Mercurial > repos > iracooke > xtandem

annotate tandem.xml @ 19:fc1decb780ba draft

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:47:33 -0400
parents 529ea20c1e6c
children 9765dd041c04
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19
fc1decb780ba planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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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5 <requirement type="package" version="1.4.3">protk</requirement>
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6 </requirements>
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7 <command>
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8 #if $database.source_select=="built_in":
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9 tandem_search.rb -d $database.dbkey
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10 #else
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11 tandem_search.rb -d $database.fasta_file
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12 #end if
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13
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14 #if $tandem_params.source_select=="built_in":
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15 -T $tandem_params.paramskey
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16 #else
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17 -T $tandem_params.params_file
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18 #end if
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21 --var-mods='
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22 $variable_mods
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23 #for $custom_variable_mod in $custom_variable_mods:
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24 ,${custom_variable_mod.custom_mod}
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25 #end for
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26 '
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28 --fix-mods='
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29 $fixed_mods
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30 #for $custom_fix_mod in $custom_fix_mods:
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31 ,${custom_fix_mod.custom_mod}
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32 #end for
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33 '
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34
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35 $input_file -o $output -r
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36
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37 --enzyme=$enzyme
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38
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39 --precursor-ion-tol-units=$precursor_tolu
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40 -v $missed_cleavages
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41 -f $fragment_ion_tol
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42 -p $precursor_ion_tol
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43 $allow_multi_isotope_search
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44 $acetyl_protein_nterm
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45 $cleavage_semi
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46 $keep_spectra
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47 --threads "\${GALAXY_SLOTS:-12}"
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48
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49 </command>
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50 <inputs>
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51 <conditional name="database">
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52 <param name="source_select" type="select" label="Database source">
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53 <option value="built_in">Built-In</option>
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54 <option value="input_ref" selected="true">Your Upload File</option>
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55 </param>
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56 <when value="built_in">
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57 <param name="dbkey" type="select" format="text" >
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58 <label>Database</label>
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59 <options from_file="pepxml_databases.loc">
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60 <column name="name" index="0" />
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61 <column name="value" index="2" />
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62 </options>
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63 </param>
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64 </when>
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65 <when value="input_ref">
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66 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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67 </when>
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68 </conditional>
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69 <conditional name="tandem_params">
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70 <param name="source_select" type="select" label="Baseline Parameters">
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71 <option value="built_in" selected="true">Built-In</option>
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72 <option value="input_ref">Custom parameter file</option>
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73 </param>
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74 <when value="built_in">
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75 <param name="paramskey" type="select" format="text" >
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76 <label>Paramset</label>
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77 <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option>
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78 <option value="isb_native">ISB Native</option>
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79 <option value="gpm">GPM</option>
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80 </param>
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81 </when>
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82 <when value="input_ref">
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83 <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
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84 </when>
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85 </conditional>
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86
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87 <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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88
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89 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
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90 clicking to select multiple items">
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91 <options from_file="tandem_mods.loc">
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92 <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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93 <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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94 </options>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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95 </param>
17
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simonalpha
parents:
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96
18
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iracooke
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97 <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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98 <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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99 </param>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
diff changeset
100 </repeat>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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101
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iracooke
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102 <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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103 clicking to select multiple items">
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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104 <options from_file="tandem_mods.loc">
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
parents: 17
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105 <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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106 <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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107 </options>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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108 </param>
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simonalpha
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109
18
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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110 <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
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111 <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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112 </param>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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113 </repeat>
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114
18
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115 <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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116 <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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117 <label>Missed Cleavages Allowed</label>
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iracooke
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118 <option value="0">0</option>
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iracooke
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119 <option value="1">1</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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120 <option selected="true" value="2">2</option>
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iracooke
parents: 17
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121 </param>
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simonalpha
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122
18
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123 <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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124 <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>
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125
18
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iracooke
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126 <param name="enzyme" type="select" format="text">
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iracooke
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127 <label>Enzyme</label>
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iracooke
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128 <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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129 <option value="[X]__pc__[D]">aspn - [X]|[D]</option>
19
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130 <option value="[FLWY]__pc__{P}">chymotrypsin - [FLWY]|{P}</option>
18
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131 <option value="[R]__pc__[X]">clostripain - [R]|[X]</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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132 <option value="[M]__pc__{X}">cnbr - [M]|{X}</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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133 <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option>
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iracooke
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134 <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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135 <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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136 <option value="[E]__pc__{P}">gluc_bicarb - [E]|{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="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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138 <option value="[K]__pc__{P}">lysc - [K]|{P}</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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139 <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
iracooke
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140 <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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141 <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</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__[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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143 <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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144 <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option>
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iracooke
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145 <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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146 <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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147 <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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148 <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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149 <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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150 <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option>
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iracooke
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151 </param>
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152
18
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153 <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
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154 <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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155 <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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156 <label>Precursor Ion Tolerance Units</label>
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157 <option value="ppm">ppm</option>
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158 <option value="Da">Da</option>
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159 </param>
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160 <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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161 </inputs>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
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162 <outputs>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
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163 <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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164 </outputs>
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165 <tests>
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iracooke
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166 <!-- Just test that the tool runs and produces vaguely correct output -->
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167 <test>
529ea20c1e6c planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 5d6553181ff8adae2c12c30eaf10e74563e8f1aa
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168 <param name="source_select" value="input_ref"/>
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169 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
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170 <param name="input_file" value="tiny.mzML" format="mzml"/>
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171 <output name="output" format="tandem">
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172 <assert_contents>
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173 <has_text text="tandem-style" />
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174 </assert_contents>
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175 </output>
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176 </test>
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177 </tests>
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178 <help>
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179
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180 **What it does**
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181
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182 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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183
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184 ----
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185
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186 **References**
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187
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188 Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
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189
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190 </help>
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191
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192 </tool>