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1 <tool id="tagrecon" name="TagRecon" version="0.1.0">
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2 <description></description>
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3 <command>
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4 #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
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5 #if $output_type.value == "mzid"
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6 #set $output_ext="mzid"
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7 #set $output_format="mzIdentML"
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8 #else
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9 #set $output_ext="pepXML"
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10 #set $output_format="pepXML"
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11 #end if
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12 #set $input_name = $input.display_name
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13 #set $tags_name = $input_name.split(".")[0] + ".tags"
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14 #set $output_name = $input_name.split(".")[0] + "." + $output_ext
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15 #set $static_mods_str = ""
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16 #for $static_mod in $static_mods
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17 #set $static_mods_str = $static_mods_str + "" + str($static_mod.aa) + " " + str($static_mod.mass)
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18 #end for
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19 #set $dynamic_mods_str = ""
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20 #set $dynamic_mod_index = 0
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21 #for $dynamic_mod in $dynamic_mods
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22 #set $dynamic_mods_str = $dynamic_mods_str + "" + str($dynamic_mod.motif) + " " + $mod_rep_chars[$dynamic_mod_index] + " " + str($dynamic_mod.mass)
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23 #set $dynamic_mod_index = $dynamic_mod_index + 1
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24 #end for
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25 ln -s '$input' '${input_name}';
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26 ln -s '$input_database' '${db_name}';
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27 cp \${TAGRECON_UNIMOD_PATH:-${GALAXY_DATA_INDEX_DIR}/unimod.xml} .;
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28 cp \${TAGRECON_BLOSUM_PATH:-${GALAXY_DATA_INDEX_DIR}/blosum62.fas} .;
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29 directag '${input_name}' \
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30 -StaticMods '${static_mods_str}' \
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31 -DynamicMods '${dynamic_mods_str}' \
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32 -MaxDynamicMods '$max_dynamic_mods' \
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33 -MaxResults ${max_tags} \
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34 -FragmentMzTolerance ${tag_mz_tolerance} \
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35 #if $advanced_charge_options.specify
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36 -UseChargeStateFromMS $advanced_charge_options.use_ms_charge_state \
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37 #end if
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38 #if $tag_weights.specify
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39 -IntensityScoreWeight $tag_weights.intensity \
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40 -MzFidelityScoreWeight $tag_weights.mz \
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41 -ComplementScoreWeight $tag_weights.complement \
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42 #end if
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43 ;
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44 tagrecon -DecoyPrefix '${decoy_prefix}' \
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45 -ProteinDatabase '${db_name}' \
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46 -OutputFormat '${$output_format}' \
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47 -StaticMods '${static_mods_str}' \
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48 -DynamicMods '${dynamic_mods_str}' \
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49 -MaxDynamicMods '$max_dynamic_mods' \
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50 -CleavageRules '${protease}' \
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51 -MaxMissedCleavages ${max_missed_cleavages} \
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52 #if $advanced_cleavage_options.specify
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53 -MinTerminiCleavages $advanced_cleavage_options.min_termini_cleavages \
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54 -UseNETAdjustment $advanced_cleavage_options.use_net_adjustment \
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55 #end if
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56 #if $advanced_charge_options.specify
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57 -UseChargeStateFromMS $advanced_charge_options.use_ms_charge_state \
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58 #end if
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59 #if $search_untagged.search
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60 -SearchUntaggedSpectra true \
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61 -UntaggedSpectraPrecMZTol $search_untagged.precursor_mz_tolerance
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62 #end if
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63 '${tags_name}';
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64 mv '$output_name' output
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65 </command>
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66 <stdio>
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67 <exit_code range="1:" level="fatal" description="Job Failed" />
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68 <regex match="^Could not find the default configuration file.*$"
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69 source="both"
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70 level="warning" />
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71 </stdio>
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72 <inputs>
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73 <conditional name="type">
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74 <param name="input_type" type="select" label="Input Type">
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75 <option value="mzml">mzML</option>
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76 <option value="mzxml">mzXML</option>
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77 <option value="mgf">mgf</option>
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78 <option value="ms2">ms2</option>
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79 </param>
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80 <when value="mzml">
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81 <param format="mzml" name="input" type="data" label="Input mzML"/>
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82 </when>
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83 <when value="mzxml">
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84 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
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85 </when>
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86 <when value="mgf">
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87 <param format="mgf" name="input" type="data" label="Input mgf"/>
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88 </when>
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89 <when value="ms2">
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90 <param format="ms2" name="input" type="data" label="Input ms2"/>
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91 </when>
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92 </conditional>
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93 <param name="output_type" type="select" label="Output Type">
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94 <option value="raw_pepxml">pepXML</option>
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95 <option value="mzid">mzIdentML</option>
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96 </param>
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97 <param format="fasta" name="input_database" type="data" label="Protein Database"/>
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98 <param name="decoy_prefix" type="text" label="Decoy Prefix"/>
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99 <repeat name="static_mods" title="Static Modifications (used by both directag and tagrecon) ">
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100 <param name="aa" type="text" label="Amino Acid" />
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101 <param name="mass" type="float" label="Mass" value="0" />
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102 </repeat>
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103 <repeat name="dynamic_mods" title="Dynamic Modifications (used by both directag and tagrecon)" max="7">
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104 <param name="motif" type="text" label="Amino Acid Motif" />
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105 <param name="mass" type="float" label="Mass" value="0" />
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106 </repeat>
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107 <param name="max_dynamic_mods" type="integer" label="Maximum Dynamic Mods per Sequence" value="2" />
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108 <param name="tag_length" type="integer" label="Tag Length" value="3" help="A sequence tag is generated from the gaps between a number of peaks equal to this parameter plus one. Longer tag lengths are more specific, but harder to find because many consecutive ion fragments are rare." />
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109 <param name="max_tags" type="integer" label="Maximum Number of Tags per Spectrum" value="20" />
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110 <param name="tag_mz_tolerance" type="float" label="Fragment m/z Tolerance during Tag Generation (Da/z)" value=".5" />
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111 <param name="protease" type="select" label="Protease">
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112 <options from_file="proteases.loc">
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113 <column name="name" index="0" />
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114 <column name="value" index="1" />
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115 </options>
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116 </param>
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117 <param name="max_missed_cleavages" label="Maximum Number of Missed Cleavages" type="integer" value="-1" />
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118 <conditional name="advanced_cleavage_options">
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119 <param name="specify" type="boolean" label="Specify advanced cleavage options" help="" truevalue="true" falsevalue="false" />
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120 <when value="false" />
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121 <when value="true">
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122 <param name="min_termini_cleavages" type="select" label="Minimum Termini Cleavages" value="2" help="A peptide must start after a cleavage and end before a cleavage. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified above.">
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123 <option value="2">2</option>
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124 <option value="1">1</option>
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125 <option value="0">0</option>
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126 </param>
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127 <param name="use_net_adjustment" type="boolean" label="Use NET Adjustment" help="When enabled, TagRecon adds a probabilistic bonus to peptide scores depending on whether the peptides are fully-enzymatic, semi-enzymatic, or non-enzymatic." truevalue="true" falsevalue="false" />
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128 </when>
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129 </conditional>
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130 <conditional name="advanced_charge_options">
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131 <param name="specify" type="boolean" label="Specify Advanced Charge State Handling Options" help="" truevalue="true" falsevalue="false" />
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132 <when value="false" />
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133 <when value="true">
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134 <param name="use_ms_charge_state" type="boolean" label="Use Charge State from MS" truevalue="true" falsevalue="false" help="When enabled, DirecTag and TagRecon will not use their internal algorithm to determine charge state of a spectrum when it is available in the input file." />
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135 <!-- TODO: Add DuplicateSpectra, NumChargeStates -->
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136 </when>
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137 </conditional>
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138 <!-- TODO: Advanced Peptide Filtering: Min/Max Peptide Mass/Length -->
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139 <conditional name="tag_weights">
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140 <param name="specify" type="boolean" label="Override Default Tag Weighting" help="By default equal weights are assigned to intensity, m/z fidelity, and complement scores." truevalue="true" falsevalue="false" />
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141 <when value="false" />
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142 <when value="true">
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143 <param name="intensity" type="float" label="Intensity Score Weight" help="" value="1.0" />
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144 <param name="mz" type="float" label="m/z Fidelity Score Weight" help="" value="1.0" />
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145 <param name="complement" type="float" label="Complement Score Weight" help="" value="1.0" />
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146 </when>
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147 </conditional>
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148 <conditional name="search_untagged">
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149 <param name="search" type="boolean" label="Search Untagged Spectra" help="Search untagged spectra like a database search." truevalue="true" falsevalue="false" />
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150 <when value="false" />
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151 <when value="true">
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152 <param name="precursor_mz_tolerance" type="float" label="Untagged Spectra Precursor m/z Tolerance" value="1.25" />
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153 </when>
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154 </conditional>
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155 <conditional name="unknown_mass_shifts">
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156 <param name="how" type="select" label="Explaination for Unknown Mass Shifts">
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157 <option value="">None, disable delta mass interpretation by TagRecon</option>
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158 <option value="blindptms">Blind PTMs</option>
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159 <option value="mutations">Mutations</option>
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160 <!-- TODO: Add preferredptms -->
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161 </param>
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162 <when value="blindptms">
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163 <!-- BlindPTMResidues ??? -->
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164 </when>
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165 <when value="mutations">
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166 <!-- BlosumScoreThreshold ??? BlosumThreshold ???-->
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167 </when>
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168 <when value="" />
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169 </conditional>
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170 </inputs>
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171 <!--
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172 Both:
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173 AdjustPrecursorMass (defaults to false)
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174
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175 TagRecon:
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176 Skip for now: ComputeXCorr
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177 Skip forever: ProteinSampleSize
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178
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179 TO ADD:
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180
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181 Both: Advanced, ClassSizeMultiplier, float 2.0.
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182 -->
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183 <outputs>
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184 <data format="raw_pepxml" name="output" from_work_dir="output">
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185 <change_format>
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186 <when input="output_type" value="mzid" format="mzid" />
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187 </change_format>
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188 </data>
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189 </outputs>
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190
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191 <requirements>
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192 <requirement type="package" version="1.2.62">directag</requirement>
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193 <requirement type="package" version="1.4.63">tagrecon</requirement>
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194 </requirements>
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195
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196 <help>
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197 **What it does**
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198
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199 Performs protein identification via Directag and TagRecon.
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200
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201 ------
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202
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203 **Citation**
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204
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205 For the underlying tool, please cite `TODO`.
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206
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207 If you use this tool in Galaxy, please cite TODO.
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208 </help>
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209 </tool>
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210
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