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1 <tool name="X!Tandem" id="masscomb_xtandem200" version="2.0.0">
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2 <description>MS/MS DB search</description>
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3 <!--
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4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
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5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
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6 -->
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7 <command interpreter="java -jar">
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8 MassComb.jar
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9 -action XTANDEMSEARCH
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10 -outputFile $outputFile
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11 -fileGrouping $fileType.type
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12 -inputFile $fileType.inputFile
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13 -parametersFile $parametersFile
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14 -outputTsv $outTsv
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15 -outReport $htmlReportFile
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16 -outReportPicturesPath $htmlReportFile.files_path
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17 </command>
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18 <inputs>
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19 <conditional name="fileType">
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20 <param name="type" type="select" label="select MS/MS input type">
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21 <option value="single" selected="true">single-File</option>
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22 <option value="fileSet">fileSet</option>
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23 </param>
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24 <when value="single">
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25 <param name="inputFile" type="data" format="mzml" label="MS/MS input file (mzml)"/>
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26 </when>
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27 <when value="fileSet">
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28 <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/>
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29 </when>
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30 </conditional>
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31
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32 <param name="precursor_mass_tolerance_lower" type="text" size="30" label="precursor monoisotopic mass_tolerance_lower" value="100" help=""/>
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33 <param name="precursor_mass_tolerance_upper" type="text" size="30" label="precursor monoisotopic mass_tolerance_upper" value="100" help=""/>
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34 <param name="precursor_error_units" type="select" label="precursor_error_units" help="">
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35 <option value="ppm" selected="true">ppm</option>
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36 <option value="Daltons">Daltons</option>
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37 </param>
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38 <param name="fragment_mass_tolerance" type="text" size="30" label="fragment_mass_tolerance" value="0.4" help=""/>
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39 <param name="fragment_error_units" type="select" label="fragment_error_units" help="">
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40 <option value="ppm">ppm</option>
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41 <option value="Daltons" selected="true">Daltons</option>
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42 </param>
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43 <param name="database" type="data" format="fasta" label="Protein sequences DB (FASTA)"/>
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44 <!--
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45 <param name="min_precursor_charge" type="text" size="30" label="min_precursor_charge" value="1" help=""/>
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46 <param name="max_precursor_charge" type="text" size="30" label="max_precursor_charge" value="4" help=""/>-->
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47 <param name="fixed_modifications" type="select" display="checkboxes" multiple="true" label="Complete modifications" help="">
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48 <option value="57.021464@C">Carbamidomethyl (C)</option>
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49 <option value="57.021464@C,10.008269@R,8.014199@K">Cam+SILAC (8@K,10@R)</option>
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50 <option value="57.021464@C,4.025107@K,6.020129@R">Cam+SILAC (4@K,6@R)</option>
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51 <option value="57.021464@C,4.025107@K,6.020129@R,6.020129@L">Cam+SILAC (4@K,6@R,6@L)</option>
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52 <option value="58.005479@C">Carboxymethyl (C)</option>
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53 <option value="45.987721@C">Methylthio (C)</option>
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54 <option value="47.984744@C">Trioxidation (C)</option>
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55 <option value="442.224991@C">ICAT-D (C)</option>
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56 <option value="450.275205@C">ICAT-D:2H(8) (C)</option>
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57 <option value="227.126991@C">ICAT-C (C)</option>
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58 <option value="236.157185@C">ICAT-C:13C(9) (C)</option>
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59 <option value="58.005479@C">Carboxymethyl (C)</option>
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60 <option value="105.057849@C">Pyridylethyl (C)</option>
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61 <option value="71.037114@C">Propionamide (C)</option>
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62 <option value="125.047679@C">Nethylmaleimide (C)</option>
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63 <option value="144.102063@[,144.102063@K">iTRAQ (N-term,K)</option>
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64 <option value="57.021464@C,144.102063@[,144.102063@K">Cam + iTRAQ (C,N-term,K)</option>
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65 <option value="57.021464@C,224.152478@K,224.152478@[">Cam + TMT (C,K,nt)</option>
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66 <option value="57.021464@C,225.155833@K,225.155833@[">Cam + TMT2plex (C,K,nt)</option>
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67 <option value="57.021464@C,229.1629328@K,229.1629328@[">Cam + TMT6plex (C,K,nt)</option>
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68 <option value="57.021464@C,28.0313@[,28.0313@K">Cam + Dimethyl (C,28@N-term,K)</option>
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69 <option value="57.021464@C,32.0564@[,32.0564@K">Cam + Dimethyl (C,32@N-term,K)</option>
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70 <option value="57.021464@C,36.0757@[,36.0757@K">Cam + Dimethyl (C,36@N-term,K)</option>
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71 <option value="45.987721@C,144.102063@[,144.102063@K">Methylthio + iTRAQ (C,N-term,K)</option>
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72 <option value="45.987721@C,224.152478@K,224.152478@[">Methylthio + TMT (C,K,nt)</option>
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73 <option value="45.987721@C,225.155833@K,225.155833@[">Methylthio + TMT2plex (C,K,nt)</option>
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74 <option value="45.987721@C,229.1629328@K,229.1629328@[">Methylthio + TMT6plex (C,K,nt)</option>
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75 <option value="14.0156@],14.0156@D,14.0156@E">Methy +14Da (D,E,C-term)</option>
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76 </param>
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77 <param name="potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications" help="">
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78 <option value="15.994915@M">Oxidation (M)</option>
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79 <option value="15.994915@W">Oxidation (W)</option>
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80 <option value="0.984016@N">Deamidation (N)</option>
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81 <option value="0.984016@Q">Deamidation (Q)</option>
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82 <option value="79.966331@S">Phospho (S)</option>
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83 <option value="79.966331@T">Phospho (T)</option>
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84 <option value="79.966331@Y">Phospho (Y)</option>
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85 <option value="79.956815@Y">Sulfo (Y)</option>
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86 <option value="42.010565@K">Acetyl (K)</option>
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87 <option value="43.005814@[">Carbamyl (nt)</option>
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88 <option value="43.005814@K">Carbamyl (K)</option>
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89 <option value="72.021129@[">Carboxyethyl (nt)</option>
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90 <option value="72.021129@K">Carboxyethyl (K)</option>
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91 <option value="57.021464@[">Carbamidomethyl (nt)</option>
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92 <option value="57.021464@K">Carbamidomethyl (K)</option>
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93 <option value="57.021464@C">Carbamidomethyl (C)</option>
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94 <option value="58.005479@C">Carboxymethyl (C)</option>
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95 <option value="45.987721@C">Methylthio (C)</option>
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96 <option value="125.047679@C">Nethylmaleimide (C)</option>
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97 <option value="31.989829@C">Dioxidation (C)</option>
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98 <option value="47.984744@C">Trioxidation (C)</option>
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99 <option value="27.994915@K">formyl (K)</option>
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100 <option value="27.994915@[">formyl (nt)</option>
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101 <option value="114.042927@K">GlyGly (K)</option>
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102 <option value="8.0502@C">ICAT-D:2H(8) (C)</option>
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103 <option value="9.0302@C">ICAT-C:13C(9) (C)</option>
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104 <option value="144.102063@[">iTRAQ (N-term)</option>
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105 <option value="144.102063@K">iTRAQ (K)</option>
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106 <option value="6.020129@L">Label:13C(6) (L)</option>
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107 <option value="6.020129@K">Label:13C(6) (K)</option>
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108 <option value="8.014199@K">Label:13C(6)15N(2) (K)</option>
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109 <option value="6.020129@R">Label:13C(6) (R)</option>
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110 <option value="4.025107@K">Label:2H(4) (K)</option>
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111 <option value="125.047679@C">Nethylmaleimide (C)</option>
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112 <option value="31.005814@C">Sulfinamide (C)</option>
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113 <option value="224.152478@K,224.152478@[">TMT (K,nt)</option>
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114 <option value="225.155833@K,225.155833@[">TMT2plex (K,nt)</option>
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115 <option value="229.1629328@K,229.1629328@[">TMT6plex (K,nt)</option>
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116 </param>
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117 <!--
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118 <param name="missed_cleavages" type="text" size="30" label="missed_cleavages" value="1" help="Nr. of possible cleavage sites missed by the enzyme"/>-->
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119 <param name="minimum_fragment_mz" type="text" size="30" label="minimum_fragment_mz" value="150" help=""/>
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120 <param name="cleavage_site" type="select" label="cleavage_site" help="">
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121 <option selected="true" value="[RK]|{P}">trypsin, [RK]|{P}</option>
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122 <option value="[R]|[X]">endo-arg-C, [R]|[X]</option>
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123 <option value="[K]|[X]">endo-lys-C, [K]|[X]</option>
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124 <option value="[E]|[X]">endo-glu-C, [E]|[X]</option>
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125 <option value="[X]|[D]">endo-asp-N, [X]|[D]</option>
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126 <option value="[ED]|[X]">V8, [ED]|[X]</option>
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127 <option value="[FYWL]|{P}">chymotrypsin, [FYWL]|{P}</option>
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128 </param>
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129 <param name="maximum_missed_cleavage_sites" type="integer" size="10" value="1"
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130 label="maximum missed cleavage sites"
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131 help="maximum number of missed cleavage sites allowed within a peptide. For a specific,
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132 aggressive enzyme such as trypsin, the number of missed sites will be low: a value of 1 or 2 is appropriate.
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133 For a non-specific enzyme, such as pepsin, then a value of 50 is more appropriate."/>
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134 <param name="max_valid_expect" type="text" size="30" label="maximum valid expectation value" value="0.1"
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135 help="Max E-Value of a hit to be reported. All results with expectation values less than this value
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136 are considered to be statisitically significant and are recorded. "/>
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137 <conditional name="refinementOpt">
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138 <param name="refinement" type="select" label="Refine search" help="Select this to enable a second round of more
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139 detailed searching, using only the set of proteins found by the contraints above. E.g.
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140 Rather than entering the 'potential modifications' in the options above, try entering them here only. This is
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141 faster and limits this more thorough searching to a set of proteins for which there is already some evidence.">
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142 <option value="yes">Yes</option>
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143 <option value="no" selected="true">No</option>
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144 </param>
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145 <when value="yes">
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146 <param name="refine_point_mutation" type="select" label="Allow for point mutations (substitutions)"
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147 help="Test the selected sequences for the possibility of a point mutation in each one of the
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148 peptides generated with the initial cleavage chemistry.">
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149 <option value="yes" selected="true">Yes</option>
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150 <option value="no">No</option>
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151 </param>
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152 <param name="refine_potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications to look for in refined search" help="">
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153 <option value="15.994915@M">Oxidation (M)</option>
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154 <option value="15.994915@W">Oxidation (W)</option>
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155 <option value="0.984016@N">Deamidation (N)</option>
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156 <option value="0.984016@Q">Deamidation (Q)</option>
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157 <option value="79.966331@S">Phospho (S)</option>
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158 <option value="79.966331@T">Phospho (T)</option>
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159 <option value="79.966331@Y">Phospho (Y)</option>
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160 <option value="79.956815@Y">Sulfo (Y)</option>
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161 <option value="42.010565@K">Acetyl (K)</option>
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162 <option value="43.005814@[">Carbamyl (nt)</option>
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163 <option value="43.005814@K">Carbamyl (K)</option>
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164 <option value="72.021129@[">Carboxyethyl (nt)</option>
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165 <option value="72.021129@K">Carboxyethyl (K)</option>
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166 <option value="57.021464@[">Carbamidomethyl (nt)</option>
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167 <option value="57.021464@K">Carbamidomethyl (K)</option>
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168 <option value="57.021464@C">Carbamidomethyl (C)</option>
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169 <option value="58.005479@C">Carboxymethyl (C)</option>
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170 <option value="45.987721@C">Methylthio (C)</option>
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171 <option value="125.047679@C">Nethylmaleimide (C)</option>
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172 <option value="31.989829@C">Dioxidation (C)</option>
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173 <option value="47.984744@C">Trioxidation (C)</option>
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174 <option value="27.994915@K">formyl (K)</option>
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175 <option value="27.994915@[">formyl (nt)</option>
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176 <option value="114.042927@K">GlyGly (K)</option>
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177 <option value="8.0502@C">ICAT-D:2H(8) (C)</option>
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178 <option value="9.0302@C">ICAT-C:13C(9) (C)</option>
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179 <option value="144.102063@[">iTRAQ (N-term)</option>
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180 <option value="144.102063@K">iTRAQ (K)</option>
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181 <option value="6.020129@L">Label:13C(6) (L)</option>
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182 <option value="6.020129@K">Label:13C(6) (K)</option>
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183 <option value="8.014199@K">Label:13C(6)15N(2) (K)</option>
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184 <option value="6.020129@R">Label:13C(6) (R)</option>
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185 <option value="4.025107@K">Label:2H(4) (K)</option>
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186 <option value="125.047679@C">Nethylmaleimide (C)</option>
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187 <option value="31.005814@C">Sulfinamide (C)</option>
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188 <option value="224.152478@K,224.152478@[">TMT (K,nt)</option>
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189 <option value="225.155833@K,225.155833@[">TMT2plex (K,nt)</option>
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190 <option value="229.1629328@K,229.1629328@[">TMT6plex (K,nt)</option>
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191 </param>
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192 <param name="refine_max_valid_expect" type="text" size="30" label="maximum valid expectation value for identifications coming from refine step" value="0.01"
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193 help="Max E-Value of a 'refine based' hit to be reported. Notice that the default value here is stricter than
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194 the same parameter for 'non-refine based' identifications above. "/>
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195 </when>
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196 </conditional>
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197 <param name="reverse_scoring" type="select" label="Scoring, include reverse" help=" Use the X! Tandem protein sequence reverse method (sequences are reversed in memory and searched again, the tag ':reversed' is added to the protein description).">
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198 <option value="yes">Yes</option>
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199 <option value="no" selected="true">No</option>
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200 <option value="only">Only</option>
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201 </param>
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202
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203 </inputs>
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204 <configfiles>
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205 <configfile name="parametersFile"><?xml version="1.0" encoding="UTF-8"?>
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206 <tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper">
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207 <Files/>
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208 <Parameters>
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209 <Attribute attributeName="xtandemLocation" value="/home/lukas007/galaxy-dist/tool-data/prims/tandem-linux-12-10-01-1/bin/" type="Unknown" description=""/>
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210 <Attribute attributeName="database" value="${database}" type="Unknown" description=""/>
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211 <Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/>
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212 <Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/>
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213 <Attribute attributeName="precursor_error_units" toolSpecificName="spectrum, parent monoisotopic mass error units" value="${precursor_error_units}" type="Unknown" description=""/>
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214 <Attribute attributeName="fragment_mass_tolerance" toolSpecificName="spectrum, fragment monoisotopic mass error" value="${fragment_mass_tolerance}" type="Unknown" description=""/>
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215 <Attribute attributeName="fragment_error_units" toolSpecificName="spectrum, fragment monoisotopic mass error units" value="${fragment_error_units}" type="Unknown" description=""/>
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216 <Attribute attributeName="fixed_modifications" toolSpecificName="residue, modification mass" value="${fixed_modifications}" type="Unknown" description=""/>
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217 <Attribute attributeName="potential_modifications" toolSpecificName="residue, potential modification mass" value="${potential_modifications}" type="Unknown" description=""/>
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218 <Attribute attributeName="minimum_fragment_mz" toolSpecificName="spectrum, minimum fragment mz" value="${minimum_fragment_mz}" type="Unknown" description=""/>
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219 <Attribute attributeName="cleavage_site" toolSpecificName="protein, cleavage site" value="${cleavage_site}" type="Unknown" description=""/>
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220 <Attribute attributeName="maximum_missed_cleavage_sites" toolSpecificName="scoring, maximum missed cleavage sites" value="${maximum_missed_cleavage_sites}" type="Unknown" description=""/>
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221 <Attribute attributeName="max_valid_expect" toolSpecificName="output, maximum valid expectation value" value="${max_valid_expect}" type="Unknown" description=""/>
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222 <Attribute attributeName="refinement" toolSpecificName="refine" value="${refinementOpt.refinement}" type="Unknown" description=""/>
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223 #if $refinementOpt.refinement == "yes"
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224 <Attribute attributeName="refine_point_mutation" toolSpecificName="refine, point mutations" value="${refinementOpt.refine_point_mutation}" type="Unknown" description=""/>
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225 <Attribute attributeName="refine_potential_modifications" toolSpecificName="refine, potential modification mass" value="${refinementOpt.refine_potential_modifications}" type="Unknown" description=""/>
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226 <Attribute attributeName="refine_max_valid_expect" toolSpecificName="refine, maximum valid expectation value" value="${refinementOpt.refine_max_valid_expect}" type="Unknown" description=""/>
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227 #end if
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228 <Attribute attributeName="reverse_scoring" toolSpecificName="scoring, include reverse" value="${reverse_scoring}" type="Unknown" description=""/>
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229 </Parameters>
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230 </tns:Program>
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231 </configfile>
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232 </configfiles>
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233 <outputs>
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234 <data name="outputFile" format="bioml" label="${tool.name} on ${on_string} - Results XML">
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235 <change_format>
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236 <when input="fileType.type" value="fileSet" format="prims.fileset.zip" />
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237 </change_format>
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238 </data>
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239 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"> </data>
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240 <data name="outTsv" format="tabular" label="${tool.name} on ${on_string} - TSV report"> </data>
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241 </outputs>
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242 <tests>
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243 <test>
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244 </test>
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245 </tests>
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246 <help>
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247
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248 .. class:: infomark
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249
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250 This tool searches MS/MS spectra against a database using X!Tandem.
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251
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252 For a complete set of parameters and their default values see `the X!Tandem parameters documentation page`_ .
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253 Parameters that are not
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254 made available in the UI above but are listed in the given link are submitted with their
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255 default values.
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256
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257 For more information on the refine step see: `Why should I use "refinement" to find modifications?`_ .
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258
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259 For more information on the expectation value calculation see:
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260 `A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes`_
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261 , David Fenyö and Ronald C. Beavis, Anal. Chem., 2003, 75, 768-774.
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262 This reference describes how peptides are scored by X!Tandem.
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263 The expectation values on the individual peptides are calculated using this method.
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264 <!-- Add this from Ron's email ? :
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265 They are an estimate of the spectrum-to-peptide match E-value associated with the
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266 null-hypothesis "all spectrum-to-peptide matches are stochasitic".
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267 -->
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268
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269 .. _the X!Tandem parameters documentation page: http://www.thegpm.org/tandem/api/index.html
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270
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271 .. _Why should I use "refinement" to find modifications?: http://www.thegpm.org/GPM/refine.html
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272
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273 .. _A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes: http://www.ncbi.nlm.nih.gov/pubmed/12622365
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274
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275 -----
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276
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277 **Output**
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278
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279 This tools returns the X!Tandem XML output which can be converted to MzIdentML using the DBSearch converter tool.
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280
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281 It also returns an HTML file with the list of peptides and the option to visualize the peptide to spectrum match
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282 using an embedded spectrum viewer.
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283
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284 .. image:: $PATH_TO_IMAGES/xtandem_results_viewer.png
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285
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286 Last but not least, it returns the list of identifications in TSV (tab separated values) format for users that are satisfied with this
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287 and do not need further processing steps like protein inference.
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288
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289 For the GPM web UI of X!Tandem see:
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290 http://ppp.thegpm.org/tandem/thegpm_ppp.html
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291
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292 </help>
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293 </tool> |
