Mercurial > repos > iracooke > xtandem

annotate tandem.xml @ 20:9765dd041c04 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Wed, 21 Oct 2015 02:28:53 -0400
parents fc1decb780ba
children
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iracooke
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1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.1">
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2 <description>Run an X!Tandem Search</description>
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3 <requirements>
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iracooke
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4 <container type="docker">iracooke/protk-1.4.3</container>
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iracooke
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5 <requirement type="package" version="1.4.3">protk</requirement>
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iracooke
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6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
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7 </requirements>
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8 <command>
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9 #if $database.source_select=="built_in":
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10 tandem_search.rb -d $database.dbkey
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11 #else
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12 tandem_search.rb -d $database.fasta_file
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13 #end if
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14
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15 #if $tandem_params.source_select=="built_in":
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16 -T $tandem_params.paramskey
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17 #else
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18 -T $tandem_params.params_file
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19 #end if
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22 --var-mods='
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23 $variable_mods
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24 #for $custom_variable_mod in $custom_variable_mods:
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25 ,${custom_variable_mod.custom_mod}
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26 #end for
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27 '
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29 --fix-mods='
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30 $fixed_mods
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31 #for $custom_fix_mod in $custom_fix_mods:
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32 ,${custom_fix_mod.custom_mod}
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33 #end for
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34 '
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35
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36 $input_file -o $output -r
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38 --enzyme=$enzyme
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39
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40 --precursor-ion-tol-units=$precursor_tolu
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41 -v $missed_cleavages
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42 -f $fragment_ion_tol
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43 -p $precursor_ion_tol
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44 $allow_multi_isotope_search
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45 $acetyl_protein_nterm
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46 $cleavage_semi
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47 $keep_spectra
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48 --threads "\${GALAXY_SLOTS:-12}"
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49
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50 </command>
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51 <inputs>
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52 <conditional name="database">
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53 <param name="source_select" type="select" label="Database source">
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54 <option value="built_in">Built-In</option>
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55 <option value="input_ref" selected="true">Your Upload File</option>
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56 </param>
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57 <when value="built_in">
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58 <param name="dbkey" type="select" format="text" >
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59 <label>Database</label>
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60 <options from_file="pepxml_databases.loc">
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61 <column name="name" index="0" />
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62 <column name="value" index="2" />
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63 </options>
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64 </param>
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65 </when>
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66 <when value="input_ref">
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67 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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68 </when>
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69 </conditional>
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70 <conditional name="tandem_params">
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71 <param name="source_select" type="select" label="Baseline Parameters">
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72 <option value="built_in" selected="true">Built-In</option>
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73 <option value="input_ref">Custom parameter file</option>
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74 </param>
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75 <when value="built_in">
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76 <param name="paramskey" type="select" format="text" >
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77 <label>Paramset</label>
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78 <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option>
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79 <option value="isb_native">ISB Native</option>
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80 <option value="gpm">GPM</option>
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81 </param>
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82 </when>
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83 <when value="input_ref">
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84 <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
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85 </when>
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86 </conditional>
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87
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88 <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/>
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89
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90 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
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91 clicking to select multiple items">
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92 <options from_file="tandem_mods.loc">
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iracooke
parents: 17
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93 <column name="name" index="0" />
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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94 <column name="value" index="2" />
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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95 </options>
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iracooke
parents: 17
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96 </param>
17
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simonalpha
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97
18
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iracooke
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98 <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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99 <param name="custom_mod" type="text">
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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100 </param>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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101 </repeat>
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iracooke
parents: 17
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102
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iracooke
parents: 17
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103 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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104 clicking to select multiple items">
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iracooke
parents: 17
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105 <options from_file="tandem_mods.loc">
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iracooke
parents: 17
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106 <column name="name" index="0" />
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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107 <column name="value" index="2" />
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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108 </options>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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109 </param>
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simonalpha
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110
18
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iracooke
parents: 17
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111 <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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112 <param name="custom_mod" type="text">
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iracooke
parents: 17
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113 </param>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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114 </repeat>
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simonalpha
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115
18
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iracooke
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116 <param name="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" />
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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117 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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118 <label>Missed Cleavages Allowed</label>
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iracooke
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119 <option value="0">0</option>
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iracooke
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120 <option value="1">1</option>
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iracooke
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121 <option selected="true" value="2">2</option>
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iracooke
parents: 17
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122 </param>
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simonalpha
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123
18
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
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124 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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125 <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>
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126
18
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iracooke
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127 <param name="enzyme" type="select" format="text">
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iracooke
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128 <label>Enzyme</label>
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iracooke
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129 <option value="[R]__pc__{P}">argc - [R]|{P}</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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130 <option value="[X]__pc__[D]">aspn - [X]|[D]</option>
19
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131 <option value="[FLWY]__pc__{P}">chymotrypsin - [FLWY]|{P}</option>
18
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132 <option value="[R]__pc__[X]">clostripain - [R]|[X]</option>
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iracooke
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133 <option value="[M]__pc__{X}">cnbr - [M]|{X}</option>
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iracooke
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134 <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option>
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iracooke
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135 <option value="[D]__pc__{P}">formicacid - [D]|{P}</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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136 <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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137 <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option>
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iracooke
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138 <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option>
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iracooke
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139 <option value="[K]__pc__{P}">lysc - [K]|{P}</option>
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iracooke
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140 <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option>
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iracooke
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141 <option value="[X]__pc__[K]">lysn - [X]|[K]</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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142 <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option>
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iracooke
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143 <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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144 <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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145 <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option>
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iracooke
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146 <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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147 <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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148 <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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149 <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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150 <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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151 <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option>
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iracooke
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152 </param>
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153
18
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154 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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155 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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156 <param name="precursor_tolu" type="select" format="text">
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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157 <label>Precursor Ion Tolerance Units</label>
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158 <option value="ppm">ppm</option>
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159 <option value="Da">Da</option>
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iracooke
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160 </param>
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161 <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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162 </inputs>
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163 <outputs>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
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164 <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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165 </outputs>
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166 <tests>
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iracooke
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167 <!-- Just test that the tool runs and produces vaguely correct output -->
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168 <test>
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169 <param name="source_select" value="input_ref"/>
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170 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
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171 <param name="input_file" value="tiny.mzML" format="mzml"/>
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iracooke
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172 <output name="output" format="tandem">
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173 <assert_contents>
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174 <has_text text="tandem-style" />
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175 </assert_contents>
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176 </output>
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177 </test>
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178 </tests>
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179 <help>
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180
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181 **What it does**
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182
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183 Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
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184
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185 ----
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186
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187 **References**
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188
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189 Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
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190
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191 </help>
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192
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193 </tool>