Mercurial > repos > galaxyp > openms_metaprosip

annotate MetaProSIP.xml @ 2:21644dec106d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Wed, 18 Oct 2017 15:29:01 -0400
parents a25d96e0d837
children fdb3fbfef4cc
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f0e3cb65a6bd 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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MetaProSIP" name="MetaProSIP" version="2.2.0.1">
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5 <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MetaProSIP</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
2
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12 <expand macro="requirements">
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13 <requirement type="package" version="3.3.1">r-base</requirement>
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14 </expand>
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15 <command>MetaProSIP
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f0e3cb65a6bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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17 #if $param_in_mzML:
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18 -in_mzML $param_in_mzML
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19 #end if
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20 #if $param_in_fasta:
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21 -in_fasta $param_in_fasta
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22 #end if
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23 #if $param_out_csv:
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24 -out_csv $param_out_csv
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25 #end if
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26 #if $param_out_peptide_centric_csv:
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27 -out_peptide_centric_csv $param_out_peptide_centric_csv
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28 #end if
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29 #if $param_in_featureXML:
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30 -in_featureXML $param_in_featureXML
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31 #end if
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21644dec106d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
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33 -r_executable 'R'
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34
0
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35 #if $param_mz_tolerance_ppm:
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36 -mz_tolerance_ppm $param_mz_tolerance_ppm
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37 #end if
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38 #if $param_rt_tolerance_s:
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39 -rt_tolerance_s $param_rt_tolerance_s
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40 #end if
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41 #if $param_intensity_threshold:
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42 -intensity_threshold $param_intensity_threshold
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43 #end if
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44 #if $param_correlation_threshold:
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45 -correlation_threshold $param_correlation_threshold
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46 #end if
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47 #if $param_xic_threshold:
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48 -xic_threshold $param_xic_threshold
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49 #end if
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50 #if $param_decomposition_threshold:
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51 -decomposition_threshold $param_decomposition_threshold
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52 #end if
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53 #if $param_weight_merge_window:
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54 -weight_merge_window $param_weight_merge_window
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55 #end if
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56 #if $param_plot_extension:
1
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57 -plot_extension
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58 #if " " in str($param_plot_extension):
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59 "$param_plot_extension"
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60 #else
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61 $param_plot_extension
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62 #end if
0
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63 #end if
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64 #if $param_qc_output_directory:
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65 -qc_output_directory "$param_qc_output_directory"
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66 #end if
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67 #if $param_labeling_element:
1
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68 -labeling_element
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69 #if " " in str($param_labeling_element):
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70 "$param_labeling_element"
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71 #else
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72 $param_labeling_element
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73 #end if
0
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74 #end if
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75 #if $param_use_unassigned_ids:
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76 -use_unassigned_ids
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77 #end if
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78 #if $param_use_averagine_ids:
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79 -use_averagine_ids
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80 #end if
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81 #if $param_report_natural_peptides:
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82 -report_natural_peptides
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83 #end if
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84 #if $param_filter_monoisotopic:
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85 -filter_monoisotopic
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86 #end if
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87 #if $param_cluster:
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88 -cluster
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89 #end if
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90 #if $adv_opts.adv_opts_selector=='advanced':
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91 #if $adv_opts.param_min_correlation_distance_to_averagine:
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92 -min_correlation_distance_to_averagine $adv_opts.param_min_correlation_distance_to_averagine
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93 #end if
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94 #if $adv_opts.param_pattern_15N_TIC_threshold:
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95 -pattern_15N_TIC_threshold $adv_opts.param_pattern_15N_TIC_threshold
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96 #end if
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97 #if $adv_opts.param_pattern_13C_TIC_threshold:
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98 -pattern_13C_TIC_threshold $adv_opts.param_pattern_13C_TIC_threshold
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99 #end if
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100 #if $adv_opts.param_pattern_2H_TIC_threshold:
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101 -pattern_2H_TIC_threshold $adv_opts.param_pattern_2H_TIC_threshold
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102 #end if
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103 #if $adv_opts.param_pattern_18O_TIC_threshold:
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104 -pattern_18O_TIC_threshold $adv_opts.param_pattern_18O_TIC_threshold
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105 #end if
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106 #if $adv_opts.param_heatmap_bins:
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107 -heatmap_bins $adv_opts.param_heatmap_bins
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108 #end if
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109 #if $adv_opts.param_observed_peak_fraction:
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110 -observed_peak_fraction $adv_opts.param_observed_peak_fraction
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111 #end if
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112 #if $adv_opts.param_min_consecutive_isotopes:
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113 -min_consecutive_isotopes $adv_opts.param_min_consecutive_isotopes
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114 #end if
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115 #if $adv_opts.param_score_plot_yaxis_min:
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116 -score_plot_yaxis_min $adv_opts.param_score_plot_yaxis_min
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117 #end if
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118 #if $adv_opts.param_collect_method:
1
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119 -collect_method
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120 #if " " in str($adv_opts.param_collect_method):
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121 "$adv_opts.param_collect_method"
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122 #else
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123 $adv_opts.param_collect_method
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124 #end if
0
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125 #end if
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126 #if $adv_opts.param_lowRIA_correlation_threshold:
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127 -lowRIA_correlation_threshold $adv_opts.param_lowRIA_correlation_threshold
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128 #end if
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129 #if $adv_opts.param_force:
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130 -force
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131 #end if
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132 #end if
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133 </command>
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134 <inputs>
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135 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
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136 <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
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137 <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
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138 <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
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139 <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
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140 <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
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141 <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
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142 <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
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143 <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R^2 of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/>
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144 <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/>
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145 <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) ">
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146 <option value="png" selected="true">png</option>
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147 <option value="svg">svg</option>
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148 <option value="pdf">pdf</option>
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149 </param>
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150 <param name="param_qc_output_directory" type="text" size="30" label="Output directory for the quality report" help="(-qc_output_directory) ">
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151 <sanitizer>
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152 <valid initial="string.printable">
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153 <remove value="'"/>
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154 <remove value="&quot;"/>
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155 </valid>
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156 </sanitizer>
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157 </param>
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158 <param name="param_labeling_element" display="radio" type="select" optional="False" value="C" label="Which element (single letter code) is labeled" help="(-labeling_element) ">
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159 <option value="C" selected="true">C</option>
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160 <option value="N">N</option>
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161 <option value="H">H</option>
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162 <option value="O">O</option>
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163 </param>
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164 <param name="param_use_unassigned_ids" display="radio" type="boolean" truevalue="-use_unassigned_ids" falsevalue="" checked="false" optional="True" label="Include identifications not assigned to a feature in pattern detection" help="(-use_unassigned_ids) "/>
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165 <param name="param_use_averagine_ids" display="radio" type="boolean" truevalue="-use_averagine_ids" falsevalue="" checked="false" optional="True" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help="(-use_averagine_ids) "/>
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166 <param name="param_report_natural_peptides" display="radio" type="boolean" truevalue="-report_natural_peptides" falsevalue="" checked="false" optional="True" label="Whether purely natural peptides are reported in the quality report" help="(-report_natural_peptides) "/>
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167 <param name="param_filter_monoisotopic" display="radio" type="boolean" truevalue="-filter_monoisotopic" falsevalue="" checked="false" optional="True" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help="(-filter_monoisotopic) "/>
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168 <param name="param_cluster" display="radio" type="boolean" truevalue="-cluster" falsevalue="" checked="false" optional="True" label="Perform grouping" help="(-cluster) "/>
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169 <expand macro="advanced_options">
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170 <param name="param_min_correlation_distance_to_averagine" type="float" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="(-min_correlation_distance_to_averagine) Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
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171 <param name="param_pattern_15N_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_15N_TIC_threshold) "/>
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172 <param name="param_pattern_13C_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_13C_TIC_threshold) "/>
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173 <param name="param_pattern_2H_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_2H_TIC_threshold) "/>
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174 <param name="param_pattern_18O_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_18O_TIC_threshold) "/>
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175 <param name="param_heatmap_bins" type="integer" value="20" label="Number of RIA bins for heat map generation" help="(-heatmap_bins) "/>
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176 <param name="param_observed_peak_fraction" type="float" value="0.5" label="Fraction of observed/expected peaks" help="(-observed_peak_fraction) "/>
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177 <param name="param_min_consecutive_isotopes" type="integer" value="2" label="Minimum number of consecutive isotopic intensities needed" help="(-min_consecutive_isotopes) "/>
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178 <param name="param_score_plot_yaxis_min" type="float" value="0.0" label="The minimum value of the score axis" help="(-score_plot_yaxis_min) Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
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179 <param name="param_collect_method" display="radio" type="select" optional="False" value="correlation_maximum" label="How RIAs are collected" help="(-collect_method) ">
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180 <option value="correlation_maximum" selected="true">correlation_maximum</option>
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181 <option value="decomposition_maximum">decomposition_maximum</option>
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182 </param>
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183 <param name="param_lowRIA_correlation_threshold" type="float" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="(-lowRIA_correlation_threshold) Disable and take correlation_threshold value for negative values"/>
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184 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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185 </expand>
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186 </inputs>
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187 <outputs>
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188 <data name="param_out_csv" format="tabular"/>
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189 <data name="param_out_peptide_centric_csv" format="tabular"/>
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190 </outputs>
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191 <help>Performs proteinSIP on peptide features for elemental flux analysis.
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192
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193
1
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194 For more information, visit http://www.openms.de/comp/metaprosip/</help>
0
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195 </tool>