Mercurial > repos > galaxyp > openms_textexporter

annotate TextExporter.xml @ 13:1b03536aa3c9 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 19:08:22 +0000
parents 1c596fdaf34a
children b5de4c3efbdd
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be5c2f82c8ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [File Handling]-->
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4 <tool id="TextExporter" name="TextExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Exports various XML formats to a text file.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">TextExporter</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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15
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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($in.ext)' &&
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19 mkdir out &&
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20 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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21 mkdir consensus_centroids &&
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22 #end if
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23 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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24 mkdir consensus_elements &&
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be5c2f82c8ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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25 #end if
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26 #if "features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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27 mkdir consensus_features &&
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28 #end if
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30 ## Main program call
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32 set -o pipefail &&
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33 @EXECUTABLE@ -write_ctd ./ &&
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34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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36 -in
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37 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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38 -out
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39 'out/output.${out_type}'
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40 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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41 -consensus:centroids
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42 'consensus_centroids/output.${gxy2omsext("csv")}'
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43 #end if
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44 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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45 -consensus:elements
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46 'consensus_elements/output.${gxy2omsext("csv")}'
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47 #end if
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48 #if "features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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49 -consensus:features
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50 'consensus_features/output.${gxy2omsext("csv")}'
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51 #end if
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52 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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53 | tee '$stdout'
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54 #end if
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55
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56 ## Postprocessing
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57 && mv 'out/output.${out_type}' '$out'
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58 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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59 && mv 'consensus_centroids/output.${gxy2omsext("csv")}' '$consensus_centroids'
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60 #end if
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61 #if "elements_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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62 && mv 'consensus_elements/output.${gxy2omsext("csv")}' '$consensus_elements'
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63 #end if
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64 #if "features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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65 && mv 'consensus_features/output.${gxy2omsext("csv")}' '$consensus_features'
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66 #end if
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67 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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68 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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69 #end if]]></command>
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70 <configfiles>
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71 <inputs name="args_json" data_style="paths"/>
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72 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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73 </configfiles>
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74 <inputs>
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75 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
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76 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension, ambiguous file extensions are interpreted as tsv" help="">
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77 <option value="csv">csv</option>
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78 <option value="tsv">tabular (tsv)</option>
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79 <option value="txt">txt</option>
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80 <expand macro="list_string_san" name="out_type"/>
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81 </param>
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82 <param argument="-replacement" type="text" optional="true" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="">
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83 <expand macro="list_string_san" name="replacement"/>
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84 </param>
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85 <param argument="-quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
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86 <option value="none" selected="true">none</option>
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87 <option value="double">double</option>
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88 <option value="escape">escape</option>
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89 <expand macro="list_string_san" name="quoting"/>
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90 </param>
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91 <param argument="-no_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppresses output of identification data" help=""/>
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92 <section name="feature" title="Options for featureXML input files" help="" expanded="false">
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93 <param name="minimal" argument="-feature:minimal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to write only three attributes: RT, m/z, and intensity" help=""/>
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94 <param name="add_metavalues" argument="-feature:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
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95 </section>
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96 <section name="id" title="Options for idXML input files" help="" expanded="false">
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97 <param name="proteins_only" argument="-id:proteins_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only protein information from an idXML file" help=""/>
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98 <param name="peptides_only" argument="-id:peptides_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only peptide information from an idXML file" help=""/>
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99 <param name="protein_groups" argument="-id:protein_groups" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want to also write indist" help="group information from an idXML file"/>
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100 <param name="first_dim_rt" argument="-id:first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" help=""/>
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101 <param name="add_metavalues" argument="-id:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideID (=spectrum) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
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102 <param name="add_hit_metavalues" argument="-id:add_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideHit (=PSM) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
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103 <param name="add_protein_hit_metavalues" argument="-id:add_protein_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values on protein level which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
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104 </section>
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105 <section name="consensus" title="Options for consensusXML input files" help="" expanded="false">
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106 <param name="sorting_method" argument="-consensus:sorting_method" type="select" optional="true" label="Sorting options can be combined" help="The precedence is: sort_by_size, sort_by_maps, sorting_method">
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107 <option value="none" selected="true">none</option>
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108 <option value="RT">RT</option>
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109 <option value="MZ">MZ</option>
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110 <option value="RT_then_MZ">RT_then_MZ</option>
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111 <option value="intensity">intensity</option>
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112 <option value="quality_decreasing">quality_decreasing</option>
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113 <option value="quality_increasing">quality_increasing</option>
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114 <expand macro="list_string_san" name="sorting_method"/>
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115 </param>
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116 <param name="sort_by_maps" argument="-consensus:sort_by_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by the covered maps, lexicographically" help=""/>
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117 <param name="sort_by_size" argument="-consensus:sort_by_size" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by decreasing size" help="(i.e., the number of elements)"/>
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118 </section>
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119 <expand macro="adv_opts_macro">
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120 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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121 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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122 <expand macro="list_string_san" name="test"/>
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123 </param>
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124 </expand>
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125 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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126 <option value="centroids_FLAG">centroids (Output file for centroids of consensus features)</option>
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127 <option value="elements_FLAG">elements (Output file for elements of consensus features)</option>
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128 <option value="features_FLAG">features (Output file for consensus features and contained elements from all maps (writes 'nan's if elements are missing))</option>
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129 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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130 </param>
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131 </inputs>
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132 <outputs>
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133 <data name="out" label="${tool.name} on ${on_string}: out" format="csv">
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134 <change_format>
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135 <when input="out_type" value="tsv" format="tabular"/>
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136 <when input="out_type" value="txt" format="txt"/>
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137 </change_format>
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138 </data>
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139 <data name="consensus_centroids" label="${tool.name} on ${on_string}: consensus:centroids" format="csv">
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140 <filter>OPTIONAL_OUTPUTS is not None and "centroids_FLAG" in OPTIONAL_OUTPUTS</filter>
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141 </data>
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142 <data name="consensus_elements" label="${tool.name} on ${on_string}: consensus:elements" format="csv">
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143 <filter>OPTIONAL_OUTPUTS is not None and "elements_FLAG" in OPTIONAL_OUTPUTS</filter>
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144 </data>
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145 <data name="consensus_features" label="${tool.name} on ${on_string}: consensus:features" format="csv">
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146 <filter>OPTIONAL_OUTPUTS is not None and "features_FLAG" in OPTIONAL_OUTPUTS</filter>
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147 </data>
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148 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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149 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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150 </data>
0
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151 </outputs>
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152 <tests><!-- TOPP_TextExporter_1 -->
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153 <test expect_num_outputs="2">
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154 <section name="adv_opts">
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155 <param name="force" value="false"/>
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156 <param name="test" value="true"/>
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157 </section>
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158 <param name="in" value="TextExporter_1_input.featureXML"/>
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159 <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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160 <param name="out_type" value="txt"/>
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161 <param name="replacement" value="_"/>
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162 <param name="quoting" value="none"/>
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163 <param name="no_ids" value="false"/>
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164 <section name="feature">
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165 <param name="minimal" value="false"/>
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166 <param name="add_metavalues" value="-1"/>
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167 </section>
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168 <section name="id">
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169 <param name="proteins_only" value="false"/>
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170 <param name="peptides_only" value="false"/>
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171 <param name="protein_groups" value="false"/>
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172 <param name="first_dim_rt" value="false"/>
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173 <param name="add_metavalues" value="-1"/>
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174 <param name="add_hit_metavalues" value="-1"/>
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175 <param name="add_protein_hit_metavalues" value="-1"/>
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176 </section>
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177 <section name="consensus">
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178 <param name="sorting_method" value="none"/>
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179 <param name="sort_by_maps" value="false"/>
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180 <param name="sort_by_size" value="false"/>
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181 </section>
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182 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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183 <output name="ctd_out" ftype="xml">
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184 <assert_contents>
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185 <is_valid_xml/>
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186 </assert_contents>
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187 </output>
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188 </test>
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189 <!-- TOPP_TextExporter_2 -->
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190 <test expect_num_outputs="5">
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191 <section name="adv_opts">
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192 <param name="force" value="false"/>
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193 <param name="test" value="true"/>
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194 </section>
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195 <param name="in" value="TextExporter_2_input.consensusXML"/>
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196 <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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197 <param name="out_type" value="tsv"/>
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198 <param name="replacement" value="_"/>
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199 <param name="quoting" value="none"/>
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200 <param name="no_ids" value="true"/>
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201 <section name="feature">
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202 <param name="minimal" value="false"/>
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203 <param name="add_metavalues" value="-1"/>
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204 </section>
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205 <section name="id">
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206 <param name="proteins_only" value="false"/>
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207 <param name="peptides_only" value="false"/>
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208 <param name="protein_groups" value="false"/>
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209 <param name="first_dim_rt" value="false"/>
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210 <param name="add_metavalues" value="-1"/>
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211 <param name="add_hit_metavalues" value="-1"/>
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212 <param name="add_protein_hit_metavalues" value="-1"/>
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213 </section>
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214 <section name="consensus">
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215 <param name="sorting_method" value="RT_then_MZ"/>
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216 <param name="sort_by_maps" value="true"/>
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217 <param name="sort_by_size" value="true"/>
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218 </section>
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219 <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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220 <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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221 <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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222 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
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223 <output name="ctd_out" ftype="xml">
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224 <assert_contents>
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225 <is_valid_xml/>
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226 </assert_contents>
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227 </output>
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228 </test>
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229 <!-- TOPP_TextExporter_3 -->
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230 <test expect_num_outputs="2">
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231 <section name="adv_opts">
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232 <param name="force" value="false"/>
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233 <param name="test" value="true"/>
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234 </section>
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235 <param name="in" value="TextExporter_3_input.idXML"/>
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236 <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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237 <param name="out_type" value="txt"/>
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238 <param name="replacement" value="_"/>
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239 <param name="quoting" value="none"/>
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240 <param name="no_ids" value="false"/>
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241 <section name="feature">
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242 <param name="minimal" value="false"/>
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243 <param name="add_metavalues" value="-1"/>
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244 </section>
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245 <section name="id">
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246 <param name="proteins_only" value="false"/>
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247 <param name="peptides_only" value="false"/>
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248 <param name="protein_groups" value="false"/>
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249 <param name="first_dim_rt" value="false"/>
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250 <param name="add_metavalues" value="-1"/>
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251 <param name="add_hit_metavalues" value="-1"/>
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252 <param name="add_protein_hit_metavalues" value="-1"/>
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253 </section>
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254 <section name="consensus">
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255 <param name="sorting_method" value="none"/>
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256 <param name="sort_by_maps" value="false"/>
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257 <param name="sort_by_size" value="false"/>
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258 </section>
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259 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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260 <output name="ctd_out" ftype="xml">
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261 <assert_contents>
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262 <is_valid_xml/>
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263 </assert_contents>
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264 </output>
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265 </test>
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266 <!-- TOPP_TextExporter_4 -->
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267 <test expect_num_outputs="2">
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268 <section name="adv_opts">
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269 <param name="force" value="false"/>
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270 <param name="test" value="true"/>
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271 </section>
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272 <param name="in" value="TextExporter_3_input.idXML"/>
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273 <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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274 <param name="out_type" value="txt"/>
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275 <param name="replacement" value="_"/>
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276 <param name="quoting" value="none"/>
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277 <param name="no_ids" value="false"/>
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278 <section name="feature">
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279 <param name="minimal" value="false"/>
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280 <param name="add_metavalues" value="-1"/>
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281 </section>
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282 <section name="id">
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283 <param name="proteins_only" value="true"/>
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284 <param name="peptides_only" value="false"/>
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285 <param name="protein_groups" value="false"/>
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286 <param name="first_dim_rt" value="false"/>
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287 <param name="add_metavalues" value="-1"/>
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288 <param name="add_hit_metavalues" value="-1"/>
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289 <param name="add_protein_hit_metavalues" value="-1"/>
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290 </section>
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291 <section name="consensus">
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292 <param name="sorting_method" value="none"/>
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293 <param name="sort_by_maps" value="false"/>
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294 <param name="sort_by_size" value="false"/>
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295 </section>
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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_TextExporter_5 -->
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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="force" value="false"/>
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307 <param name="test" value="true"/>
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308 </section>
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309 <param name="in" value="TextExporter_5_input.idXML"/>
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310 <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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311 <param name="out_type" value="txt"/>
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312 <param name="replacement" value="_"/>
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313 <param name="quoting" value="none"/>
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314 <param name="no_ids" value="false"/>
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315 <section name="feature">
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316 <param name="minimal" value="false"/>
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317 <param name="add_metavalues" value="-1"/>
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318 </section>
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319 <section name="id">
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320 <param name="proteins_only" value="false"/>
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321 <param name="peptides_only" value="true"/>
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322 <param name="protein_groups" value="false"/>
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323 <param name="first_dim_rt" value="true"/>
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324 <param name="add_metavalues" value="-1"/>
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325 <param name="add_hit_metavalues" value="-1"/>
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326 <param name="add_protein_hit_metavalues" value="-1"/>
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327 </section>
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328 <section name="consensus">
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329 <param name="sorting_method" value="none"/>
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330 <param name="sort_by_maps" value="false"/>
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331 <param name="sort_by_size" value="false"/>
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332 </section>
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333 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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334 <output name="ctd_out" ftype="xml">
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335 <assert_contents>
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336 <is_valid_xml/>
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337 </assert_contents>
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338 </output>
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339 </test>
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340 <!-- TOPP_TextExporter_6 -->
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341 <test expect_num_outputs="2">
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342 <section name="adv_opts">
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343 <param name="force" value="false"/>
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344 <param name="test" value="true"/>
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345 </section>
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346 <param name="in" value="TextExporter_6_input.featureXML"/>
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347 <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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348 <param name="out_type" value="txt"/>
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349 <param name="replacement" value="_"/>
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350 <param name="quoting" value="none"/>
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351 <param name="no_ids" value="true"/>
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352 <section name="feature">
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353 <param name="minimal" value="false"/>
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354 <param name="add_metavalues" value="-1"/>
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355 </section>
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356 <section name="id">
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357 <param name="proteins_only" value="false"/>
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358 <param name="peptides_only" value="false"/>
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359 <param name="protein_groups" value="false"/>
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360 <param name="first_dim_rt" value="false"/>
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361 <param name="add_metavalues" value="-1"/>
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362 <param name="add_hit_metavalues" value="-1"/>
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363 <param name="add_protein_hit_metavalues" value="-1"/>
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364 </section>
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365 <section name="consensus">
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366 <param name="sorting_method" value="none"/>
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367 <param name="sort_by_maps" value="false"/>
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368 <param name="sort_by_size" value="false"/>
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369 </section>
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370 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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371 <output name="ctd_out" ftype="xml">
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372 <assert_contents>
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373 <is_valid_xml/>
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374 </assert_contents>
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375 </output>
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376 </test>
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377 <!-- TOPP_TextExporter_7 -->
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378 <test expect_num_outputs="2">
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379 <section name="adv_opts">
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380 <param name="force" value="false"/>
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381 <param name="test" value="true"/>
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382 </section>
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383 <param name="in" value="TextExporter_7_input.consensusXML"/>
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384 <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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385 <param name="out_type" value="tsv"/>
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386 <param name="replacement" value="_"/>
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387 <param name="quoting" value="none"/>
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388 <param name="no_ids" value="false"/>
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389 <section name="feature">
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390 <param name="minimal" value="false"/>
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391 <param name="add_metavalues" value="-1"/>
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392 </section>
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393 <section name="id">
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394 <param name="proteins_only" value="false"/>
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395 <param name="peptides_only" value="false"/>
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396 <param name="protein_groups" value="false"/>
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397 <param name="first_dim_rt" value="false"/>
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398 <param name="add_metavalues" value="-1"/>
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399 <param name="add_hit_metavalues" value="-1"/>
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400 <param name="add_protein_hit_metavalues" value="-1"/>
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401 </section>
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402 <section name="consensus">
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403 <param name="sorting_method" value="RT_then_MZ"/>
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404 <param name="sort_by_maps" value="true"/>
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405 <param name="sort_by_size" value="true"/>
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406 </section>
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407 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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408 <output name="ctd_out" ftype="xml">
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409 <assert_contents>
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410 <is_valid_xml/>
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411 </assert_contents>
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412 </output>
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413 </test>
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414 <!-- TOPP_TextExporter_8 -->
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415 <test expect_num_outputs="2">
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416 <section name="adv_opts">
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417 <param name="force" value="false"/>
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418 <param name="test" value="true"/>
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419 </section>
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420 <param name="in" value="TextExporter_1_input.featureXML"/>
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421 <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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422 <param name="out_type" value="txt"/>
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423 <param name="replacement" value="_"/>
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424 <param name="quoting" value="none"/>
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425 <param name="no_ids" value="true"/>
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426 <section name="feature">
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427 <param name="minimal" value="false"/>
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428 <param name="add_metavalues" value="-1"/>
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429 </section>
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430 <section name="id">
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431 <param name="proteins_only" value="false"/>
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432 <param name="peptides_only" value="false"/>
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433 <param name="protein_groups" value="false"/>
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434 <param name="first_dim_rt" value="false"/>
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435 <param name="add_metavalues" value="-1"/>
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436 <param name="add_hit_metavalues" value="-1"/>
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437 <param name="add_protein_hit_metavalues" value="-1"/>
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438 </section>
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439 <section name="consensus">
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440 <param name="sorting_method" value="none"/>
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441 <param name="sort_by_maps" value="false"/>
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442 <param name="sort_by_size" value="false"/>
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443 </section>
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444 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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445 <output name="ctd_out" ftype="xml">
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446 <assert_contents>
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447 <is_valid_xml/>
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448 </assert_contents>
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449 </output>
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450 </test>
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451 <!-- TOPP_TextExporter_9 -->
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452 <test expect_num_outputs="2">
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453 <section name="adv_opts">
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454 <param name="force" value="false"/>
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455 <param name="test" value="true"/>
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456 </section>
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457 <param name="in" value="TextExporter_9_input.idXML"/>
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458 <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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459 <param name="out_type" value="txt"/>
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460 <param name="replacement" value="_"/>
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461 <param name="quoting" value="none"/>
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462 <param name="no_ids" value="false"/>
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463 <section name="feature">
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464 <param name="minimal" value="false"/>
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465 <param name="add_metavalues" value="-1"/>
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466 </section>
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467 <section name="id">
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468 <param name="proteins_only" value="false"/>
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469 <param name="peptides_only" value="false"/>
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470 <param name="protein_groups" value="false"/>
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471 <param name="first_dim_rt" value="false"/>
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472 <param name="add_metavalues" value="0"/>
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473 <param name="add_hit_metavalues" value="0"/>
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474 <param name="add_protein_hit_metavalues" value="-1"/>
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475 </section>
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476 <section name="consensus">
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477 <param name="sorting_method" value="none"/>
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478 <param name="sort_by_maps" value="false"/>
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479 <param name="sort_by_size" value="false"/>
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480 </section>
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481 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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482 <output name="ctd_out" ftype="xml">
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483 <assert_contents>
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484 <is_valid_xml/>
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485 </assert_contents>
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486 </output>
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487 </test>
9
27aeff17fd2e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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488 </tests>
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489 <help><![CDATA[Exports various XML formats to a text file.
0
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490
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491
13
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492 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_TextExporter.html]]></help>
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27aeff17fd2e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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493 <expand macro="references"/>
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be5c2f82c8ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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494 </tool>