annotate ProteinQuantifier.xml @ 13:d426affe977c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:18:55 +0000
parents bb1e75938909
children 89ece0562fe0
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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: [Quantitation]-->
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4 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Compute peptide and protein abundances</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ProteinQuantifier</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 #if $protein_groups:
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20 mkdir protein_groups &&
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21 ln -s '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' &&
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22 #end if
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23 #if $design:
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24 mkdir design &&
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25 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
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26 #end if
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27 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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28 mkdir out &&
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29 #end if
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30 #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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31 mkdir peptide_out &&
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32 #end if
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33 #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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34 mkdir mztab &&
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35 #end if
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36
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37 ## Main program call
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38
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39 set -o pipefail &&
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40 @EXECUTABLE@ -write_ctd ./ &&
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41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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43 -in
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44 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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45 #if $protein_groups:
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46 -protein_groups
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47 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)'
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48 #end if
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49 #if $design:
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50 -design
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51 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
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52 #end if
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53 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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54 -out
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55 'out/output.${gxy2omsext("csv")}'
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56 #end if
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57 #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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58 -peptide_out
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59 'peptide_out/output.${gxy2omsext("csv")}'
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60 #end if
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61 #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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62 -mztab
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63 'mztab/output.${gxy2omsext("mztab")}'
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64 #end if
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65 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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66 | tee '$stdout'
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67 #end if
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68
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69 ## Postprocessing
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70 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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71 && mv 'out/output.${gxy2omsext("csv")}' '$out'
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72 #end if
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73 #if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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74 && mv 'peptide_out/output.${gxy2omsext("csv")}' '$peptide_out'
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75 #end if
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76 #if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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77 && mv 'mztab/output.${gxy2omsext("mztab")}' '$mztab'
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78 #end if
9
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79 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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80 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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81 #end if]]></command>
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82 <configfiles>
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83 <inputs name="args_json" data_style="paths"/>
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84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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85 </configfiles>
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86 <inputs>
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87 <param argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
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88 <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/>
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89 <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
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90 <param argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/>
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91 <param argument="-average" type="select" optional="true" label="Averaging method used to compute protein abundances from peptide abundances" help="">
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92 <option value="median" selected="true">median</option>
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93 <option value="mean">mean</option>
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94 <option value="weighted_mean">weighted_mean</option>
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95 <option value="sum">sum</option>
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96 <expand macro="list_string_san" name="average"/>
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97 </param>
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98 <param argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/>
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99 <param argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/>
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100 <param argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/>
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101 <param argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/>
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102 <param argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/>
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103 <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false">
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104 <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/>
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105 <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0',all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
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106 </section>
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107 <section name="format" title="Output formatting options" help="" expanded="false">
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108 <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="">
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109 <expand macro="list_string_san" name="separator"/>
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110 </param>
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111 <param name="quoting" argument="-format: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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112 <option value="none">none</option>
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113 <option value="double" selected="true">double</option>
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114 <option value="escape">escape</option>
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115 <expand macro="list_string_san" name="quoting"/>
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116 </param>
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117 <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="">
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118 <expand macro="list_string_san" name="replacement"/>
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119 </param>
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120 </section>
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121 <expand macro="adv_opts_macro">
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122 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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123 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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124 <expand macro="list_string_san" name="test"/>
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125 </param>
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126 </expand>
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127 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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128 <option value="out_FLAG">out (Output file for protein abundances)</option>
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129 <option value="peptide_out_FLAG">peptide_out (Output file for peptide abundances)</option>
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130 <option value="mztab_FLAG">mztab (Output file (mzTab))</option>
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131 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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132 </param>
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133 </inputs>
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134 <outputs>
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135 <data name="out" label="${tool.name} on ${on_string}: out" format="csv">
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136 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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137 </data>
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138 <data name="peptide_out" label="${tool.name} on ${on_string}: peptide_out" format="csv">
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139 <filter>OPTIONAL_OUTPUTS is not None and "peptide_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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140 </data>
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141 <data name="mztab" label="${tool.name} on ${on_string}: mztab" format="mztab">
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142 <filter>OPTIONAL_OUTPUTS is not None and "mztab_FLAG" in OPTIONAL_OUTPUTS</filter>
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143 </data>
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144 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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145 <filter>OPTIONAL_OUTPUTS is None</filter>
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146 </data>
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147 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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148 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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149 </data>
0
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150 </outputs>
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151 <tests><!-- TOPP_ProteinQuantifier_1 -->
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152 <test expect_num_outputs="3">
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153 <section name="adv_opts">
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154 <param name="force" value="false"/>
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155 <param name="test" value="true"/>
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156 </section>
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157 <param name="in" value="ProteinQuantifier_input.featureXML"/>
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158 <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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159 <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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160 <param name="top" value="3"/>
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161 <param name="average" value="median"/>
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162 <param name="include_all" value="false"/>
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163 <param name="best_charge_and_fraction" value="false"/>
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164 <param name="greedy_group_resolution" value="false"/>
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165 <param name="ratios" value="false"/>
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166 <param name="ratiosSILAC" value="false"/>
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167 <section name="consensus">
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168 <param name="normalize" value="false"/>
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169 <param name="fix_peptides" value="false"/>
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170 </section>
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171 <section name="format">
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172 <param name="separator" value=""/>
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173 <param name="quoting" value="double"/>
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174 <param name="replacement" value="_"/>
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175 </section>
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176 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
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177 <output name="ctd_out" ftype="xml">
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178 <assert_contents>
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179 <is_valid_xml/>
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180 </assert_contents>
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181 </output>
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182 </test>
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183 <!-- TOPP_ProteinQuantifier_2 -->
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184 <test expect_num_outputs="3">
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185 <section name="adv_opts">
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186 <param name="force" value="false"/>
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187 <param name="test" value="true"/>
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188 </section>
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189 <param name="in" value="ProteinQuantifier_input.featureXML"/>
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190 <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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191 <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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192 <param name="top" value="2"/>
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193 <param name="average" value="sum"/>
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194 <param name="include_all" value="true"/>
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195 <param name="best_charge_and_fraction" value="true"/>
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196 <param name="greedy_group_resolution" value="false"/>
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197 <param name="ratios" value="false"/>
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198 <param name="ratiosSILAC" value="false"/>
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199 <section name="consensus">
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200 <param name="normalize" value="false"/>
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201 <param name="fix_peptides" value="false"/>
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202 </section>
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203 <section name="format">
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204 <param name="separator" value=""/>
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205 <param name="quoting" value="double"/>
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206 <param name="replacement" value="_"/>
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207 </section>
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208 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
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209 <output name="ctd_out" ftype="xml">
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210 <assert_contents>
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211 <is_valid_xml/>
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212 </assert_contents>
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213 </output>
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214 </test>
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215 <!-- TOPP_ProteinQuantifier_3 -->
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216 <test expect_num_outputs="3">
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217 <section name="adv_opts">
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218 <param name="force" value="false"/>
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219 <param name="test" value="true"/>
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220 </section>
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221 <param name="in" value="ProteinQuantifier_3_input.featureXML"/>
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222 <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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223 <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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224 <param name="top" value="2"/>
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225 <param name="average" value="mean"/>
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226 <param name="include_all" value="true"/>
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227 <param name="best_charge_and_fraction" value="false"/>
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228 <param name="greedy_group_resolution" value="false"/>
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229 <param name="ratios" value="false"/>
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230 <param name="ratiosSILAC" value="false"/>
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231 <section name="consensus">
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232 <param name="normalize" value="false"/>
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233 <param name="fix_peptides" value="false"/>
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234 </section>
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235 <section name="format">
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236 <param name="separator" value=""/>
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237 <param name="quoting" value="double"/>
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238 <param name="replacement" value="_"/>
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239 </section>
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240 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_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_ProteinQuantifier_4 -->
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248 <test expect_num_outputs="2">
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249 <section name="adv_opts">
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250 <param name="force" value="false"/>
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251 <param name="test" value="true"/>
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252 </section>
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253 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
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254 <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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255 <param name="top" value="0"/>
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256 <param name="average" value="sum"/>
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257 <param name="include_all" value="false"/>
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258 <param name="best_charge_and_fraction" value="false"/>
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259 <param name="greedy_group_resolution" value="false"/>
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260 <param name="ratios" value="false"/>
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261 <param name="ratiosSILAC" value="false"/>
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262 <section name="consensus">
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263 <param name="normalize" value="false"/>
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264 <param name="fix_peptides" value="false"/>
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265 </section>
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266 <section name="format">
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267 <param name="separator" value=""/>
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268 <param name="quoting" value="double"/>
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269 <param name="replacement" value="_"/>
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270 </section>
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271 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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272 <output name="ctd_out" ftype="xml">
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273 <assert_contents>
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274 <is_valid_xml/>
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275 </assert_contents>
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276 </output>
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277 </test>
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278 <!-- TOPP_ProteinQuantifier_5 -->
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279 <test expect_num_outputs="2">
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280 <section name="adv_opts">
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281 <param name="force" value="false"/>
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282 <param name="test" value="true"/>
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283 </section>
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284 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
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285 <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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286 <param name="top" value="3"/>
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287 <param name="average" value="sum"/>
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288 <param name="include_all" value="false"/>
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289 <param name="best_charge_and_fraction" value="false"/>
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290 <param name="greedy_group_resolution" value="false"/>
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291 <param name="ratios" value="false"/>
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292 <param name="ratiosSILAC" value="false"/>
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293 <section name="consensus">
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294 <param name="normalize" value="false"/>
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295 <param name="fix_peptides" value="false"/>
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296 </section>
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297 <section name="format">
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298 <param name="separator" value=""/>
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299 <param name="quoting" value="double"/>
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300 <param name="replacement" value="_"/>
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301 </section>
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302 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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303 <output name="ctd_out" ftype="xml">
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304 <assert_contents>
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305 <is_valid_xml/>
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306 </assert_contents>
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307 </output>
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308 </test>
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309 <!-- TOPP_ProteinQuantifier_6 -->
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310 <test expect_num_outputs="2">
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311 <section name="adv_opts">
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312 <param name="force" value="false"/>
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313 <param name="test" value="true"/>
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314 </section>
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315 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
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316 <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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317 <param name="top" value="3"/>
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318 <param name="average" value="sum"/>
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319 <param name="include_all" value="true"/>
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320 <param name="best_charge_and_fraction" value="false"/>
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321 <param name="greedy_group_resolution" value="false"/>
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322 <param name="ratios" value="false"/>
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323 <param name="ratiosSILAC" value="false"/>
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324 <section name="consensus">
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325 <param name="normalize" value="false"/>
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326 <param name="fix_peptides" value="false"/>
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327 </section>
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328 <section name="format">
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329 <param name="separator" value=""/>
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330 <param name="quoting" value="double"/>
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331 <param name="replacement" value="_"/>
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332 </section>
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333 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,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_ProteinQuantifier_7 -->
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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="ProteinQuantifier_input.consensusXML"/>
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347 <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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348 <param name="top" value="0"/>
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349 <param name="average" value="sum"/>
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350 <param name="include_all" value="false"/>
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351 <param name="best_charge_and_fraction" value="false"/>
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352 <param name="greedy_group_resolution" value="false"/>
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galaxyp
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353 <param name="ratios" value="false"/>
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354 <param name="ratiosSILAC" value="false"/>
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355 <section name="consensus">
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356 <param name="normalize" value="false"/>
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357 <param name="fix_peptides" value="true"/>
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358 </section>
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359 <section name="format">
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360 <param name="separator" value=""/>
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361 <param name="quoting" value="double"/>
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362 <param name="replacement" value="_"/>
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363 </section>
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364 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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365 <output name="ctd_out" ftype="xml">
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366 <assert_contents>
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367 <is_valid_xml/>
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368 </assert_contents>
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369 </output>
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370 </test>
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371 <!-- TOPP_ProteinQuantifier_8 -->
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372 <test expect_num_outputs="2">
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373 <section name="adv_opts">
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374 <param name="force" value="false"/>
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375 <param name="test" value="true"/>
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376 </section>
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377 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
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378 <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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diff changeset
379 <param name="top" value="3"/>
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galaxyp
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diff changeset
380 <param name="average" value="sum"/>
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381 <param name="include_all" value="false"/>
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diff changeset
382 <param name="best_charge_and_fraction" value="false"/>
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galaxyp
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diff changeset
383 <param name="greedy_group_resolution" value="false"/>
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galaxyp
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diff changeset
384 <param name="ratios" value="false"/>
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385 <param name="ratiosSILAC" value="false"/>
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galaxyp
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386 <section name="consensus">
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387 <param name="normalize" value="false"/>
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388 <param name="fix_peptides" value="true"/>
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389 </section>
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390 <section name="format">
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diff changeset
391 <param name="separator" value=""/>
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diff changeset
392 <param name="quoting" value="double"/>
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diff changeset
393 <param name="replacement" value="_"/>
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394 </section>
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diff changeset
395 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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396 <output name="ctd_out" ftype="xml">
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397 <assert_contents>
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398 <is_valid_xml/>
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399 </assert_contents>
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400 </output>
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401 </test>
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402 <!-- TOPP_ProteinQuantifier_9 -->
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galaxyp
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diff changeset
403 <test expect_num_outputs="3">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
404 <section name="adv_opts">
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galaxyp
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diff changeset
405 <param name="force" value="false"/>
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diff changeset
406 <param name="test" value="true"/>
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diff changeset
407 </section>
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galaxyp
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diff changeset
408 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
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diff changeset
409 <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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diff changeset
410 <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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galaxyp
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diff changeset
411 <param name="top" value="3"/>
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galaxyp
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diff changeset
412 <param name="average" value="sum"/>
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galaxyp
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diff changeset
413 <param name="include_all" value="true"/>
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galaxyp
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diff changeset
414 <param name="best_charge_and_fraction" value="false"/>
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galaxyp
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diff changeset
415 <param name="greedy_group_resolution" value="false"/>
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galaxyp
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diff changeset
416 <param name="ratios" value="false"/>
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galaxyp
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417 <param name="ratiosSILAC" value="false"/>
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galaxyp
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diff changeset
418 <section name="consensus">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
419 <param name="normalize" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
420 <param name="fix_peptides" value="true"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
421 </section>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
422 <section name="format">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
423 <param name="separator" value=""/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
424 <param name="quoting" value="double"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
425 <param name="replacement" value="_"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
426 </section>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
427 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
428 <output name="ctd_out" ftype="xml">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
429 <assert_contents>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
430 <is_valid_xml/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
431 </assert_contents>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
432 </output>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
433 </test>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
434 <!-- TOPP_ProteinQuantifier_12 -->
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
435 <test expect_num_outputs="2">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
436 <section name="adv_opts">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
437 <param name="force" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
438 <param name="test" value="true"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
439 </section>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
440 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
441 <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
442 <param name="top" value="3"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
443 <param name="average" value="sum"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
444 <param name="include_all" value="true"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
445 <param name="best_charge_and_fraction" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
446 <param name="greedy_group_resolution" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
447 <param name="ratios" value="true"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
448 <param name="ratiosSILAC" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
449 <section name="consensus">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
450 <param name="normalize" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
451 <param name="fix_peptides" value="true"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
452 </section>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
453 <section name="format">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
454 <param name="separator" value=""/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
455 <param name="quoting" value="double"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
456 <param name="replacement" value="_"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
457 </section>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
458 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
459 <output name="ctd_out" ftype="xml">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
460 <assert_contents>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
461 <is_valid_xml/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
462 </assert_contents>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
463 </output>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
464 </test>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
465 <!-- TOPP_ProteinQuantifier_13 -->
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
466 <test expect_num_outputs="2">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
467 <section name="adv_opts">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
468 <param name="force" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
469 <param name="test" value="true"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
470 </section>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
471 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
472 <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
473 <param name="top" value="3"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
474 <param name="average" value="sum"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
475 <param name="include_all" value="true"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
476 <param name="best_charge_and_fraction" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
477 <param name="greedy_group_resolution" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
478 <param name="ratios" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
479 <param name="ratiosSILAC" value="true"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
480 <section name="consensus">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
481 <param name="normalize" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
482 <param name="fix_peptides" value="true"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
483 </section>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
484 <section name="format">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
485 <param name="separator" value=""/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
486 <param name="quoting" value="double"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
487 <param name="replacement" value="_"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
488 </section>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
489 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
490 <output name="ctd_out" ftype="xml">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
491 <assert_contents>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
492 <is_valid_xml/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
493 </assert_contents>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
494 </output>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
495 </test>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
496 <!-- TOPP_ProteinQuantifier_14 -->
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
497 <test expect_num_outputs="3">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
498 <section name="adv_opts">
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
499 <param name="force" value="false"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
500 <param name="test" value="true"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
501 </section>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
502 <param name="in" value="ProteinQuantifier_input.idXML"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
503 <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
diff changeset
504 <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
d426affe977c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 11
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505 <param name="top" value="0"/>
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506 <param name="average" value="sum"/>
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507 <param name="include_all" value="false"/>
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508 <param name="best_charge_and_fraction" value="false"/>
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509 <param name="greedy_group_resolution" value="false"/>
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510 <param name="ratios" value="false"/>
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511 <param name="ratiosSILAC" value="false"/>
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512 <section name="consensus">
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513 <param name="normalize" value="false"/>
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514 <param name="fix_peptides" value="false"/>
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515 </section>
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516 <section name="format">
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517 <param name="separator" value=""/>
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518 <param name="quoting" value="double"/>
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519 <param name="replacement" value="_"/>
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520 </section>
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521 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
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522 <output name="ctd_out" ftype="xml">
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523 <assert_contents>
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524 <is_valid_xml/>
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525 </assert_contents>
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526 </output>
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527 </test>
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528 </tests>
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529 <help><![CDATA[Compute peptide and protein abundances
0
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530
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531
13
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532 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinQuantifier.html]]></help>
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533 <expand macro="references"/>
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534 </tool>