Mercurial > repos > galaxyp > openms_featurefindermultiplex

annotate FeatureFinderMultiplex.xml @ 7:3a462c96f2bd draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
author galaxyp
date Mon, 12 Feb 2018 10:29:47 -0500
parents 9ef0f56e82df
children 45fffe3eb041
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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: [Quantitation]-->
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4 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.2.0.1">
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5 <description>Determination of peak ratios in LC-MS data</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureFinderMultiplex</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"/>
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12 <expand macro="requirements"/>
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13 <command>FeatureFinderMultiplex
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_out_features:
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22 -out_features $param_out_features
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23 #end if
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24 #if $param_out_mzq:
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25 -out_mzq $param_out_mzq
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26 #end if
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27
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28 -algorithm:labels '$param_algorithm_labels'
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29
0
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30 #if $param_algorithm_charge:
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31 -algorithm:charge "$param_algorithm_charge"
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32 #end if
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33 #if $param_algorithm_rt_typical:
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34 -algorithm:rt_typical $param_algorithm_rt_typical
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35 #end if
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36 #if $param_algorithm_rt_min:
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37 -algorithm:rt_min $param_algorithm_rt_min
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38 #end if
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39 #if $param_algorithm_mz_tolerance:
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40 -algorithm:mz_tolerance $param_algorithm_mz_tolerance
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41 #end if
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42 #if $param_algorithm_mz_unit:
1
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43 -algorithm:mz_unit
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44 #if " " in str($param_algorithm_mz_unit):
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45 "$param_algorithm_mz_unit"
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46 #else
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47 $param_algorithm_mz_unit
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48 #end if
0
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49 #end if
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50 #if $param_algorithm_intensity_cutoff:
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51 -algorithm:intensity_cutoff $param_algorithm_intensity_cutoff
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52 #end if
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53 #if $param_algorithm_peptide_similarity:
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54 -algorithm:peptide_similarity $param_algorithm_peptide_similarity
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55 #end if
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56 #if $param_algorithm_averagine_similarity:
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57 -algorithm:averagine_similarity $param_algorithm_averagine_similarity
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58 #end if
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59 #if $param_algorithm_missed_cleavages:
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60 -algorithm:missed_cleavages $param_algorithm_missed_cleavages
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61 #end if
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62 #if $adv_opts.adv_opts_selector=='advanced':
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63 #if $adv_opts.param_force:
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64 -force
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65 #end if
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66 #if $adv_opts.param_algorithm_isotopes_per_peptide:
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67 -algorithm:isotopes_per_peptide "$adv_opts.param_algorithm_isotopes_per_peptide"
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68 #end if
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69 #if $adv_opts.param_algorithm_averagine_similarity_scaling:
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70 -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling
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71 #end if
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72 #if $adv_opts.param_algorithm_knock_out:
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73 -algorithm:knock_out
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74 #end if
3
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75 #if $adv_opts.param_algorithm_spectrum_type:
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76 -algorithm:spectrum_type
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77 #if " " in str($adv_opts.param_algorithm_spectrum_type):
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78 "$adv_opts.param_algorithm_spectrum_type"
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79 #else
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80 $adv_opts.param_algorithm_spectrum_type
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81 #end if
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82 #end if
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83 #if $adv_opts.param_algorithm_averagine_type:
1
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84 -algorithm:averagine_type
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85 #if " " in str($adv_opts.param_algorithm_averagine_type):
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86 "$adv_opts.param_algorithm_averagine_type"
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87 #else
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88 $adv_opts.param_algorithm_averagine_type
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89 #end if
0
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90 #end if
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91 #if $adv_opts.param_labels_Arg6:
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92 -labels:Arg6 $adv_opts.param_labels_Arg6
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93 #end if
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94 #if $adv_opts.param_labels_Arg10:
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95 -labels:Arg10 $adv_opts.param_labels_Arg10
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96 #end if
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97 #if $adv_opts.param_labels_Lys4:
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98 -labels:Lys4 $adv_opts.param_labels_Lys4
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99 #end if
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100 #if $adv_opts.param_labels_Lys6:
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101 -labels:Lys6 $adv_opts.param_labels_Lys6
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102 #end if
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103 #if $adv_opts.param_labels_Lys8:
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104 -labels:Lys8 $adv_opts.param_labels_Lys8
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105 #end if
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106 #if $adv_opts.param_labels_Leu3:
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107 -labels:Leu3 $adv_opts.param_labels_Leu3
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108 #end if
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109 #if $adv_opts.param_labels_Dimethyl0:
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110 -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0
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111 #end if
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112 #if $adv_opts.param_labels_Dimethyl4:
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113 -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4
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114 #end if
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115 #if $adv_opts.param_labels_Dimethyl6:
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116 -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6
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117 #end if
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118 #if $adv_opts.param_labels_Dimethyl8:
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119 -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8
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120 #end if
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121 #if $adv_opts.param_labels_ICPL0:
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122 -labels:ICPL0 $adv_opts.param_labels_ICPL0
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123 #end if
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124 #if $adv_opts.param_labels_ICPL4:
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125 -labels:ICPL4 $adv_opts.param_labels_ICPL4
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126 #end if
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127 #if $adv_opts.param_labels_ICPL6:
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128 -labels:ICPL6 $adv_opts.param_labels_ICPL6
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129 #end if
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130 #if $adv_opts.param_labels_ICPL10:
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131 -labels:ICPL10 $adv_opts.param_labels_ICPL10
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132 #end if
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133 #end if
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134 </command>
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135 <inputs>
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136 <param name="param_in" type="data" format="mzml" optional="False" label="LC-MS dataset in centroid or profile mode" help="(-in) "/>
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137 <param name="param_algorithm_labels" type="text" size="30" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="(-labels) [...] specifies the labels for a single sample. For example &lt;br&gt; &lt;br&gt;[][Lys8,Arg10] ... SILAC &lt;br&gt;[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC &lt;br&gt;[Dimethyl0][Dimethyl6] ... Dimethyl &lt;br&gt;[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl &lt;br&gt;[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
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138 <sanitizer>
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139 <valid initial="string.printable">
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140 <remove value="'"/>
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141 <remove value="&quot;"/>
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142 </valid>
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143 </sanitizer>
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144 </param>
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145 <param name="param_algorithm_charge" type="text" size="30" value="1:4" label="Range of charge states in the sample, i.e" help="(-charge) min charge : max charge">
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146 <sanitizer>
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147 <valid initial="string.printable">
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148 <remove value="'"/>
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149 <remove value="&quot;"/>
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150 </valid>
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151 </sanitizer>
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152 </param>
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153 <param name="param_algorithm_rt_typical" type="float" min="0.0" optional="True" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(-rt_typical) (This is not an upper bound. Peptides that elute for longer will be reported.)"/>
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154 <param name="param_algorithm_rt_min" type="float" min="0.0" optional="True" value="2.0" label="Lower bound for the retention time [s]" help="(-rt_min) (Any peptides seen for a shorter time period are not reported.)"/>
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155 <param name="param_algorithm_mz_tolerance" type="float" min="0.0" optional="True" value="6.0" label="m/z tolerance for search of peak patterns" help="(-mz_tolerance) "/>
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156 <param name="param_algorithm_mz_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of the 'mz_tolerance' paramete" help="(-mz_unit) ">
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157 <option value="Da">Da</option>
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158 <option value="ppm" selected="true">ppm</option>
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159 </param>
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160 <param name="param_algorithm_intensity_cutoff" type="float" min="0.0" optional="True" value="1000.0" label="Lower bound for the intensity of isotopic peaks" help="(-intensity_cutoff) "/>
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161 <param name="param_algorithm_peptide_similarity" type="float" min="-1.0" max="1.0" optional="True" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="(-peptide_similarity) This parameter is a lower bound on their similarity"/>
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162 <param name="param_algorithm_averagine_similarity" type="float" min="-1.0" max="1.0" optional="True" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="(-averagine_similarity) This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/>
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163 <param name="param_algorithm_missed_cleavages" type="integer" min="0" optional="True" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(-missed_cleavages) (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
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164 <expand macro="advanced_options">
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165 <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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166 <param name="param_algorithm_isotopes_per_peptide" type="text" size="30" value="3:6" label="Range of isotopes per peptide in the sample" help="(-isotopes_per_peptide) For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. ">
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167 <sanitizer>
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168 <valid initial="string.printable">
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169 <remove value="'"/>
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170 <remove value="&quot;"/>
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171 </valid>
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172 </sanitizer>
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173 </param>
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174 <param name="param_algorithm_averagine_similarity_scaling" type="float" min="0.0" max="1.0" optional="True" value="0.75" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="(-averagine_similarity_scaling) For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
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175 <param name="param_algorithm_knock_out" display="radio" type="boolean" truevalue="-algorithm:knock_out" falsevalue="" checked="false" optional="True" label="Is it likely that knock-outs are present?" help="(-knock_out) (Supported for doublex, triplex and quadruplex experiments only.)"/>
3
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176 <param name="param_algorithm_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Type of MS1 spectra in input mzML file" help="(-spectrum_type) 'automatic' determines the spectrum type directly from the input mzML file">
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177 <option value="profile">profile</option>
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178 <option value="centroid">centroid</option>
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179 <option value="automatic" selected="true">automatic</option>
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180 </param>
0
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181 <param name="param_algorithm_averagine_type" display="radio" type="select" optional="False" value="peptide" label="The type of averagine to use, currently RNA, DNA or peptide" help="(-averagine_type) ">
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182 <option value="peptide" selected="true">peptide</option>
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183 <option value="RNA">RNA</option>
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184 <option value="DNA">DNA</option>
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185 </param>
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186 <param name="param_labels_Arg6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Arg6) "/>
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187 <param name="param_labels_Arg10" type="float" min="0.0" optional="True" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help="(-Arg10) "/>
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188 <param name="param_labels_Lys4" type="float" min="0.0" optional="True" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help="(-Lys4) "/>
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189 <param name="param_labels_Lys6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help="(-Lys6) "/>
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190 <param name="param_labels_Lys8" type="float" min="0.0" optional="True" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help="(-Lys8) "/>
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191 <param name="param_labels_Leu3" type="float" min="0.0" optional="True" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help="(-Leu3) "/>
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192 <param name="param_labels_Dimethyl0" type="float" min="0.0" optional="True" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help="(-Dimethyl0) "/>
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193 <param name="param_labels_Dimethyl4" type="float" min="0.0" optional="True" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help="(-Dimethyl4) "/>
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194 <param name="param_labels_Dimethyl6" type="float" min="0.0" optional="True" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help="(-Dimethyl6) "/>
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195 <param name="param_labels_Dimethyl8" type="float" min="0.0" optional="True" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help="(-Dimethyl8) "/>
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196 <param name="param_labels_ICPL0" type="float" min="0.0" optional="True" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help="(-ICPL0) "/>
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197 <param name="param_labels_ICPL4" type="float" min="0.0" optional="True" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help="(-ICPL4) "/>
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198 <param name="param_labels_ICPL6" type="float" min="0.0" optional="True" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help="(-ICPL6) "/>
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199 <param name="param_labels_ICPL10" type="float" min="0.0" optional="True" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help="(-ICPL10) "/>
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200 </expand>
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201 </inputs>
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202 <outputs>
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203 <data name="param_out" format="consensusxml"/>
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204 <data name="param_out_features" format="featurexml"/>
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205 <data name="param_out_mzq" format="mzq"/>
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206 </outputs>
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207 <help>Determination of peak ratios in LC-MS data
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208
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209
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210 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html</help>
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211 </tool>