Mercurial > repos > galaxyp > openms_fileconverter

annotate FileConverter.xml @ 15:2a93a25f0599 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:09:16 +0000
parents 62e19948b50f
children 8b6336c903ef
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [File Handling]-->
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4 <tool id="FileConverter" name="FileConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Converts between different MS file formats.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FileConverter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 mkdir out &&
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21 ## Main program call
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23 set -o pipefail &&
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24 @EXECUTABLE@ -write_ctd ./ &&
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25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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27 -in
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28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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29 -out
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30 'out/output.${out_type}'
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31
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32 ## Postprocessing
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33 && mv 'out/output.${out_type}' '$out'
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34 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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35 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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36 #end if]]></command>
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37 <configfiles>
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38 <inputs name="args_json" data_style="paths"/>
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39 <configfile name="hardcoded_json"><![CDATA[{"ThermoRaw_executable": "ThermoRawFileParser.exe", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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40 </configfiles>
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41 <inputs>
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42 <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,sqlite,tabular,thermo.raw" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,sqlite,tabular,thermo.raw data sets(s)"/>
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43 <param argument="-out_type" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
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44 <option value="consensusXML">consensusxml</option>
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45 <option value="csv">csv</option>
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46 <option value="dta2d">dta2d</option>
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47 <option value="edta">edta</option>
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48 <option value="featureXML">featurexml</option>
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49 <option value="mgf">mgf</option>
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50 <option value="mzData">mzdata</option>
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51 <option value="mzML">mzml</option>
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52 <option value="mzXML">mzxml</option>
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53 <option value="oms">sqlite (oms)</option>
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54 <expand macro="list_string_san" name="out_type"/>
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55 </param>
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56 <expand macro="adv_opts_macro">
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57 <param argument="-UID_postprocessing" type="select" optional="true" label="unique ID post-processing for output data" help="'none' keeps current IDs even if invalid.. 'ensure' keeps current IDs but reassigns invalid ones.. 'reassign' assigns new unique IDs">
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58 <option value="none">none</option>
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59 <option value="ensure" selected="true">ensure</option>
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60 <option value="reassign">reassign</option>
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61 <expand macro="list_string_san" name="UID_postprocessing"/>
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62 </param>
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63 <param argument="-TIC_DTA2D" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help=""/>
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64 <param argument="-MGF_compact" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help=""/>
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65 <param argument="-force_MaxQuant_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help=""/>
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66 <param argument="-force_TPP_compatibility" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help=""/>
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67 <param argument="-convert_to_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[mzML output only] Assumes that the provided spectra represent data in SRM mode or targeted MS1 mode and converts them to chromatogram data" help=""/>
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68 <param argument="-change_im_format" type="select" optional="true" label="[mzML output only] How to store ion mobility scans (none: no change in format; multiple_spectra: store each IM frame as multiple scans (one per drift time value); concatenated: store whole frame as single scan with IM values in a FloatDataArray" help="">
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69 <option value="none" selected="true">none</option>
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70 <option value="concatenated">concatenated</option>
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71 <option value="multiple_spectra">multiple_spectra</option>
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72 <option value="mixed">mixed</option>
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73 <expand macro="list_string_san" name="change_im_format"/>
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74 </param>
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75 <param argument="-write_scan_index" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Append an index when writing mzML or mzXML files" help="Some external tools might rely on it"/>
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76 <param argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use numpress compression to achieve optimally small file size using linear compression for m/z domain and slof for intensity and float data arrays (attention: may cause small loss of precision; only for mzML data)" help=""/>
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77 <param argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
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78 <param argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/>
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79 <param argument="-no_peak_picking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables vendor peak picking for raw files" help=""/>
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80 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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81 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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82 <expand macro="list_string_san" name="test"/>
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83 </param>
0
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84 </expand>
13
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85 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
11
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86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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87 </param>
0
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88 </inputs>
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89 <outputs>
15
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90 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml">
11
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91 <change_format>
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92 <when input="out_type" value="csv" format="csv"/>
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93 <when input="out_type" value="dta2d" format="dta2d"/>
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94 <when input="out_type" value="edta" format="edta"/>
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95 <when input="out_type" value="featureXML" format="featurexml"/>
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96 <when input="out_type" value="mgf" format="mgf"/>
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97 <when input="out_type" value="mzData" format="mzdata"/>
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98 <when input="out_type" value="mzML" format="mzml"/>
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99 <when input="out_type" value="mzXML" format="mzxml"/>
15
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100 <when input="out_type" value="oms" format="sqlite"/>
11
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101 </change_format>
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102 </data>
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103 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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104 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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105 </data>
0
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106 </outputs>
15
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107 <tests><!-- TOPP_FileConverter_1 -->
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108 <test expect_num_outputs="2">
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109 <section name="adv_opts">
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110 <param name="UID_postprocessing" value="ensure"/>
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111 <param name="TIC_DTA2D" value="false"/>
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112 <param name="MGF_compact" value="false"/>
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113 <param name="force_MaxQuant_compatibility" value="false"/>
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114 <param name="force_TPP_compatibility" value="false"/>
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115 <param name="convert_to_chromatograms" value="false"/>
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116 <param name="change_im_format" value="none"/>
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117 <param name="write_scan_index" value="true"/>
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118 <param name="lossy_compression" value="false"/>
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119 <param name="lossy_mass_accuracy" value="-1.0"/>
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120 <param name="process_lowmemory" value="false"/>
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121 <param name="no_peak_picking" value="false"/>
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122 <param name="force" value="false"/>
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123 <param name="test" value="true"/>
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124 </section>
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125 <param name="in" value="FileConverter_1_input.mzData"/>
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126 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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127 <param name="out_type" value="mzML"/>
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128 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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129 <output name="ctd_out" ftype="xml">
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130 <assert_contents>
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131 <is_valid_xml/>
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132 </assert_contents>
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133 </output>
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134 </test>
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135 <!-- TOPP_FileConverter_2 -->
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136 <test expect_num_outputs="2">
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137 <section name="adv_opts">
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138 <param name="UID_postprocessing" value="ensure"/>
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139 <param name="TIC_DTA2D" value="false"/>
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140 <param name="MGF_compact" value="false"/>
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141 <param name="force_MaxQuant_compatibility" value="false"/>
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142 <param name="force_TPP_compatibility" value="false"/>
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143 <param name="convert_to_chromatograms" value="false"/>
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144 <param name="change_im_format" value="none"/>
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145 <param name="write_scan_index" value="true"/>
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146 <param name="lossy_compression" value="false"/>
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147 <param name="lossy_mass_accuracy" value="-1.0"/>
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148 <param name="process_lowmemory" value="false"/>
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149 <param name="no_peak_picking" value="false"/>
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150 <param name="force" value="false"/>
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151 <param name="test" value="true"/>
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152 </section>
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153 <param name="in" value="FileConverter_2_input.someInputDTA2D"/>
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154 <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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155 <param name="out_type" value="mzML"/>
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156 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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157 <output name="ctd_out" ftype="xml">
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158 <assert_contents>
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159 <is_valid_xml/>
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160 </assert_contents>
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161 </output>
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162 </test>
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163 <!-- TOPP_FileConverter_3 -->
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164 <test expect_num_outputs="2">
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165 <section name="adv_opts">
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166 <param name="UID_postprocessing" value="ensure"/>
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167 <param name="TIC_DTA2D" value="false"/>
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168 <param name="MGF_compact" value="false"/>
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169 <param name="force_MaxQuant_compatibility" value="false"/>
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170 <param name="force_TPP_compatibility" value="false"/>
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171 <param name="convert_to_chromatograms" value="false"/>
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172 <param name="change_im_format" value="none"/>
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173 <param name="write_scan_index" value="true"/>
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174 <param name="lossy_compression" value="false"/>
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175 <param name="lossy_mass_accuracy" value="-1.0"/>
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176 <param name="process_lowmemory" value="false"/>
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177 <param name="no_peak_picking" value="false"/>
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178 <param name="force" value="false"/>
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179 <param name="test" value="true"/>
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180 </section>
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181 <param name="in" value="FileConverter_3_input.featureXML"/>
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182 <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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183 <param name="out_type" value="mzML"/>
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184 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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185 <output name="ctd_out" ftype="xml">
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186 <assert_contents>
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187 <is_valid_xml/>
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188 </assert_contents>
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189 </output>
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190 </test>
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191 <!-- TOPP_FileConverter_4 -->
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192 <test expect_num_outputs="2">
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193 <section name="adv_opts">
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194 <param name="UID_postprocessing" value="ensure"/>
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195 <param name="TIC_DTA2D" value="false"/>
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196 <param name="MGF_compact" value="false"/>
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197 <param name="force_MaxQuant_compatibility" value="false"/>
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198 <param name="force_TPP_compatibility" value="false"/>
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199 <param name="convert_to_chromatograms" value="false"/>
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200 <param name="change_im_format" value="none"/>
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201 <param name="write_scan_index" value="true"/>
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202 <param name="lossy_compression" value="false"/>
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203 <param name="lossy_mass_accuracy" value="-1.0"/>
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204 <param name="process_lowmemory" value="false"/>
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205 <param name="no_peak_picking" value="false"/>
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206 <param name="force" value="false"/>
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207 <param name="test" value="true"/>
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208 </section>
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209 <param name="in" value="FileConverter_4_input.mzXML"/>
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210 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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211 <param name="out_type" value="mzML"/>
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212 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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213 <output name="ctd_out" ftype="xml">
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214 <assert_contents>
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215 <is_valid_xml/>
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216 </assert_contents>
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217 </output>
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218 </test>
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219 <!-- TOPP_FileConverter_5 -->
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220 <test expect_num_outputs="2">
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221 <section name="adv_opts">
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222 <param name="UID_postprocessing" value="ensure"/>
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223 <param name="TIC_DTA2D" value="false"/>
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224 <param name="MGF_compact" value="false"/>
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225 <param name="force_MaxQuant_compatibility" value="false"/>
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226 <param name="force_TPP_compatibility" value="false"/>
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227 <param name="convert_to_chromatograms" value="false"/>
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228 <param name="change_im_format" value="none"/>
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229 <param name="write_scan_index" value="true"/>
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230 <param name="lossy_compression" value="false"/>
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231 <param name="lossy_mass_accuracy" value="-1.0"/>
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232 <param name="process_lowmemory" value="false"/>
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233 <param name="no_peak_picking" value="false"/>
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234 <param name="force" value="false"/>
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235 <param name="test" value="true"/>
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236 </section>
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237 <param name="in" value="FileConverter_5_input.mzML"/>
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238 <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
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239 <param name="out_type" value="mzXML"/>
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240 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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241 <output name="ctd_out" ftype="xml">
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242 <assert_contents>
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243 <is_valid_xml/>
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244 </assert_contents>
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245 </output>
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246 </test>
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247 <!-- TOPP_FileConverter_6 -->
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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="UID_postprocessing" value="ensure"/>
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251 <param name="TIC_DTA2D" value="false"/>
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252 <param name="MGF_compact" value="false"/>
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253 <param name="force_MaxQuant_compatibility" value="false"/>
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254 <param name="force_TPP_compatibility" value="false"/>
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255 <param name="convert_to_chromatograms" value="false"/>
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256 <param name="change_im_format" value="none"/>
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257 <param name="write_scan_index" value="true"/>
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258 <param name="lossy_compression" value="false"/>
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259 <param name="lossy_mass_accuracy" value="-1.0"/>
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260 <param name="process_lowmemory" value="false"/>
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261 <param name="no_peak_picking" value="false"/>
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262 <param name="force" value="false"/>
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263 <param name="test" value="true"/>
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264 </section>
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265 <param name="in" value="FileConverter_6_input.mzML"/>
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266 <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
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267 <param name="out_type" value="mzXML"/>
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268 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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269 <output name="ctd_out" ftype="xml">
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270 <assert_contents>
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271 <is_valid_xml/>
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272 </assert_contents>
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273 </output>
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274 </test>
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275 <!-- TOPP_FileConverter_7 -->
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276 <test expect_num_outputs="2">
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277 <section name="adv_opts">
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278 <param name="UID_postprocessing" value="ensure"/>
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279 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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280 <param name="MGF_compact" value="false"/>
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281 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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282 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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283 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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284 <param name="change_im_format" value="none"/>
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285 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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286 <param name="lossy_compression" value="false"/>
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287 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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288 <param name="process_lowmemory" value="false"/>
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289 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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290 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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291 <param name="test" value="true"/>
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292 </section>
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293 <param name="in" value="FileConverter_7_input.consensusXML"/>
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294 <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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295 <param name="out_type" value="featureXML"/>
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296 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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297 <output name="ctd_out" ftype="xml">
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298 <assert_contents>
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299 <is_valid_xml/>
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300 </assert_contents>
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301 </output>
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302 </test>
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303 <!-- TOPP_FileConverter_8 -->
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304 <test expect_num_outputs="2">
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305 <section name="adv_opts">
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306 <param name="UID_postprocessing" value="ensure"/>
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307 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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308 <param name="MGF_compact" value="false"/>
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309 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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310 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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311 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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312 <param name="change_im_format" value="none"/>
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313 <param name="write_scan_index" value="true"/>
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314 <param name="lossy_compression" value="false"/>
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315 <param name="lossy_mass_accuracy" value="-1.0"/>
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316 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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317 <param name="no_peak_picking" value="false"/>
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318 <param name="force" value="false"/>
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319 <param name="test" value="true"/>
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320 </section>
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321 <param name="in" value="FileConverter_8_input.mzML"/>
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322 <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta_frac="0.7" ftype="mzdata"/>
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323 <param name="out_type" value="mzData"/>
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324 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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325 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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326 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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327 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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328 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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329 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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330 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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331 <!-- TOPP_FileConverter_9 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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332 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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333 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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334 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
335 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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336 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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337 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
338 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
339 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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340 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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341 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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342 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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343 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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344 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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345 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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346 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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347 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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348 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
349 <param name="in" value="FileConverter_9_input.consensusXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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350 <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
351 <param name="out_type" value="featureXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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352 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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353 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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354 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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355 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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356 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
357 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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358 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
359 <!-- TOPP_FileConverter_10 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
360 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
361 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
362 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
363 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
364 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
365 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
366 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
367 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
368 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
369 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
370 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
371 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
372 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
373 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
374 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
375 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
376 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
377 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
378 <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
379 <param name="out_type" value="featureXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
380 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
381 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
382 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
383 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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384 </assert_contents>
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diff changeset
385 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
386 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
387 <!-- TOPP_FileConverter_11 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
388 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
389 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
390 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
391 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
392 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
393 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
394 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
395 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
396 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
397 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
398 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
399 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
400 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
401 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
402 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
403 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
404 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
405 <param name="in" value="FileConverter_11_input.peplist"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
406 <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
407 <param name="out_type" value="featureXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
408 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
409 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
410 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
411 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
412 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
413 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
414 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
415 <!-- TOPP_FileConverter_12 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
416 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
417 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
418 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
419 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
420 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
421 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
422 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
423 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
424 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
425 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
426 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
427 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
428 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
429 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
430 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
431 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
432 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
433 <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
434 <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
435 <param name="out_type" value="featureXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
436 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
437 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
438 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
439 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
440 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
441 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
442 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
443 <!-- TOPP_FileConverter_13 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
444 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
445 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
446 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
447 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
448 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
449 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
450 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
451 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
452 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
453 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
454 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
455 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
456 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
457 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
458 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
459 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
460 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
461 <param name="in" value="FileConverter_13_input.peptides.kroenik"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
462 <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
463 <param name="out_type" value="featureXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
464 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
465 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
466 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
467 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
468 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
469 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
470 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
471 <!-- TOPP_FileConverter_14 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
472 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
473 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
474 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
475 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
476 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
477 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
478 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
479 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
480 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
481 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
482 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
483 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
484 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
485 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
486 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
487 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
488 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
489 <param name="in" value="FileConverter_9_output.featureXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
490 <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
491 <param name="out_type" value="consensusXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
492 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
493 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
494 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
495 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
496 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
497 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
498 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
499 <!-- TOPP_FileConverter_15 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
500 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
501 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
502 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
503 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
504 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
505 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
506 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
507 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
508 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
509 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
510 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
511 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
512 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
513 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
514 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
515 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
516 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
517 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
518 <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
519 <param name="out_type" value="consensusXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
520 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
521 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
522 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
523 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
524 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
525 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
526 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
527 <!-- TOPP_FileConverter_16 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
528 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
529 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
530 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
531 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
532 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
533 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
534 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
535 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
536 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
537 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
538 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
539 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
540 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
541 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
542 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
543 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
544 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
545 <param name="in" value="FileConverter_16_input.edta" ftype="edta"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
546 <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
547 <param name="out_type" value="consensusXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
548 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
549 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
550 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
551 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
552 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
553 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
554 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
555 <!-- TOPP_FileConverter_17 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
556 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
557 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
558 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
559 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
560 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
561 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
562 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
563 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
564 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
565 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
566 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
567 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
568 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
569 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
570 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
571 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
572 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
573 <param name="in" value="FileConverter_17_input.consensusXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
574 <output name="out" file="FileConverter_17.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
575 <param name="out_type" value="csv"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
576 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
577 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
578 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
579 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
580 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
581 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
582 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
583 <!-- TOPP_FileConverter_18 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
584 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
585 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
586 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
587 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
588 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
589 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
590 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
591 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
592 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
593 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
594 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
595 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
596 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
597 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
598 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
599 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
600 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
601 <param name="in" value="FileConverter_17_input.consensusXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
602 <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
603 <param name="out_type" value="csv"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
604 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
605 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
606 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
607 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
608 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
609 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
610 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
611 <!-- TOPP_FileConverter_19 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
612 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
613 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
614 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
615 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
616 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
617 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
618 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
619 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
620 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
621 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
622 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
623 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
624 <param name="process_lowmemory" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
625 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
626 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
627 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
628 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
629 <param name="in" value="FileFilter_1_input.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
630 <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
631 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
632 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
633 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
634 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
635 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
636 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
637 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
638 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
639 <!-- TOPP_FileConverter_20 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
640 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
641 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
642 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
643 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
644 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
645 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
646 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
647 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
648 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
649 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
650 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
651 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
652 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
653 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
654 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
655 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
656 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
657 <param name="in" value="FileConverter_20_input.featureXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
658 <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
659 <param name="out_type" value="featureXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
660 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
661 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
662 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
663 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
664 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
665 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
666 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
667 <!-- TOPP_FileConverter_21 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
668 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
669 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
670 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
671 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
672 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
673 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
674 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
675 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
676 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
677 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
678 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
679 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
680 <param name="process_lowmemory" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
681 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
682 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
683 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
684 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
685 <param name="in" value="FileConverter_4_input.mzXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
686 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
687 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
688 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
689 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
690 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
691 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
692 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
693 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
694 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
695 <!-- TOPP_FileConverter_23 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
696 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
697 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
698 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
699 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
700 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
701 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
702 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
703 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
704 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
705 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
706 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
707 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
708 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
709 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
710 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
711 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
712 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
713 <param name="in" value="FileConverter_23_input.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
714 <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
715 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
716 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
717 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
718 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
719 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
720 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
721 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
722 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
723 <!-- TOPP_FileConverter_24 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
724 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
725 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
726 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
727 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
728 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
729 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
730 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
731 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
732 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
733 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
734 <param name="lossy_compression" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
735 <param name="lossy_mass_accuracy" value="0.0001"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
736 <param name="process_lowmemory" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
737 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
738 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
739 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
740 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
741 <param name="in" value="FileFilter_1_input.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
742 <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
743 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
744 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
745 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
746 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
747 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
748 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
749 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
750 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
751 <!-- TOPP_FileConverter_25 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
752 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
753 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
754 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
755 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
756 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
757 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
758 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
759 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
760 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
761 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
762 <param name="lossy_compression" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
763 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
764 <param name="process_lowmemory" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
765 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
766 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
767 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
768 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
769 <param name="in" value="FileFilter_1_input.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
770 <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
771 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
772 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
773 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
774 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
775 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
776 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
777 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
778 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
779 <!-- TOPP_FileConverter_26 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
780 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
781 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
782 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
783 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
784 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
785 <param name="force_MaxQuant_compatibility" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
786 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
787 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
788 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
789 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
790 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
791 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
792 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
793 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
794 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
795 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
796 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
797 <param name="in" value="FileFilter_1_input.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
798 <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
799 <param name="out_type" value="mzXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
800 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
801 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
802 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
803 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
804 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
805 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
806 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
807 <!-- TOPP_FileConverter_26-2 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
808 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
809 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
810 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
811 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
812 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
813 <param name="force_MaxQuant_compatibility" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
814 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
815 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
816 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
817 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
818 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
819 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
820 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
821 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
822 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
823 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
824 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
825 <param name="in" value="FileConverter_26_output.mzXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
826 <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta_frac="0.7" ftype="mzxml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
827 <param name="out_type" value="mzXML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
828 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
829 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
830 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
831 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
832 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
833 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
834 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
835 <!-- TOPP_FileConverter_27 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
836 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
837 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
838 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
839 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
840 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
841 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
842 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
843 <param name="convert_to_chromatograms" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
844 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
845 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
846 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
847 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
848 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
849 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
850 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
851 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
852 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
853 <param name="in" value="FileConverter_27_input.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
854 <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
855 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
856 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
857 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
858 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
859 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
860 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
861 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
862 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
863 <!-- TOPP_FileConverter_28 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
864 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
865 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
866 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
867 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
868 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
869 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
870 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
871 <param name="convert_to_chromatograms" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
872 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
873 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
874 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
875 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
876 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
877 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
878 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
879 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
880 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
881 <param name="in" value="FileConverter_28_input.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
882 <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
883 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
884 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
885 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
886 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
887 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
888 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
889 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
890 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
891 <!-- TOPP_FileConverter_29 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
892 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
893 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
894 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
895 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
896 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
897 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
898 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
899 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
900 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
901 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
902 <param name="lossy_compression" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
903 <param name="lossy_mass_accuracy" value="1e-05"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
904 <param name="process_lowmemory" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
905 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
906 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
907 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
908 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
909 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
910 <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
911 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
912 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
913 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
914 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
915 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
916 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
917 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
918 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
919 <!-- TOPP_FileConverter_29_back -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
920 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
921 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
922 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
923 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
924 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
925 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
926 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
927 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
928 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
929 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
930 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
931 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
932 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
933 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
934 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
935 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
936 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
937 <param name="in" value="FileConverter_29_output.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
938 <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta_frac="0.7"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
939 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
940 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
941 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
942 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
943 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
944 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
945 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
946 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
947 <!-- TOPP_FileConverter_30 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
948 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
949 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
950 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
951 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
952 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
953 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
954 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
955 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
956 <param name="change_im_format" value="multiple_spectra"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
957 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
958 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
959 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
960 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
961 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
962 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
963 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
964 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
965 <param name="in" value="FileConverter_30_input.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
966 <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
967 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
968 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
969 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
970 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
971 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
972 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
973 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
974 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
975 <!-- TOPP_FileConverter_31 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
976 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
977 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
978 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
979 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
980 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
981 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
982 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
983 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
984 <param name="change_im_format" value="concatenated"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
985 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
986 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
987 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
988 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
989 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
990 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
991 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
992 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
993 <param name="in" value="FileConverter_30_output.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
994 <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
995 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
996 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
997 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
998 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
999 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1000 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1001 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1002 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1003 <!-- TOPP_FileConverter_32 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1004 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1005 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1006 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1007 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1008 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1009 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1010 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1011 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1012 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1013 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1014 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1015 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1016 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1017 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1018 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1019 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1020 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1021 <param name="in" value="FileConverter_32_input.mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1022 <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1023 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1024 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1025 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1026 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1027 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1028 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1029 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1030 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1031 <!-- TOPP_IDFileConverter_32_File_Conversion -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1032 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1033 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1034 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1035 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1036 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1037 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1038 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1039 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1040 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1041 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1042 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1043 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1044 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1045 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1046 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1047 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1048 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1049 <param name="in" value="IDFileConverter_32_output.tmp"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1050 <output name="out" file="IDFileConverter_32_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1051 <param name="out_type" value="mgf"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1052 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1053 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1054 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1055 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1056 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1057 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1058 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1059 <!-- TOPP_IDFileConverter_33_File_Conversion -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1060 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1061 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1062 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1063 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1064 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1065 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1066 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1067 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1068 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1069 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1070 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1071 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1072 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1073 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1074 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1075 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1076 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1077 <param name="in" value="IDFileConverter_33_output.tmp"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1078 <output name="out" file="IDFileConverter_33_output.mgf" compare="sim_size" delta_frac="0.7" ftype="mgf"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1079 <param name="out_type" value="mgf"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1080 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1081 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1082 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1083 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1084 </assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1085 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1086 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1087 <!-- TOPP_THERMORAWFILEPARSER_1 -->
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1088 <test expect_num_outputs="2">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1089 <section name="adv_opts">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1090 <param name="UID_postprocessing" value="ensure"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1091 <param name="TIC_DTA2D" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1092 <param name="MGF_compact" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1093 <param name="force_MaxQuant_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1094 <param name="force_TPP_compatibility" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1095 <param name="convert_to_chromatograms" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1096 <param name="change_im_format" value="none"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1097 <param name="write_scan_index" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1098 <param name="lossy_compression" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1099 <param name="lossy_mass_accuracy" value="-1.0"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1100 <param name="process_lowmemory" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1101 <param name="no_peak_picking" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1102 <param name="force" value="false"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1103 <param name="test" value="true"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1104 </section>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1105 <param name="in" value="ginkgotoxin-ms-switching.raw"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1106 <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1107 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1108 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1109 <output name="ctd_out" ftype="xml">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1110 <assert_contents>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1111 <is_valid_xml/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1112 </assert_contents>
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diff changeset
1113 </output>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1114 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1115 <test expect_num_outputs="1">
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1116 <param name="in" value="FileConverter_1_input.mzData"/>
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parents: 13
diff changeset
1117 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 13
diff changeset
1118 <param name="out_type" value="mzML"/>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 13
diff changeset
1119 </test>
2a93a25f0599 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1120 </tests>
11
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diff changeset
1121 <help><![CDATA[Converts between different MS file formats.
0
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1122
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1123
15
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diff changeset
1124 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileConverter.html]]></help>
11
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1125 <expand macro="references"/>
0
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1126 </tool>