>
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225 <param name="use_uis_scores" argument="-algorithm:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/>
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226 <param name="use_ionseries_scores" argument="-algorithm:Scores:use_ionseries_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use MS2-level b/y ion-series scores for peptidoform identification" help=""/>
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227 <param name="use_ms2_isotope_scores" argument="-algorithm:Scores:use_ms2_isotope_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use MS2-level isotope scores (pearson &amp; manhattan) across product transitions (based on ID if annotated or averagine)" help=""/>
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228 </section>
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229 </section>
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230 <expand macro="adv_opts_macro">
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231 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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232 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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233 <expand macro="list_string_san" name="test"/>
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234 </param>
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235 </expand>
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236 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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237 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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238 </param>
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239 </inputs>
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240 <outputs>
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241 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
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242 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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243 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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244 </data>
0
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245 </outputs>
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246 <tests>
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247 <!-- TOPP_OpenSwathAnalyzer_test_1 -->
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248 <test expect_num_outputs="2">
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249 <section name="adv_opts">
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250 <param name="force" value="false"/>
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251 <param name="test" value="true"/>
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252 </section>
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253 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
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254 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
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255 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
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256 <output name="out" value="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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257 <param name="no_strict" value="false"/>
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258 <param name="min_upper_edge_dist" value="0.0"/>
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259 <section name="model">
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260 <param name="type" value="linear"/>
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261 <param name="symmetric_regression" value="false"/>
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262 </section>
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263 <section name="algorithm">
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264 <param name="stop_report_after_feature" value="-1"/>
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265 <param name="rt_extraction_window" value="-1.0"/>
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266 <param name="rt_normalization_factor" value="1.0"/>
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267 <param name="quantification_cutoff" value="0.0"/>
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268 <param name="write_convex_hull" value="false"/>
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269 <param name="spectrum_addition_method" value="simple"/>
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270 <param name="add_up_spectra" value="1"/>
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271 <param name="spacing_for_spectra_resampling" value="0.005"/>
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272 <param name="uis_threshold_sn" value="-1"/>
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273 <param name="uis_threshold_peak_area" value="0"/>
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274 <param name="scoring_model" value="default"/>
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275 <param name="im_extra_drift" value="0.0"/>
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276 <param name="strict" value="true"/>
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277 <section name="TransitionGroupPicker">
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278 <param name="stop_after_feature" value="-1"/>
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279 <param name="stop_after_intensity_ratio" value="0.0001"/>
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280 <param name="min_peak_width" value="0.001"/>
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281 <param name="peak_integration" value="original"/>
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282 <param name="background_subtraction" value="none"/>
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283 <param name="recalculate_peaks" value="false"/>
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284 <param name="use_precursors" value="false"/>
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285 <param name="use_consensus" value="true"/>
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286 <param name="recalculate_peaks_max_z" value="1.0"/>
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287 <param name="minimal_quality" value="-10000.0"/>
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288 <param name="resample_boundary" value="15.0"/>
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289 <param name="compute_peak_quality" value="false"/>
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290 <param name="compute_peak_shape_metrics" value="false"/>
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291 <param name="compute_total_mi" value="false"/>
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292 <param name="boundary_selection_method" value="largest"/>
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293 <section name="PeakPickerMRM">
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294 <param name="sgolay_frame_length" value="15"/>
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295 <param name="sgolay_polynomial_order" value="3"/>
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296 <param name="gauss_width" value="50.0"/>
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297 <param name="use_gauss" value="true"/>
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298 <param name="peak_width" value="40.0"/>
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299 <param name="signal_to_noise" value="1.0"/>
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300 <param name="sn_win_len" value="1000.0"/>
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301 <param name="sn_bin_count" value="30"/>
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302 <param name="write_sn_log_messages" value="false"/>
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303 <param name="remove_overlapping_peaks" value="false"/>
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304 <param name="method" value="legacy"/>
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305 </section>
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306 <section name="PeakIntegrator">
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307 <param name="integration_type" value="intensity_sum"/>
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308 <param name="baseline_type" value="base_to_base"/>
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309 <param name="fit_EMG" value="false"/>
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310 </section>
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311 </section>
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312 <section name="DIAScoring">
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313 <param name="dia_extraction_window" value="0.05"/>
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314 <param name="dia_extraction_unit" value="Th"/>
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315 <param name="dia_centroided" value="false"/>
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316 <param name="dia_byseries_intensity_min" value="300.0"/>
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317 <param name="dia_byseries_ppm_diff" value="10.0"/>
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318 <param name="dia_nr_isotopes" value="4"/>
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319 <param name="dia_nr_charges" value="4"/>
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320 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
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321 </section>
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322 <section name="EMGScoring">
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323 <param name="interpolation_step" value="0.2"/>
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324 <param name="tolerance_stdev_bounding_box" value="3.0"/>
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325 <param name="max_iteration" value="500"/>
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326 <param name="init_mom" value="false"/>
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327 <section name="statistics">
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328 <param name="mean" value="1.0"/>
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329 <param name="variance" value="1.0"/>
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330 </section>
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331 </section>
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332 <section name="Scores">
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333 <param name="use_shape_score" value="true"/>
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334 <param name="use_coelution_score" value="true"/>
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335 <param name="use_rt_score" value="true"/>
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336 <param name="use_library_score" value="true"/>
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337 <param name="use_elution_model_score" value="true"/>
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338 <param name="use_intensity_score" value="true"/>
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339 <param name="use_nr_peaks_score" value="true"/>
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340 <param name="use_total_xic_score" value="true"/>
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341 <param name="use_total_mi_score" value="false"/>
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342 <param name="use_sn_score" value="true"/>
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343 <param name="use_mi_score" value="false"/>
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344 <param name="use_dia_scores" value="true"/>
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345 <param name="use_ms1_correlation" value="false"/>
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346 <param name="use_sonar_scores" value="false"/>
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347 <param name="use_ion_mobility_scores" value="false"/>
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348 <param name="use_ms1_fullscan" value="false"/>
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349 <param name="use_ms1_mi" value="false"/>
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350 <param name="use_uis_scores" value="false"/>
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351 <param name="use_ionseries_scores" value="true"/>
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352 <param name="use_ms2_isotope_scores" value="true"/>
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353 </section>
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354 </section>
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355 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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356 <output name="ctd_out" ftype="xml">
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357 <assert_contents>
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358 <is_valid_xml/>
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359 </assert_contents>
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360 </output>
14
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361 <assert_stdout>
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362 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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363 </assert_stdout>
13
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364 </test>
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365 <!-- TOPP_OpenSwathAnalyzer_test_2 -->
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366 <test expect_num_outputs="2">
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367 <section name="adv_opts">
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368 <param name="force" value="false"/>
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369 <param name="test" value="true"/>
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370 </section>
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371 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
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372 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
14
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373 <output name="out" value="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
13
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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374 <param name="no_strict" value="false"/>
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galaxyp
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diff changeset
375 <conditional name="swath_files_cond">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
376 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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377 </conditional>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
378 <param name="min_upper_edge_dist" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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379 <section name="model">
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galaxyp
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diff changeset
380 <param name="type" value="linear"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
381 <param name="symmetric_regression" value="false"/>
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galaxyp
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382 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
383 <section name="algorithm">
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galaxyp
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384 <param name="stop_report_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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385 <param name="rt_extraction_window" value="-1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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386 <param name="rt_normalization_factor" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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387 <param name="quantification_cutoff" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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388 <param name="write_convex_hull" value="false"/>
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galaxyp
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389 <param name="spectrum_addition_method" value="simple"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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390 <param name="add_up_spectra" value="1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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391 <param name="spacing_for_spectra_resampling" value="0.005"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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392 <param name="uis_threshold_sn" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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393 <param name="uis_threshold_peak_area" value="0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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394 <param name="scoring_model" value="default"/>
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galaxyp
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diff changeset
395 <param name="im_extra_drift" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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396 <param name="strict" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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397 <section name="TransitionGroupPicker">
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galaxyp
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398 <param name="stop_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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399 <param name="stop_after_intensity_ratio" value="0.0001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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400 <param name="min_peak_width" value="0.001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
401 <param name="peak_integration" value="original"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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402 <param name="background_subtraction" value="none"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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403 <param name="recalculate_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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404 <param name="use_precursors" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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405 <param name="use_consensus" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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406 <param name="recalculate_peaks_max_z" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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407 <param name="minimal_quality" value="-10000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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408 <param name="resample_boundary" value="15.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
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409 <param name="compute_peak_quality" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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410 <param name="compute_peak_shape_metrics" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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411 <param name="compute_total_mi" value="false"/>
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galaxyp
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412 <param name="boundary_selection_method" value="largest"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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413 <section name="PeakPickerMRM">
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galaxyp
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414 <param name="sgolay_frame_length" value="15"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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415 <param name="sgolay_polynomial_order" value="3"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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416 <param name="gauss_width" value="50.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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417 <param name="use_gauss" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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418 <param name="peak_width" value="40.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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419 <param name="signal_to_noise" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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420 <param name="sn_win_len" value="1000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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421 <param name="sn_bin_count" value="30"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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422 <param name="write_sn_log_messages" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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423 <param name="remove_overlapping_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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424 <param name="method" value="legacy"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
425 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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426 <section name="PeakIntegrator">
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galaxyp
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diff changeset
427 <param name="integration_type" value="intensity_sum"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
428 <param name="baseline_type" value="base_to_base"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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429 <param name="fit_EMG" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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430 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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431 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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432 <section name="DIAScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
433 <param name="dia_extraction_window" value="0.05"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
434 <param name="dia_extraction_unit" value="Th"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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435 <param name="dia_centroided" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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436 <param name="dia_byseries_intensity_min" value="300.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
437 <param name="dia_byseries_ppm_diff" value="10.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
438 <param name="dia_nr_isotopes" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
439 <param name="dia_nr_charges" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
440 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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441 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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442 <section name="EMGScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
443 <param name="interpolation_step" value="0.2"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
444 <param name="tolerance_stdev_bounding_box" value="3.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
445 <param name="max_iteration" value="500"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
446 <param name="init_mom" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
447 <section name="statistics">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
448 <param name="mean" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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449 <param name="variance" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
450 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
451 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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452 <section name="Scores">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
453 <param name="use_shape_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
454 <param name="use_coelution_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
455 <param name="use_rt_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
456 <param name="use_library_score" value="true"/>
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galaxyp
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diff changeset
457 <param name="use_elution_model_score" value="true"/>
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galaxyp
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458 <param name="use_intensity_score" value="true"/>
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galaxyp
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diff changeset
459 <param name="use_nr_peaks_score" value="true"/>
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galaxyp
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460 <param name="use_total_xic_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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461 <param name="use_total_mi_score" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
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462 <param name="use_sn_score" value="true"/>
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galaxyp
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463 <param name="use_mi_score" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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464 <param name="use_dia_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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465 <param name="use_ms1_correlation" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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466 <param name="use_sonar_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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467 <param name="use_ion_mobility_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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468 <param name="use_ms1_fullscan" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
469 <param name="use_ms1_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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470 <param name="use_uis_scores" value="false"/>
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galaxyp
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471 <param name="use_ionseries_scores" value="true"/>
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galaxyp
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472 <param name="use_ms2_isotope_scores" value="true"/>
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473 </section>
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474 </section>
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galaxyp
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diff changeset
475 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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476 <output name="ctd_out" ftype="xml">
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477 <assert_contents>
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478 <is_valid_xml/>
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479 </assert_contents>
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480 </output>
14
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481 <assert_stdout>
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482 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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483 </assert_stdout>
13
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484 </test>
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485 <!-- TOPP_OpenSwathAnalyzer_test_5_mod -->
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galaxyp
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486 <test expect_num_outputs="2">
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487 <section name="adv_opts">
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488 <param name="force" value="false"/>
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galaxyp
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diff changeset
489 <param name="test" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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490 </section>
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491 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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492 <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/>
14
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493 <output name="out" value="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
13
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494 <param name="no_strict" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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495 <conditional name="swath_files_cond">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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496 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
497 </conditional>
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498 <param name="min_upper_edge_dist" value="0.0"/>
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diff changeset
499 <section name="model">
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500 <param name="type" value="linear"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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501 <param name="symmetric_regression" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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502 </section>
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galaxyp
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diff changeset
503 <section name="algorithm">
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504 <param name="stop_report_after_feature" value="-1"/>
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galaxyp
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diff changeset
505 <param name="rt_extraction_window" value="-1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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506 <param name="rt_normalization_factor" value="1.0"/>
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galaxyp
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507 <param name="quantification_cutoff" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
508 <param name="write_convex_hull" value="false"/>
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galaxyp
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diff changeset
509 <param name="spectrum_addition_method" value="simple"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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510 <param name="add_up_spectra" value="1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
511 <param name="spacing_for_spectra_resampling" value="0.005"/>
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galaxyp
parents: 11
diff changeset
512 <param name="uis_threshold_sn" value="-1"/>
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galaxyp
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513 <param name="uis_threshold_peak_area" value="0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
514 <param name="scoring_model" value="default"/>
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galaxyp
parents: 11
diff changeset
515 <param name="im_extra_drift" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
516 <param name="strict" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
517 <section name="TransitionGroupPicker">
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518 <param name="stop_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
519 <param name="stop_after_intensity_ratio" value="0.0001"/>
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galaxyp
parents: 11
diff changeset
520 <param name="min_peak_width" value="-1.0"/>
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galaxyp
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diff changeset
521 <param name="peak_integration" value="original"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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522 <param name="background_subtraction" value="none"/>
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diff changeset
523 <param name="recalculate_peaks" value="false"/>
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galaxyp
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524 <param name="use_precursors" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
525 <param name="use_consensus" value="true"/>
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parents: 11
diff changeset
526 <param name="recalculate_peaks_max_z" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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527 <param name="minimal_quality" value="-10000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
528 <param name="resample_boundary" value="15.0"/>
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galaxyp
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diff changeset
529 <param name="compute_peak_quality" value="false"/>
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galaxyp
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530 <param name="compute_peak_shape_metrics" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
531 <param name="compute_total_mi" value="false"/>
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galaxyp
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diff changeset
532 <param name="boundary_selection_method" value="largest"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
533 <section name="PeakPickerMRM">
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galaxyp
parents: 11
diff changeset
534 <param name="sgolay_frame_length" value="15"/>
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535 <param name="sgolay_polynomial_order" value="3"/>
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galaxyp
parents: 11
diff changeset
536 <param name="gauss_width" value="50.0"/>
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galaxyp
parents: 11
diff changeset
537 <param name="use_gauss" value="true"/>
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galaxyp
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diff changeset
538 <param name="peak_width" value="40.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
539 <param name="signal_to_noise" value="1.0"/>
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parents: 11
diff changeset
540 <param name="sn_win_len" value="1000.0"/>
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parents: 11
diff changeset
541 <param name="sn_bin_count" value="30"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
542 <param name="write_sn_log_messages" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
543 <param name="remove_overlapping_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
544 <param name="method" value="legacy"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
545 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
546 <section name="PeakIntegrator">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
547 <param name="integration_type" value="intensity_sum"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
548 <param name="baseline_type" value="base_to_base"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
549 <param name="fit_EMG" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
550 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
551 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
552 <section name="DIAScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
553 <param name="dia_extraction_window" value="0.05"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
554 <param name="dia_extraction_unit" value="Th"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
555 <param name="dia_centroided" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
556 <param name="dia_byseries_intensity_min" value="8.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
557 <param name="dia_byseries_ppm_diff" value="15.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
558 <param name="dia_nr_isotopes" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
559 <param name="dia_nr_charges" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
560 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
561 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
562 <section name="EMGScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
563 <param name="interpolation_step" value="0.2"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
564 <param name="tolerance_stdev_bounding_box" value="3.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
565 <param name="max_iteration" value="500"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
566 <param name="init_mom" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
567 <section name="statistics">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
568 <param name="mean" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
569 <param name="variance" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
570 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
571 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
572 <section name="Scores">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
573 <param name="use_shape_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
574 <param name="use_coelution_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
575 <param name="use_rt_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
576 <param name="use_library_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
577 <param name="use_elution_model_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
578 <param name="use_intensity_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
579 <param name="use_nr_peaks_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
580 <param name="use_total_xic_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
581 <param name="use_total_mi_score" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
582 <param name="use_sn_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
583 <param name="use_mi_score" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
584 <param name="use_dia_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
585 <param name="use_ms1_correlation" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
586 <param name="use_sonar_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
587 <param name="use_ion_mobility_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
588 <param name="use_ms1_fullscan" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
589 <param name="use_ms1_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
590 <param name="use_uis_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
591 <param name="use_ionseries_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
592 <param name="use_ms2_isotope_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
593 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
594 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
595 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
596 <output name="ctd_out" ftype="xml">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
597 <assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
598 <is_valid_xml/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
599 </assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
600 </output>
14
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
601 <assert_stdout>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 13
diff changeset
602 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
603 </assert_stdout>
13
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
604 </test>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 11
diff changeset
605 <!-- TOPP_OpenSwathAnalyzer_test_6_nomod -->
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
606 <test expect_num_outputs="2">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
607 <section name="adv_opts">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
608 <param name="force" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
609 <param name="test" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
610 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
611 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
612 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
14
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parents: 13
diff changeset
613 <output name="out" value="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
13
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parents: 11
diff changeset
614 <param name="no_strict" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
615 <conditional name="swath_files_cond">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
616 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
617 </conditional>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
618 <param name="min_upper_edge_dist" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
619 <section name="model">
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diff changeset
620 <param name="type" value="linear"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
621 <param name="symmetric_regression" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
622 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
623 <section name="algorithm">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
624 <param name="stop_report_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
625 <param name="rt_extraction_window" value="-1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
626 <param name="rt_normalization_factor" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
627 <param name="quantification_cutoff" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
628 <param name="write_convex_hull" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
629 <param name="spectrum_addition_method" value="simple"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
630 <param name="add_up_spectra" value="1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
631 <param name="spacing_for_spectra_resampling" value="0.005"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
632 <param name="uis_threshold_sn" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
633 <param name="uis_threshold_peak_area" value="0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
634 <param name="scoring_model" value="default"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
635 <param name="im_extra_drift" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
636 <param name="strict" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
637 <section name="TransitionGroupPicker">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
638 <param name="stop_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
639 <param name="stop_after_intensity_ratio" value="0.0001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
640 <param name="min_peak_width" value="-1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
641 <param name="peak_integration" value="original"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
642 <param name="background_subtraction" value="none"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
643 <param name="recalculate_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
644 <param name="use_precursors" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
645 <param name="use_consensus" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
646 <param name="recalculate_peaks_max_z" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
647 <param name="minimal_quality" value="-10000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
648 <param name="resample_boundary" value="15.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
649 <param name="compute_peak_quality" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
650 <param name="compute_peak_shape_metrics" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
651 <param name="compute_total_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
652 <param name="boundary_selection_method" value="largest"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
653 <section name="PeakPickerMRM">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
654 <param name="sgolay_frame_length" value="15"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
655 <param name="sgolay_polynomial_order" value="3"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
656 <param name="gauss_width" value="50.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
657 <param name="use_gauss" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
658 <param name="peak_width" value="40.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
659 <param name="signal_to_noise" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
660 <param name="sn_win_len" value="1000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
661 <param name="sn_bin_count" value="30"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
662 <param name="write_sn_log_messages" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
663 <param name="remove_overlapping_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
664 <param name="method" value="legacy"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
665 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
666 <section name="PeakIntegrator">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
667 <param name="integration_type" value="intensity_sum"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
668 <param name="baseline_type" value="base_to_base"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
669 <param name="fit_EMG" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
670 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
671 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
672 <section name="DIAScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
673 <param name="dia_extraction_window" value="0.05"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
674 <param name="dia_extraction_unit" value="Th"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
675 <param name="dia_centroided" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
676 <param name="dia_byseries_intensity_min" value="8.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
677 <param name="dia_byseries_ppm_diff" value="15.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
678 <param name="dia_nr_isotopes" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
679 <param name="dia_nr_charges" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
680 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
681 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
682 <section name="EMGScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
683 <param name="interpolation_step" value="0.2"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
684 <param name="tolerance_stdev_bounding_box" value="3.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
685 <param name="max_iteration" value="500"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
686 <param name="init_mom" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
687 <section name="statistics">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
688 <param name="mean" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
689 <param name="variance" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
690 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
691 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
692 <section name="Scores">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
693 <param name="use_shape_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
694 <param name="use_coelution_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
695 <param name="use_rt_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
696 <param name="use_library_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
697 <param name="use_elution_model_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
698 <param name="use_intensity_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
699 <param name="use_nr_peaks_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
700 <param name="use_total_xic_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
701 <param name="use_total_mi_score" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
702 <param name="use_sn_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
703 <param name="use_mi_score" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
704 <param name="use_dia_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
705 <param name="use_ms1_correlation" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
706 <param name="use_sonar_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
707 <param name="use_ion_mobility_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
708 <param name="use_ms1_fullscan" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
709 <param name="use_ms1_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
710 <param name="use_uis_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
711 <param name="use_ionseries_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
712 <param name="use_ms2_isotope_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
713 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
714 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
715 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
716 <output name="ctd_out" ftype="xml">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
717 <assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
718 <is_valid_xml/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
719 </assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
720 </output>
14
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
721 <assert_stdout>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
722 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
723 </assert_stdout>
13
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
724 </test>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
725 <!-- TOPP_OpenSwathAnalyzer_test_7_backgroundSubtraction -->
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
726 <test expect_num_outputs="2">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
727 <section name="adv_opts">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
728 <param name="force" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
729 <param name="test" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
730 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
731 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
732 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
14
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
733 <output name="out" value="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
13
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
734 <param name="no_strict" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
735 <param name="min_upper_edge_dist" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
736 <section name="model">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
737 <param name="type" value="linear"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
738 <param name="symmetric_regression" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
739 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
740 <section name="algorithm">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
741 <param name="stop_report_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
742 <param name="rt_extraction_window" value="-1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
743 <param name="rt_normalization_factor" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
744 <param name="quantification_cutoff" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
745 <param name="write_convex_hull" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
746 <param name="spectrum_addition_method" value="simple"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
747 <param name="add_up_spectra" value="1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
748 <param name="spacing_for_spectra_resampling" value="0.005"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
749 <param name="uis_threshold_sn" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
750 <param name="uis_threshold_peak_area" value="0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
751 <param name="scoring_model" value="default"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
752 <param name="im_extra_drift" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
753 <param name="strict" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
754 <section name="TransitionGroupPicker">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
755 <param name="stop_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
756 <param name="stop_after_intensity_ratio" value="0.0001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
757 <param name="min_peak_width" value="-1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
758 <param name="peak_integration" value="original"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
759 <param name="background_subtraction" value="original"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
760 <param name="recalculate_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
761 <param name="use_precursors" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
762 <param name="use_consensus" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
763 <param name="recalculate_peaks_max_z" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
764 <param name="minimal_quality" value="-10000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
765 <param name="resample_boundary" value="15.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
766 <param name="compute_peak_quality" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
767 <param name="compute_peak_shape_metrics" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
768 <param name="compute_total_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
769 <param name="boundary_selection_method" value="largest"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
770 <section name="PeakPickerMRM">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
771 <param name="sgolay_frame_length" value="15"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
772 <param name="sgolay_polynomial_order" value="3"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
773 <param name="gauss_width" value="50.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
774 <param name="use_gauss" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
775 <param name="peak_width" value="40.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
776 <param name="signal_to_noise" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
777 <param name="sn_win_len" value="1000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
778 <param name="sn_bin_count" value="30"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
779 <param name="write_sn_log_messages" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
780 <param name="remove_overlapping_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
781 <param name="method" value="legacy"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
782 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
783 <section name="PeakIntegrator">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
784 <param name="integration_type" value="intensity_sum"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
785 <param name="baseline_type" value="base_to_base"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
786 <param name="fit_EMG" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
787 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
788 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
789 <section name="DIAScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
790 <param name="dia_extraction_window" value="0.05"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
791 <param name="dia_extraction_unit" value="Th"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
792 <param name="dia_centroided" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
793 <param name="dia_byseries_intensity_min" value="300.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
794 <param name="dia_byseries_ppm_diff" value="10.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
795 <param name="dia_nr_isotopes" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
796 <param name="dia_nr_charges" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
797 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
798 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
799 <section name="EMGScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
800 <param name="interpolation_step" value="0.2"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
801 <param name="tolerance_stdev_bounding_box" value="3.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
802 <param name="max_iteration" value="500"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
803 <param name="init_mom" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
804 <section name="statistics">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
805 <param name="mean" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
806 <param name="variance" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
807 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
808 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
809 <section name="Scores">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
810 <param name="use_shape_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
811 <param name="use_coelution_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
812 <param name="use_rt_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
813 <param name="use_library_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
814 <param name="use_elution_model_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
815 <param name="use_intensity_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
816 <param name="use_nr_peaks_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
817 <param name="use_total_xic_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
818 <param name="use_total_mi_score" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
819 <param name="use_sn_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
820 <param name="use_mi_score" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
821 <param name="use_dia_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
822 <param name="use_ms1_correlation" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
823 <param name="use_sonar_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
824 <param name="use_ion_mobility_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
825 <param name="use_ms1_fullscan" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
826 <param name="use_ms1_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
827 <param name="use_uis_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
828 <param name="use_ionseries_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
829 <param name="use_ms2_isotope_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
830 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
831 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
832 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
833 <output name="ctd_out" ftype="xml">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
834 <assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
835 <is_valid_xml/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
836 </assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
837 </output>
14
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
838 <assert_stdout>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
839 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
840 </assert_stdout>
13
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
841 </test>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
842 <!-- TOPP_OpenSwathAnalyzer_test_8 -->
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
843 <test expect_num_outputs="2">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
844 <section name="adv_opts">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
845 <param name="force" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
846 <param name="test" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
847 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
848 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
849 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
850 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
14
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
851 <output name="out" value="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
13
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
852 <param name="no_strict" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
853 <param name="min_upper_edge_dist" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
854 <section name="model">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
855 <param name="type" value="linear"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
856 <param name="symmetric_regression" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
857 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
858 <section name="algorithm">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
859 <param name="stop_report_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
860 <param name="rt_extraction_window" value="-1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
861 <param name="rt_normalization_factor" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
862 <param name="quantification_cutoff" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
863 <param name="write_convex_hull" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
864 <param name="spectrum_addition_method" value="simple"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
865 <param name="add_up_spectra" value="1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
866 <param name="spacing_for_spectra_resampling" value="0.005"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
867 <param name="uis_threshold_sn" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
868 <param name="uis_threshold_peak_area" value="0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
869 <param name="scoring_model" value="default"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
870 <param name="im_extra_drift" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
871 <param name="strict" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
872 <section name="TransitionGroupPicker">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
873 <param name="stop_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
874 <param name="stop_after_intensity_ratio" value="0.0001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
875 <param name="min_peak_width" value="0.001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
876 <param name="peak_integration" value="original"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
877 <param name="background_subtraction" value="none"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
878 <param name="recalculate_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
879 <param name="use_precursors" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
880 <param name="use_consensus" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
881 <param name="recalculate_peaks_max_z" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
882 <param name="minimal_quality" value="-10000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
883 <param name="resample_boundary" value="15.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
884 <param name="compute_peak_quality" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
885 <param name="compute_peak_shape_metrics" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
886 <param name="compute_total_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
887 <param name="boundary_selection_method" value="largest"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
888 <section name="PeakPickerMRM">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
889 <param name="sgolay_frame_length" value="15"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
890 <param name="sgolay_polynomial_order" value="3"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
891 <param name="gauss_width" value="50.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
892 <param name="use_gauss" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
893 <param name="peak_width" value="40.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
894 <param name="signal_to_noise" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
895 <param name="sn_win_len" value="1000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
896 <param name="sn_bin_count" value="30"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
897 <param name="write_sn_log_messages" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
898 <param name="remove_overlapping_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
899 <param name="method" value="legacy"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
900 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
901 <section name="PeakIntegrator">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
902 <param name="integration_type" value="intensity_sum"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
903 <param name="baseline_type" value="base_to_base"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
904 <param name="fit_EMG" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
905 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
906 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
907 <section name="DIAScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
908 <param name="dia_extraction_window" value="0.05"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
909 <param name="dia_extraction_unit" value="Th"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
910 <param name="dia_centroided" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
911 <param name="dia_byseries_intensity_min" value="300.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
912 <param name="dia_byseries_ppm_diff" value="10.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
913 <param name="dia_nr_isotopes" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
914 <param name="dia_nr_charges" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
915 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
916 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
917 <section name="EMGScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
918 <param name="interpolation_step" value="0.2"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
919 <param name="tolerance_stdev_bounding_box" value="3.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
920 <param name="max_iteration" value="500"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
921 <param name="init_mom" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
922 <section name="statistics">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
923 <param name="mean" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
924 <param name="variance" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
925 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
926 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
927 <section name="Scores">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
928 <param name="use_shape_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
929 <param name="use_coelution_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
930 <param name="use_rt_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
931 <param name="use_library_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
932 <param name="use_elution_model_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
933 <param name="use_intensity_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
934 <param name="use_nr_peaks_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
935 <param name="use_total_xic_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
936 <param name="use_total_mi_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
937 <param name="use_sn_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
938 <param name="use_mi_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
939 <param name="use_dia_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
940 <param name="use_ms1_correlation" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
941 <param name="use_sonar_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
942 <param name="use_ion_mobility_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
943 <param name="use_ms1_fullscan" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
944 <param name="use_ms1_mi" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
945 <param name="use_uis_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
946 <param name="use_ionseries_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
947 <param name="use_ms2_isotope_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
948 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
949 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
950 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
951 <output name="ctd_out" ftype="xml">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
952 <assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
953 <is_valid_xml/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
954 </assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
955 </output>
14
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
956 <assert_stdout>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
957 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
958 </assert_stdout>
13
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
959 </test>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
960 <!-- TOPP_OpenSwathAnalyzer_test_9 -->
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
961 <test expect_num_outputs="2">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
962 <section name="adv_opts">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
963 <param name="force" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
964 <param name="test" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
965 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
966 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
967 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
968 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
14
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
969 <output name="out" value="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
13
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
970 <param name="no_strict" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
971 <param name="min_upper_edge_dist" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
972 <section name="model">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
973 <param name="type" value="linear"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
974 <param name="symmetric_regression" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
975 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
976 <section name="algorithm">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
977 <param name="stop_report_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
978 <param name="rt_extraction_window" value="-1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
979 <param name="rt_normalization_factor" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
980 <param name="quantification_cutoff" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
981 <param name="write_convex_hull" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
982 <param name="spectrum_addition_method" value="simple"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
983 <param name="add_up_spectra" value="1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
984 <param name="spacing_for_spectra_resampling" value="0.005"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
985 <param name="uis_threshold_sn" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
986 <param name="uis_threshold_peak_area" value="0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
987 <param name="scoring_model" value="default"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
988 <param name="im_extra_drift" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
989 <param name="strict" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
990 <section name="TransitionGroupPicker">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
991 <param name="stop_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
992 <param name="stop_after_intensity_ratio" value="0.0001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
993 <param name="min_peak_width" value="0.001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
994 <param name="peak_integration" value="original"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
995 <param name="background_subtraction" value="none"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
996 <param name="recalculate_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
997 <param name="use_precursors" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
998 <param name="use_consensus" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
999 <param name="recalculate_peaks_max_z" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1000 <param name="minimal_quality" value="-10000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1001 <param name="resample_boundary" value="15.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1002 <param name="compute_peak_quality" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1003 <param name="compute_peak_shape_metrics" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1004 <param name="compute_total_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1005 <param name="boundary_selection_method" value="largest"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1006 <section name="PeakPickerMRM">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1007 <param name="sgolay_frame_length" value="15"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1008 <param name="sgolay_polynomial_order" value="3"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1009 <param name="gauss_width" value="50.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1010 <param name="use_gauss" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1011 <param name="peak_width" value="40.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1012 <param name="signal_to_noise" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1013 <param name="sn_win_len" value="1000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1014 <param name="sn_bin_count" value="30"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1015 <param name="write_sn_log_messages" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1016 <param name="remove_overlapping_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1017 <param name="method" value="legacy"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1018 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1019 <section name="PeakIntegrator">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1020 <param name="integration_type" value="intensity_sum"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1021 <param name="baseline_type" value="base_to_base"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1022 <param name="fit_EMG" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1023 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1024 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1025 <section name="DIAScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1026 <param name="dia_extraction_window" value="0.05"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1027 <param name="dia_extraction_unit" value="Th"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1028 <param name="dia_centroided" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1029 <param name="dia_byseries_intensity_min" value="300.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1030 <param name="dia_byseries_ppm_diff" value="10.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1031 <param name="dia_nr_isotopes" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1032 <param name="dia_nr_charges" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1033 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1034 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1035 <section name="EMGScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1036 <param name="interpolation_step" value="0.2"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1037 <param name="tolerance_stdev_bounding_box" value="3.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1038 <param name="max_iteration" value="500"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1039 <param name="init_mom" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1040 <section name="statistics">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1041 <param name="mean" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1042 <param name="variance" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1043 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1044 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1045 <section name="Scores">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1046 <param name="use_shape_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1047 <param name="use_coelution_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1048 <param name="use_rt_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1049 <param name="use_library_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1050 <param name="use_elution_model_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1051 <param name="use_intensity_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1052 <param name="use_nr_peaks_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1053 <param name="use_total_xic_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1054 <param name="use_total_mi_score" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1055 <param name="use_sn_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1056 <param name="use_mi_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1057 <param name="use_dia_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1058 <param name="use_ms1_correlation" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1059 <param name="use_sonar_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1060 <param name="use_ion_mobility_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1061 <param name="use_ms1_fullscan" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1062 <param name="use_ms1_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1063 <param name="use_uis_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1064 <param name="use_ionseries_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1065 <param name="use_ms2_isotope_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1066 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1067 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1068 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1069 <output name="ctd_out" ftype="xml">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1070 <assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1071 <is_valid_xml/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1072 </assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1073 </output>
14
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
1074 <assert_stdout>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
1075 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
1076 </assert_stdout>
13
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1077 </test>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1078 <!-- TOPP_OpenSwathAnalyzer_test_10 -->
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1079 <test expect_num_outputs="2">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1080 <section name="adv_opts">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1081 <param name="force" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1082 <param name="test" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1083 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1084 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1085 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1086 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
14
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 13
diff changeset
1087 <output name="out" value="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
13
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1088 <param name="no_strict" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1089 <param name="min_upper_edge_dist" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1090 <section name="model">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1091 <param name="type" value="linear"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1092 <param name="symmetric_regression" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1093 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1094 <section name="algorithm">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1095 <param name="stop_report_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1096 <param name="rt_extraction_window" value="-1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1097 <param name="rt_normalization_factor" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1098 <param name="quantification_cutoff" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1099 <param name="write_convex_hull" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1100 <param name="spectrum_addition_method" value="simple"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1101 <param name="add_up_spectra" value="1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1102 <param name="spacing_for_spectra_resampling" value="0.005"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1103 <param name="uis_threshold_sn" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1104 <param name="uis_threshold_peak_area" value="0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1105 <param name="scoring_model" value="default"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1106 <param name="im_extra_drift" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1107 <param name="strict" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1108 <section name="TransitionGroupPicker">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1109 <param name="stop_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1110 <param name="stop_after_intensity_ratio" value="0.0001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1111 <param name="min_peak_width" value="0.001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1112 <param name="peak_integration" value="original"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1113 <param name="background_subtraction" value="none"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1114 <param name="recalculate_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1115 <param name="use_precursors" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1116 <param name="use_consensus" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1117 <param name="recalculate_peaks_max_z" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1118 <param name="minimal_quality" value="-10000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1119 <param name="resample_boundary" value="15.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1120 <param name="compute_peak_quality" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 11
diff changeset
1121 <param name="compute_peak_shape_metrics" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1122 <param name="compute_total_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1123 <param name="boundary_selection_method" value="largest"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1124 <section name="PeakPickerMRM">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1125 <param name="sgolay_frame_length" value="15"/>
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galaxyp
parents: 11
diff changeset
1126 <param name="sgolay_polynomial_order" value="3"/>
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diff changeset
1127 <param name="gauss_width" value="50.0"/>
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galaxyp
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diff changeset
1128 <param name="use_gauss" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1129 <param name="peak_width" value="40.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1130 <param name="signal_to_noise" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1131 <param name="sn_win_len" value="1000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1132 <param name="sn_bin_count" value="30"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1133 <param name="write_sn_log_messages" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1134 <param name="remove_overlapping_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1135 <param name="method" value="legacy"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1136 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1137 <section name="PeakIntegrator">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1138 <param name="integration_type" value="intensity_sum"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1139 <param name="baseline_type" value="base_to_base"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1140 <param name="fit_EMG" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1141 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1142 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1143 <section name="DIAScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1144 <param name="dia_extraction_window" value="0.05"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1145 <param name="dia_extraction_unit" value="Th"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1146 <param name="dia_centroided" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1147 <param name="dia_byseries_intensity_min" value="300.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1148 <param name="dia_byseries_ppm_diff" value="10.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1149 <param name="dia_nr_isotopes" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1150 <param name="dia_nr_charges" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1151 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1152 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1153 <section name="EMGScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1154 <param name="interpolation_step" value="0.2"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1155 <param name="tolerance_stdev_bounding_box" value="3.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1156 <param name="max_iteration" value="500"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1157 <param name="init_mom" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1158 <section name="statistics">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1159 <param name="mean" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1160 <param name="variance" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1161 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1162 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1163 <section name="Scores">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1164 <param name="use_shape_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1165 <param name="use_coelution_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1166 <param name="use_rt_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1167 <param name="use_library_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1168 <param name="use_elution_model_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1169 <param name="use_intensity_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1170 <param name="use_nr_peaks_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1171 <param name="use_total_xic_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1172 <param name="use_total_mi_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1173 <param name="use_sn_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1174 <param name="use_mi_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1175 <param name="use_dia_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1176 <param name="use_ms1_correlation" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1177 <param name="use_sonar_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1178 <param name="use_ion_mobility_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1179 <param name="use_ms1_fullscan" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1180 <param name="use_ms1_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1181 <param name="use_uis_scores" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1182 <param name="use_ionseries_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1183 <param name="use_ms2_isotope_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1184 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1185 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1186 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1187 <output name="ctd_out" ftype="xml">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1188 <assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1189 <is_valid_xml/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1190 </assert_contents>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 11
diff changeset
1191 </output>
14
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parents: 13
diff changeset
1192 <assert_stdout>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 13
diff changeset
1193 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
9cdf469a3241 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 13
diff changeset
1194 </assert_stdout>
13
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 11
diff changeset
1195 </test>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1196 <!-- TOPP_OpenSwathAnalyzer_test_11 -->
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1197 <test expect_num_outputs="2">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1198 <section name="adv_opts">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1199 <param name="force" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1200 <param name="test" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1201 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1202 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1203 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1204 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
14
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parents: 13
diff changeset
1205 <output name="out" value="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
13
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galaxyp
parents: 11
diff changeset
1206 <param name="no_strict" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1207 <param name="min_upper_edge_dist" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 11
diff changeset
1208 <section name="model">
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galaxyp
parents: 11
diff changeset
1209 <param name="type" value="linear"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1210 <param name="symmetric_regression" value="false"/>
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diff changeset
1211 </section>
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parents: 11
diff changeset
1212 <section name="algorithm">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1213 <param name="stop_report_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1214 <param name="rt_extraction_window" value="-1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1215 <param name="rt_normalization_factor" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1216 <param name="quantification_cutoff" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1217 <param name="write_convex_hull" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1218 <param name="spectrum_addition_method" value="simple"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1219 <param name="add_up_spectra" value="1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1220 <param name="spacing_for_spectra_resampling" value="0.005"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1221 <param name="uis_threshold_sn" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1222 <param name="uis_threshold_peak_area" value="0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1223 <param name="scoring_model" value="default"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1224 <param name="im_extra_drift" value="0.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1225 <param name="strict" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1226 <section name="TransitionGroupPicker">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1227 <param name="stop_after_feature" value="-1"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1228 <param name="stop_after_intensity_ratio" value="0.0001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1229 <param name="min_peak_width" value="0.001"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1230 <param name="peak_integration" value="original"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1231 <param name="background_subtraction" value="none"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1232 <param name="recalculate_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1233 <param name="use_precursors" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1234 <param name="use_consensus" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1235 <param name="recalculate_peaks_max_z" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1236 <param name="minimal_quality" value="-10000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1237 <param name="resample_boundary" value="15.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1238 <param name="compute_peak_quality" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1239 <param name="compute_peak_shape_metrics" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1240 <param name="compute_total_mi" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1241 <param name="boundary_selection_method" value="largest"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1242 <section name="PeakPickerMRM">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1243 <param name="sgolay_frame_length" value="15"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1244 <param name="sgolay_polynomial_order" value="3"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1245 <param name="gauss_width" value="50.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1246 <param name="use_gauss" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1247 <param name="peak_width" value="40.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1248 <param name="signal_to_noise" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1249 <param name="sn_win_len" value="1000.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1250 <param name="sn_bin_count" value="30"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1251 <param name="write_sn_log_messages" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1252 <param name="remove_overlapping_peaks" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1253 <param name="method" value="legacy"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1254 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1255 <section name="PeakIntegrator">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1256 <param name="integration_type" value="intensity_sum"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1257 <param name="baseline_type" value="base_to_base"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1258 <param name="fit_EMG" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1259 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1260 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1261 <section name="DIAScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1262 <param name="dia_extraction_window" value="0.05"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1263 <param name="dia_extraction_unit" value="Th"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1264 <param name="dia_centroided" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1265 <param name="dia_byseries_intensity_min" value="300.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1266 <param name="dia_byseries_ppm_diff" value="10.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1267 <param name="dia_nr_isotopes" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1268 <param name="dia_nr_charges" value="4"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1269 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1270 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1271 <section name="EMGScoring">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1272 <param name="interpolation_step" value="0.2"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1273 <param name="tolerance_stdev_bounding_box" value="3.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1274 <param name="max_iteration" value="500"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1275 <param name="init_mom" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1276 <section name="statistics">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1277 <param name="mean" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1278 <param name="variance" value="1.0"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1279 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1280 </section>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1281 <section name="Scores">
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1282 <param name="use_shape_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1283 <param name="use_coelution_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1284 <param name="use_rt_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1285 <param name="use_library_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1286 <param name="use_elution_model_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1287 <param name="use_intensity_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1288 <param name="use_nr_peaks_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1289 <param name="use_total_xic_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1290 <param name="use_total_mi_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1291 <param name="use_sn_score" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1292 <param name="use_mi_score" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1293 <param name="use_dia_scores" value="true"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1294 <param name="use_ms1_correlation" value="false"/>
08488066d588 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
1295 <param name="use_sonar_scores" value="false"/>
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1296 <param name="use_ion_mobility_scores" value="false"/>
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1297 <param name="use_ms1_fullscan" value="false"/>
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1298 <param name="use_ms1_mi" value="false"/>
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1299 <param name="use_uis_scores" value="false"/>
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1300 <param name="use_ionseries_scores" value="true"/>
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1301 <param name="use_ms2_isotope_scores" value="true"/>
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1302 </section>
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1303 </section>
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1304 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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1305 <output name="ctd_out" ftype="xml">
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1306 <assert_contents>
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1307 <is_valid_xml/>
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1308 </assert_contents>
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1309 </output>
14
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1310 <assert_stdout>
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1311 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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1312 </assert_stdout>
13
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1313 </test>
9
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1314 </tests>
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1315 <help><![CDATA[Picks peaks and finds features in an SWATH-MS or SRM experiment.
0
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1316
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1317
14
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1318 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathAnalyzer.html]]></help>
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1319 <expand macro="references"/>
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1320 </tool>