Mercurial > repos > galaxyp > peptideshaker

annotate macros.xml @ 54:7fdd9119cc4f draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e17bb5a0e4a22c7376b2e7a70cf690262a44a0c6"
author galaxyp
date Thu, 20 Feb 2020 05:51:38 -0500
parents 864bd76db767
children
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1 <macros>
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2 <import>macros_modifications.xml</import>
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3 <xml name="stdio">
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4 <stdio>
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5 <exit_code range="1:" level="fatal" description="Job Failed" />
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6 <!-- <regex match="java.lang.OutOfMemoryError" level="fatal_oom" description="Java memory Exception"/>
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7 <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
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8 <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
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9 <regex match="Native memory allocation (malloc) failed" level="fatal_oom" description="Java memory Exception"/>-->
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10 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
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11 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
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12 <regex match="PeptideShaker ran out of memory" level="fatal" description="JVM Error"/>
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13 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
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14 </stdio>
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15 </xml>
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16
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17 <token name="@GENERAL_PARAMETERS@">
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18 -frag_tol '${precursor_options.fragment_tol}'
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19 -frag_ppm '${precursor_options.fragment_tol_units}'
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20 -prec_tol '${precursor_options.precursor_ion_tol}'
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21 -prec_ppm '${precursor_options.precursor_ion_tol_units}'
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23 -min_charge $precursor_options.min_charge
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24 -max_charge $precursor_options.max_charge
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25 -fi $precursor_options.forward_ion
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26 -ri $precursor_options.reverse_ion
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27 -min_isotope ${precursor_options.min_isotope}
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28 -max_isotope ${precursor_options.max_isotope}
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29 #if $protein_digest_options.digestion.cleavage == 'default':
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30 ## -enzyme "Trysin"
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31 -mc $protein_digest_options.digestion.missed_cleavages
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32 #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0:
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33 #set $enzymes = []
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34 #set $missed_cleavages = []
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35 ## #set $specificities = []
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36 #for $i, $digest in enumerate($protein_digest_options.digestion.digests):
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37 #silent $enzymes.append(str($digest.enzyme))
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38 #silent $missed_cleavages.append(str($digest.missed_cleavages))
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39 ## #silent $specificities.append(str($digest.specificity))
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40 #end for
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41 -enzyme "#echo ','.join($enzymes)#"
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42 -mc "#echo ','.join($missed_cleavages)#"
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43 ## -specificity "#echo ','.join($specificities)#"
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44 #else:
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45 -digestion $protein_digest_options.digestion.cleavage
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46 #end if
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48 #set $fixed_mods_str = $protein_modification_options.fixed_modifications or ''
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49 #set $variable_mods_str = $protein_modification_options.variable_modifications or ''
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50 #if $fixed_mods_str
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51 -fixed_mods "$fixed_mods_str"
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52 #end if
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53 #if $variable_mods_str
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54 -variable_mods "$variable_mods_str"
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55 #end if
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56
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57 </token>
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58
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59 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
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60 <token name="@SEARCHGUI_VERSION@">3.3.10</token>
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61 <token name="@PEPTIDESHAKER_VERSION@">1.16.36</token>
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62 <xml name="general_options">
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63
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64 <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
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65 <conditional name="digestion">
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66 <param name="cleavage" type="select" label="Digestion">
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67 <option value="0">Select Enzymes</option>
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68 <option value="1">Unspecific Cleavage</option>
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69 <option value="2">Whole Protein</option>
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70 </param>
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71 <when value="0">
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72 <repeat name="digests" min="1" title="Enzymes">
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73 <param name="enzyme" type="select" label="Enzyme"
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74 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
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75 <option value="Trypsin">Trypsin</option>
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76 <option value="Trypsin (no P rule)">Trypsin (no P rule)</option>
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77 <option value="Arg-C">Arg-C</option>
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78 <option value="Arg-C (no P rule)">Arg-C</option>
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79 <option value="Arg-N">Arg-N</option>
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80 <option value="Glu-C">Glu-C</option>
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81 <option value="Lys-C">Lys-C</option>
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82 <option value="Lys-C (no P rule)">Lys-C (no P rule)</option>
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83 <option value="Lys-N">Lys-N</option>
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84 <option value="Asp-N">Asp-N</option>
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85 <option value="Asp-N (ambic)">Asp-N (ambic)</option>
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86 <option value="Chymotrypsin">Chymotrypsin</option>
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87 <option value="Chymotrypsin (no P rule)">Chymotrypsin (no P rule)</option>
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88 <option value="Pepsin A">Pepsin A</option>
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89 <option value="CNBr">CNBr</option>
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90 <option value="Thermolysin">Thermolysin</option>
33
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91 <option value="LysargiNase">LysargiNase</option>
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92 </param>
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93 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
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94 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
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95 <!--
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96 <param name="specificity" type="select" label="Specificity">
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97 <option value="0" selected="true">Specific at both termini</option>
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98 <option value="1">Semi-Specific - one terminus</option>
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99 <option value="2">Specific at the N-terminus only</option>
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100 <option value="3">Specific at the C-terminus only</option>
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101 </param>
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102 -->
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103 </repeat>
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104 </when>
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105 <when value="1"/>
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106 <when value="2"/>
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107 </conditional>
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108 </section>
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109
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110 <section name="precursor_options" expanded="false" title="Precursor Options">
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111 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
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112 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
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113 <option value="1">Parts per million (ppm)</option>
42
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114 <option value="0">Daltons</option>
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115 </param>
37
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116 <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
33
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117 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
41
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118 <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
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119 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
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120 <option value="1">Parts per million (ppm)</option>
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121 <option value="0" selected="true">Daltons</option>
41
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122 </param>
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123 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
33
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124 help="Provide error value for fragment ions, based on instrument used"/>
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125 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
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126 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
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127 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
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128 <option value="a">a</option>
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129 <option value="b" selected="true">b</option>
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130 <option value="c">c</option>
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131 </param>
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132 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
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133 <option value="x">x</option>
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134 <option value="y" selected="true">y</option>
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135 <option value="z">z</option>
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136 </param>
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137 <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
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138 <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
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139 </section>
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140
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141 <section name="protein_modification_options" expanded="false" title="Protein Modification Options">
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142 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
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143 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
52
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144 <expand macro="modifications"/>
33
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145 </param>
43
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146 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
52
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147 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
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148 <expand macro="modifications"/>
33
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149 </param>
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150 </section>
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151
20
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152 </xml>
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153
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154 <xml name="citations">
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155 <citations>
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156 <citation type="doi">10.1186/1471-2105-12-70</citation>
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157 <citation type="doi">10.1002/pmic.201000595</citation>
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158 <citation type="doi">doi:10.1038/nbt.3109</citation>
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159 </citations>
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160 </xml>
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161
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162 </macros>