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annotate macros.xml @ 4:b4b1780ef40f draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit c624897f9f1282fe1708271a06554bf5a3465763-dirty
author jjohnson
date Thu, 12 Jul 2018 09:10:29 -0400
parents 8cf04d7a6683
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2
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1 <macros>
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2 <xml name="stdio">
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3 <stdio>
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4 <exit_code range="1:" level="fatal" description="Job Failed" />
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5 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
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6 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
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7 <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
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8 </stdio>
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9 </xml>
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10 <token name="@ENZYMESCLI@"><![CDATA[
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11 #if len($protein_digest_options.digestion.user_enzymes) > 0:
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12 #for $i, $user_enzyme in enumerate($protein_digest_options.digestion.user_enzymes):
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13 (searchgui com.compomics.cli.enzymes.EnzymesCLI -out enzymes.json -in enzymes.json
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14 -name $user_enzyme.enzyme_name
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15 #if $user_enzyme.cleave_before:
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16 -cleave_before $user_enzyme.cleave_before
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17 #end if
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18 #if $user_enzyme.cleave_after:
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19 -cleave_after $user_enzyme.cleave_after
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20 #end if
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21 #if $user_enzyme.restriction_before:
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22 -restriction_before $user_enzyme.restriction_before
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23 #end if
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24 #if $user_enzyme.restriction_after:
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25 -restriction_after $user_enzyme.restriction_after
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26 #end if
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27 ) &&
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28 #end for
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29 #end if
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30 ]]></token>
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31 <token name="@ENZYME_CONFIGUTRATION@">
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32 #if len($protein_digest_options.digestion.user_enzymes) > 0:
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33 -enzyme_configuration enzymes.json
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34 #end if
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35 </token>
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36 <token name="@GENERAL_PARAMETERS@">
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37 -frag_tol '${precursor_options.fragment_tol}'
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38 -frag_ppm '${precursor_options.fragment_tol_units}'
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39 -prec_tol '${precursor_options.precursor_ion_tol}'
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40 -prec_ppm '${precursor_options.precursor_ion_tol_units}'
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41
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42 -min_charge $precursor_options.min_charge
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43 -max_charge $precursor_options.max_charge
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44 -fi $precursor_options.forward_ion
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45 -ri $precursor_options.reverse_ion
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46 -min_isotope ${precursor_options.min_isotope}
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47 -max_isotope ${precursor_options.max_isotope}
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48 #if $protein_digest_options.digestion.cleavage == 'default':
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49 ## -enzyme "Trysin"
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50 -mc $protein_digest_options.digestion.missed_cleavages
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51 #elif $protein_digest_options.digestion.cleavage == '0':
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52 #set $enzymes = []
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53 #set $missed_cleavages = []
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54 ## #set $specificities = []
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55 #if len($protein_digest_options.digestion.digests) > 0:
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56 #for $i, $digest in enumerate($protein_digest_options.digestion.digests):
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57 #silent $enzymes.append(str($digest.enzyme))
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58 #silent $missed_cleavages.append(str($digest.missed_cleavages))
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59 ## #silent $specificities.append(str($digest.specificity))
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60 #end for
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61 #end if
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62 #if len($protein_digest_options.digestion.user_enzymes) > 0:
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63 #for $i, $user_enzyme in enumerate($protein_digest_options.digestion.user_enzymes):
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64 #silent $enzymes.append(str($user_enzyme.enzyme_name))
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65 #silent $missed_cleavages.append(str($user_enzyme.missed_cleavages))
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66 #end for
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67 #end if
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68 #if len($enzymes) > 0:
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69 -enzyme "#echo ','.join($enzymes)#"
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70 -mc "#echo ','.join($missed_cleavages)#"
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71 ## -specificity "#echo ','.join($specificities)#"
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72 #end if
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73 #else:
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74 -digestion $protein_digest_options.digestion.cleavage
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75 #end if
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76
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77 #set $fixed_mods_str = $protein_modification_options.fixed_modifications or ''
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78 #set $variable_mods_str = $protein_modification_options.variable_modifications or ''
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79 #if $fixed_mods_str
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80 -fixed_mods "$fixed_mods_str"
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81 #end if
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82 #if $variable_mods_str
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83 -variable_mods "$variable_mods_str"
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84 #end if
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85
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86 </token>
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87 <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
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88 <token name="@SEARCHGUI_VERSION@">3.3.3</token>
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89 <xml name="general_options">
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90
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91 <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
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92 <conditional name="digestion">
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93 <param name="cleavage" type="select" label="Digestion">
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94 <option value="default" selected="true">Trypsin</option>
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95 <option value="0">Select Enzymes</option>
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96 <option value="1">Unspecific Cleavage</option>
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97 <option value="2">Whole Protein</option>
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98 </param>
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99 <when value="default">
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100 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
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101 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
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102 </when>
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103 <when value="0">
4
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104 <repeat name="digests" min="0" title="Enzymes">
2
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105 <param name="enzyme" type="select" label="Enzyme"
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106 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
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107 <option value="Trypsin">Trypsin</option>
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108 <option value="Arg-C">Arg-C</option>
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109 <option value="CNBr">CNBr</option>
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110 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
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111 <option value="Formic Acid">Formic Acid</option>
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112 <option value="Lys-C">Lys-C</option>
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113 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
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114 <option value="Pepsin A">Pepsin A</option>
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115 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
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116 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
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117 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
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118 <option value="Whole Protein">Whole Protein</option>
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119 <option value="Asp-N">Asp-N</option>
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120 <option value="Glu-C">Glu-C</option>
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121 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
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122 <option value="Top-Down">Top-Down</option>
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123 <option value="Semi-Tryptic">Semi-Tryptic</option>
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124 <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
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125 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
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126 <option value="Asp-N (DE)">Asp-N (DE)</option>
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127 <option value="Glu-C (DE)">Glu-C (DE)</option>
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128 <option value="Lys-N (K)">Lys-N (K)</option>
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129 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
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130 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
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131 <option value="Semi-Glu-C">Semi-Glu-C</option>
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132 <option value="LysargiNase">LysargiNase</option>
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133 <option value="Semi-LysargiNase">Semi-LysargiNase</option>
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134 <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
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135 <option value="Semi-Arg-C">Semi-Arg-C</option>
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136 <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
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137 <option value="Arg-N">Arg-N</option>
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138 <option value="Semi-Arg-N">Semi-Arg-N</option>
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139 </param>
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140 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
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141 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
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142 <!--
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143 <param name="specificity" type="select" label="Specificity">
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144 <option value="0" selected="true">Specific at both termini</option>
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145 <option value="1">Semi-Specific - one terminus</option>
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146 <option value="2">Specific at the N-terminus only</option>
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147 <option value="3">Specific at the C-terminus only</option>
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148 </param>
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149 -->
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150 </repeat>
3
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151 <repeat name="user_enzymes" min="0" title="User Defined Enzymes">
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152 <param name="enzyme_name" type="text" value="" label="enzyme_name">
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153 <validator type="empty_field" message="Enzyme must be geiven a name"/>
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154 </param>
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155 <param name="cleave_before" type="text" value="" optional="true" label="cleave_before AAs">
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156 <validator type="regex" message="single letter amino acid codes separated by comma">^([ACDEFGHILKMNPQRSTVWY](,[ACDEFGHILKMNPQRSTVWY])*)?$</validator>
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157 </param>
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158 <param name="cleave_after" type="text" value="" optional="true" label="cleave_after AAs">
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159 <validator type="regex" message="single letter amino acid codes separated by comma">^([ACDEFGHILKMNPQRSTVWY](,[ACDEFGHILKMNPQRSTVWY])*)?$</validator>
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160 </param>
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161 <param name="restriction_before" type="text" value="" optional="true" label="restriction_before AAs">
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162 <validator type="regex" message="single letter amino acid codes separated by comma">^([ACDEFGHILKMNPQRSTVWY](,[ACDEFGHILKMNPQRSTVWY])*)?$</validator>
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163 </param>
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164 <param name="restriction_after" type="text" value="" optional="true" label="restriction_after AAs">
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165 <validator type="regex" message="single letter amino acid codes separated by comma">^([ACDEFGHILKMNPQRSTVWY](,[ACDEFGHILKMNPQRSTVWY])*)?$</validator>
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166 </param>
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167 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
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168 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
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169 </repeat>
2
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170 </when>
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171 <when value="1"/>
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172 <when value="2"/>
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173 </conditional>
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174 </section>
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175
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176 <section name="precursor_options" expanded="false" title="Precursor Options">
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177 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
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178 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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179 <option value="1">Parts per million (ppm)</option>
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180 <option value="0">Daltons</option>
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181 </param>
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182 <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
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183 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
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184 <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
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185 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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186 <option value="1">Parts per million (ppm)</option>
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187 <option value="0" selected="true">Daltons</option>
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188 </param>
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189 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
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190 help="Provide error value for fragment ions, based on instrument used"/>
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191 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
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192 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
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193 <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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194 <option value="a">a</option>
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195 <option value="b" selected="true">b</option>
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196 <option value="c">c</option>
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197 </param>
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198 <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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199 <option value="x">x</option>
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200 <option value="y" selected="true">y</option>
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201 <option value="z">z</option>
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202 </param>
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203 <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
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204 <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
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205 </section>
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206
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207 <section name="protein_modification_options" expanded="false" title="Protein Modification Options">
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208 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
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209 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
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210 <options from_file="searchgui_mods.loc">
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211 <column name="name" index="0" />
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212 <column name="value" index="0" />
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213 </options>
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214 </param>
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215 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
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216 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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217 <options from_file="searchgui_mods.loc">
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218 <column name="name" index="0" />
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219 <column name="value" index="0" />
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220 </options>
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221 </param>
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222 </section>
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223
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224 </xml>
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225
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226 <xml name="citations">
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227 <citations>
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228 <citation type="doi">10.1186/1471-2105-12-70</citation>
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229 <citation type="doi">10.1002/pmic.201000595</citation>
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230 <citation type="doi">doi:10.1038/nbt.3109</citation>
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231 </citations>
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232 </xml>
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233
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234 </macros>