Mercurial > repos > galaxyp > pepquery2

annotate pepquery2.xml @ 1:6b5ce9e2b0d0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
author galaxyp
date Sun, 02 Oct 2022 23:50:18 +0000
parents 3c45645197f6
children 3b2874c58bcd
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3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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1 <tool id="pepquery2" name="PepQuery2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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2 <description>Peptide-centric search engine for novel peptide identification and validation.</description>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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3 <macros>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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4 <import>macros.xml</import>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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5 </macros>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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6 <requirements>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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8 </requirements>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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9 <stdio>
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10 <exit_code range="1:" level="fatal" description="Failed" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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11 <regex match="Exception"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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12 source="stderr"
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13 level="fatal"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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14 description="java Exception" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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15 </stdio>
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16 <command><![CDATA[
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17 @CMD_IMPORTS@
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18 #if $req_inputs.db_type.db_type_selector == 'history'
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19 #set $db_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.db_type.db_file.display_name.split('/')[-1])) + ".fa"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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20 ln -s '$req_inputs.db_type.db_file' '$db_file' &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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21 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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22 #if $req_inputs.ms_dataset.ms_dataset_type == 'history'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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23 @INDEX_SPECTRUM_FILES@
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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24 $index_spectrum_files($ms_index.files_path, $req_inputs.ms_dataset.spectrum_files) &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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25 #elif $req_inputs.ms_dataset.ms_dataset_type == 'indexed'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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26 #if $os.path.exists($os.path.join($req_inputs.ms_dataset.index.extra_files_path, 'summary.txt'))
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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27 #set $index_dir = 'index_dir'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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28 ln -s '$req_inputs.ms_dataset.index.extra_files_path' index_dir &&
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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29 #else
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30 #raise ValueError
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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31 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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32 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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33 ## PepQuery command
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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34 pepquery
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35 #if $validation.task_type == "known"
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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36 -s 2 $validation.decoy
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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37 #else
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38 -s 1
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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39 #end if
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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40 #if $req_inputs.ms_dataset.ms_dataset_type in ['history', 'indexed']
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41 -ms '$index_dir'
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42 #elif $req_inputs.ms_dataset.ms_dataset_type in ['PepQueryDB', 'public']
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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43 -b '$req_inputs.ms_dataset.dataset'
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44 #end if
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45
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46 #if $req_inputs.db_type.db_type_selector == 'history'
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47 -db '$db_file'
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48 #else
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49 -db '$req_inputs.db_type.db_id'
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50 #end if
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51 #if $req_inputs.input_type.input_type_selector == 'peptide'
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52 -t '$req_inputs.input_type.input_type_selector'
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53 -i '$req_inputs.input_type.multiple.input'
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54 #else
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55 -t '$req_inputs.input_type.input_type_selector'
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56 #if int(str($req_inputs.input_type.input_type_selector)) == 1
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57 -i '$req_inputs.input_type.multiple.input'
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58 #else
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59 -i '$req_inputs.input_type.input'
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60 #if int(str($req_inputs.input_type.input_type_selector)) == 2
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61 #if $req_inputs.input_type.frame == 'None'
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62 -f '0'
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63 #else
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64 -f '$req_inputs.input_type.frame'
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65 #end if
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66 #else
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67 -anno '$req_inputs.input_type.anno'
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68 #end if
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69 #end if
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70 #end if
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71 -indexType $req_inputs.indexType
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72
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73 #if $modifications.fixed_mod
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74 -fixMod '$modifications.fixed_mod'
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75 #end if
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76 #if $modifications.var_mod
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77 -varMod '$modifications.var_mod'
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78 #end if
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79 #if $digestion.enzyme
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80 -e '$digestion.enzyme'
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81 #end if
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82 #if $digestion.max_missed_cleavages
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83 -c '$digestion.max_missed_cleavages'
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84 #end if
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85
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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86 #if $modifications.max_mods
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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87 -maxVar '$modifications.max_mods'
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88 #end if
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89 $modifications.unmodified
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90 $modifications.aa
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91 #if $ms_params.tolerance_params.precursor_tolerance
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92 -tol '$ms_params.tolerance_params.precursor_tolerance'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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93 #end if
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94
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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95 #if $ms_params.tolerance_params.precursor_unit
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96 -tolu '$ms_params.tolerance_params.precursor_unit'
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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97 #end if
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98 #if $ms_params.tolerance_params.tolerance
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99 -itol '$ms_params.tolerance_params.tolerance'
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100 #end if
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101 #if $ms_params.search.frag_method
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102 -fragmentMethod '$ms_params.search.frag_method'
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103 #end if
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104 #if $ms_params.search.scoring_method
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105 -m '$ms_params.search.scoring_method'
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106 #end if
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107 $ms_params.search.extra_score_validation
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108 #if $ms_params.search.max_charge
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109 -maxCharge '$ms_params.search.max_charge'
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110 #end if
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111 #if $ms_params.search.min_charge
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112 -minCharge '$ms_params.search.min_charge'
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113 #end if
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114 #if $ms_params.search.min_peaks
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115 -minPeaks '$ms_params.search.min_peaks'
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116 #end if
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117 #if $ms_params.search.isotope_error
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118 -ti '$ms_params.search.isotope_error'
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119 #end if
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120 #if $ms_params.search.min_score
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121 -minScore '$ms_params.search.min_score'
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122 #end if
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123 #if $ms_params.search.min_length
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124 -minLength '$ms_params.search.min_length'
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125 #end if
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126 #if $ms_params.search.max_length
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127 -maxLength '$ms_params.search.max_length'
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128 #end if
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129 #if $ms_params.search.num_random_peptides
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130 -n '$ms_params.search.num_random_peptides'
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131 #end if
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132 #if 'psm_annotation.txt' in $outputs_selected
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133 -plot
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134 #end if
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135 $fast
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136 -o pepquery_output
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137 | sed 's/No valid peptide/Error: No valid peptide/' | tee >(cat 1>&2)
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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138 #set $flist = str($outputs_selected).replace(',',' ')
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139 && for i in $flist; do for f in `find pepquery_output/*/* -name \$i`; do cat \$f >> pepquery_output/\${i}; done; done
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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140 && for f in `find pepquery_output/*/ -name parameter.txt`; do cp \$f pepquery_output/parameter.txt; done
0
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141 ]]>
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142 </command>
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143 <inputs>
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144 <conditional name="validation">
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145 <param name="task_type" argument="-s" type="select" label="Validation Task Type">
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146 <option value="novel" selected="true">novel peptide/protein validation</option>
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147 <option value="known">known peptide/protein validation</option>
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148 </param>
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149 <when value="novel"/>
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150 <when value="known">
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151 <param name="decoy" argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
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152 </when>
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153 </conditional>
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154 <section name="req_inputs" title="Input Data" expanded="true">
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155 <conditional name="input_type">
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156 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
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157 <option value="peptide">peptide</option>
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158 <option value="1">protein</option>
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159 <option value="2">DNA (translate to protein sequences)</option>
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160 <!-- these are not working with pepquery version 1.6
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161 <option value="3">VCF (translate to protein sequences)</option>
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162 <option value="4">BED (translate to protein sequences)</option>
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163 <option value="5">GTF (translate to protein sequences)</option>
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164 -->
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165 </param>
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166 <when value="peptide">
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167 <conditional name="multiple">
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168 <param name="peptide_input_selector" type="select" label="Peptides?">
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169 <option value="multiple">Peptide list from your history</option>
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170 <option value="single">Single peptide entered as text</option>
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171 </param>
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172 <when value="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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173 <param name="input" argument="-i" type="data" format="txt" label="Peptide Sequences (.txt)" help="Peptide sequence file containing peptides which you want to search (no column header, 1 peptide per line)." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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174 </when>
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175 <when value="single">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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176 <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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177 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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178 </param>
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179 </when>
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180 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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181 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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182 <when value="1">
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galaxyp
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183 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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184 <param name="protein_input_selector" type="select" label="Proteins?">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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185 <option value="multiple">Protein fasta from your history</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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186 <option value="single">Single protein entered as text</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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187 </param>
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188 <when value="multiple">
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189 <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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190 </when>
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galaxyp
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191 <when value="single">
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192 <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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193 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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194 </param>
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195 </when>
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196 </conditional>
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197 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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198 <when value="2">
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199 <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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200 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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201 </param>
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202 <param name="frame" argument="-f" type="select" label="Frame(s) for DNA translation" multiple="true" help="The frame(s) to translate DNA sequence to protein. Selecting nothing (default) keeps the longest frame">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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203 <option value="1">1</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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204 <option value="2">2</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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205 <option value="3">3</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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206 <option value="4">4</option>
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galaxyp
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207 <option value="5">5</option>
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208 <option value="6">6</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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209 </param>
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210 </when>
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211 <!-- these are not working with pepquery version 1.6
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212 <when value="3">
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213 <param name="input" type="data" format="vcf" label="VCF File" argument="-i" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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214 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the VCF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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215 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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216 <when value="4">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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217 <param name="input" type="data" format="bed" label="BED File" argument="-i" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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218 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the BED file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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219 </when>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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220 <when value="5">
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galaxyp
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221 <param name="input" type="data" format="gtf" label="GTF File" argument="-i" help="" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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222 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the GTF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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223 </when>
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224 -->
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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225 </conditional>
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226 <conditional name="db_type">
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227 <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" >
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228 <option value="history">history</option>
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229 <option value="download">download</option>
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230 </param>
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231 <when value="history">
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232 <param name="db_file" argument="-db" type="data" format="fasta" label="Protein Reference Database File" help="an input sequence that matches a reference will be ignored." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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233 </when>
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234 <when value="download">
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235 <param name="db_id" type="text" value="" label="Public protein sequence database">
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236 <help>Currently supported dowloads: gencode:human, swissprot:human, refseq:human</help>
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237 <option value="gencode:human">gencode:human</option>
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238 <option value="swissprot:human">swissprot:human</option>
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239 <option value="refseq:human">refseq:human</option>
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240 <validator type="regex" message="">^(swissprot|refseq|gencode):(human)$</validator>
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241 </param>
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242 </when>
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243 </conditional>
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244 <conditional name="ms_dataset">
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245 <param name="ms_dataset_type" type="select" label="MS/MS dataset to search" help="" >
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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246 <option value="history"> Spectrum Datasets from history</option>
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247 <option value="indexed">Indexed MS/MS spectrums</option>
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248 <option value="PepQueryDB">PepQueryDB</option>
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249 <option value="public">public proteomics data repositories</option>
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250 </param>
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251 <when value="history">
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252 <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml,thermo.raw" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML,Thermo RAW" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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253 </when>
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254 <when value="indexed">
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255 <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
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256 </when>
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257 <when value="PepQueryDB">
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258 <param name="dataset" argument="-b" type="text" value="" label="PepQueryDB dataset">
1
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259 <help>PepQueryDB dataset IDs (separated by commas).</help>
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260 <expand macro="pepquerydb_options" />
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261 <validator type="regex" message="PepQueryDB dataset_name(,dataset_name)">^[a-zA-Z][^,]*(,[a-zA-Z][^,]*)*$</validator>
0
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262 </param>
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263 </when>
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264 <when value="public">
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265 <param name="dataset" type="text" value="" label="Public dataset">
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266 <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD|MSV|JPST).*$</validator>
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267 </param>
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268 </when>
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269 </conditional>
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270
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271 <param name="indexType" argument="-indexType" type="select" label="Report Spectrum Scan as" help="" >
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272 <option value="1" selected="true">index (1-based) in MGF</option>
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273 <option value="2">spectrum title in MGF</option>
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274 </param>
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275 </section>
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276
1
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277 <param name="parameter_set" argument="-p" type="text" value="" optional="true" label="MS/MS searching parameter set name">
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278 <help>Currently supported set names start with: MS1 or TMT</help>
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279 <option value="MS1_H_MS2_H_LF">MS1_H_MS2_H_LF</option>
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280 <option value="MS1_H_MS2_L_LF">MS1_H_MS2_L_LF</option>
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281 <option value="TMT10_11">TMT10_11</option>
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282 <option value="TMT10_11_MS2_L">TMT10_11_MS2_L</option>
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283 <option value="TMT10_11_MS2_L_phosphorylation">TMT10_11_MS2_L_phosphorylation</option>
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284 <option value="TMT10_11_acetylation">TMT10_11_acetylation</option>
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285 <option value="TMT10_11_glycosylation">TMT10_11_glycosylation</option>
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286 <option value="TMT10_11_phosphorylation">TMT10_11_phosphorylation</option>
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287 <option value="TMT10_11_ubiquitination">TMT10_11_ubiquitination</option>
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288 </param>
0
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289
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290 <section name="modifications" title="Modifications" expanded="false">
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291 <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" optional="true">
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292 <help>default: 1: Carbamidomethylation of C [57.02146372057]</help>
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293 <expand macro="modifications" />
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294 </param>
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295 <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" optional="true">
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296 <help>default: 2: Oxidation of M [15.99491461956]</help>
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297 <expand macro="modifications" />
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298 </param>
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299
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300 <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications Default: 3" />
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301 <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" />
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302 <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
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303 </section>
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304
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305 <section name="digestion" title="Digestion" expanded="false">
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306 <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion" >
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307 <option value="0">Non enzyme</option>
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308 <option value="1" selected="true">Trypsin</option>
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309 <option value="2">Trypsin (no P rule)</option>
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310 <option value="3">Arg-C</option>
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311 <option value="4">Arg-C (no P rule)</option>
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312 <option value="5">Arg-N</option>
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313 <option value="6">Glu-C</option>
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314 <option value="7">Lys-C</option>
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315 </param>
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316 <param name="max_missed_cleavages" argument="-c" type="integer" value="" optional="true" label="Max Missed Cleavages" help="The max missed cleavages" />
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317 </section>
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318
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319 <section name="ms_params" title="Mass spectrometer" expanded="false">
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320 <section name="tolerance_params" title="Tolerance" expanded="true">
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321 <param name="precursor_tolerance" argument="-tol" type="integer" value="" optional="true" label="Precursor Tolerance" help="The error window on experimental peptide mass values. This parameter is usually set according to the mass spectrometer which was used to generate the MS/MS data. Default: 10" />
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322 <param name="precursor_unit" argument="-tolu" type="select" optional="true" label="Precursor Unit" help="The unit of precursor ion m/z tolerance">
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323 <option value="ppm" selected="true">ppm</option>
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324 <option value="Da">Da</option>
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325 </param>
1
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326 <param name="tolerance" argument="-itol" type="float" value="" optional="true" label="Tolerance" help="Error window for MS/MS fragment ion mass values in Da unit. Default: 0.6 Da" />
0
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327 </section>
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328
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329 <section name="search" title="PSM" expanded="false">
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330 <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method">
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331 <option value="1" selected="true">CID/HCD</option>
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332 <option value="2">ETD</option>
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333 </param>
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334 <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method">
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335 <option value="1" selected="true">HyperScore</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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336 <option value="2">MVH</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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337 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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338 <param name="extra_score_validation" argument="-x" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Add extra score validation" help="use two scoring algorithms for peptide identification" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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339 <param name="min_charge" argument="-minCharge" type="integer" value="" optional="true" label="Minimum Charge" help="The minimum charge to consider if the charge state is not available. Default: 2"/>
1
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340 <param name="max_charge" argument="-maxCharge" type="integer" value="" optional="true" label="Maximum Charge" help="The maximum charge to consider if the charge state is not available. Default: 3" />
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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341 <param name="min_peaks" argument="-minPeaks" type="integer" value="" optional="true" label="Minimum Peaks" help="Min peaks in spectrum. Default: 10" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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342 <param name="isotope_error" argument="-ti" type="text" value="" optional="true" label="Isotope peak error range">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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343 <help>A comma-sepated range of integers from -2 to 2, e.g. '-1,0,1,2' Default: 0</help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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344 <validator type="regex" message="">^((-2,)?-1,)?0(,1(,2)?)?$</validator>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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345 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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346 <param name="min_score" argument="-minScore" type="integer" value="" min="0" optional="true" label="Minimum Score" help="Minimum score to consider for peptide searching. Default: 12" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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347 <param name="min_length" argument="-minLength" type="integer" value="" min="0" optional="true" label="Minimum length of peptide" help="The maximum length of peptide to consider. Default: 7" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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348 <param name="max_length" argument="-maxLength" type="integer" value="" min="0" optional="true" label="Maximum length of peptide" help="The maximum length of peptide to consider. Default: 45" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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349 <param name="num_random_peptides" argument="-n" type="integer" value="" min="0" optional="true" label="Number of Random Peptides" help="The number of random peptides. Default: 1000" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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350 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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351 </section>
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352
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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353 <param name="outputs_selected" type="select" multiple="true" optional="false" label="Select outputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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354 <option value="psm.txt" selected="true">psm.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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355 <option value="psm_rank.txt" selected="true">psm_rank.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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356 <option value="psm_rank.mgf" selected="true">psm_rank.mgf</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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357 <option value="psm_annotation.txt" selected="true">psm_annotation.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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358 <option value="psm_type.txt" selected="false">psm_type.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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359 <option value="detail.txt" selected="true">detail.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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360 <option value="ptm.txt" selected="true">ptm.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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361 <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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362 <option value="ptm_detail.txt" selected="true">ptm_detail.txt</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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363 <option value="ms_index" selected="true">MS/MS Index</option>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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364 </param>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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365 <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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366 </inputs>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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367 <outputs>
1
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368 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">
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369 </data>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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370 <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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371 <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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372 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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373 <data name="psm_txt" format="tabular" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: psm.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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374 <filter>'psm.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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375 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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376 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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377 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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378 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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379 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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380
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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381 <data name="psm_rank_txt" format="tabular" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: psm_rank.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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382 <filter>'psm_rank.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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383 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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384 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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385 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,n_ptm,confident,ref_delta_score,mod_delta_score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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386 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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387 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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388
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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389 <data name="psm_rank_mgf" format="mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: psm_rank.mgf">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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390 <filter>'psm_rank.mgf' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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391 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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392 <data name="psm_type_txt" format="tabular" from_work_dir="pepquery_output/psmi_type.txt" label="${tool.name} on ${on_string}: psm_type.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
393 <filter>'psm_type.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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394 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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395 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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396 <action name="column_names" type="metadata" default="peptide,spectrum_title,type" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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397 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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398 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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399 <data name="psm_annotation_txt" format="tabular" from_work_dir="pepquery_output/psm_annotation.txt" label="${tool.name} on ${on_string}: psm_annotation.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
400 <filter>'psm_annotation.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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401 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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402 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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403 <action name="column_names" type="metadata" default="peptide,modification,Query,calc_mr,observed_mz,charge,pepSeq,m_label,m_mz,m_intensity,mz,intensity" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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parents:
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404 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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405 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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406 <data name="detail_txt" format="tabular" from_work_dir="pepquery_output/detail.txt" label="${tool.name} on ${on_string}: detail.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
407 <filter>'detail.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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408 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
409 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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410 <action name="column_names" type="metadata" default="spectrum_title,peptide,modification,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,score" />
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411 </actions>
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412 </data>
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413
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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414 <data name="ptm_txt" format="tabular" from_work_dir="pepquery_output/ptm.txt" label="${tool.name} on ${on_string}: ptm.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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415 <filter>'ptm.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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416 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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417 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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418 <action name="column_names" type="metadata" default="spectrum_title,peptide,charge,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,modification,score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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419 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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420 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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421 <data name="ptm_detail_txt" format="tabular" from_work_dir="pepquery_output/ptm_detail.txt" label="${tool.name} on ${on_string}: ptm_detail.txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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422 <filter>'ptm_detail.txt' in outputs_selected</filter>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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423 <actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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424 <action name="comment_lines" type="metadata" default="1" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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425 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,ptm_spectrum_title,ptm_peptide,ptm_charge,ptm_exp_mass,ptm_pep_mass,ptm_tol_ppm,ptm_tol_da,ptm_isotope_error,ptm_modification,ptm_score" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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426 </actions>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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427 </data>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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428
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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429 </outputs>
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430 <tests>
1
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431 <!-- Test-1 PepQueryDB peptide gencode:human -->
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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432 <test>
1
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433 <conditional name="validation">
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434 <param name="task_type" value="novel"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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435 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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436 <section name="req_inputs">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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437 <conditional name="input_type">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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438 <param name="input_type_selector" value="peptide"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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439 <conditional name="multiple">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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440 <param name="peptide_input_selector" value="single" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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441 <param name="input" value="LVVVGADGVGK"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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442 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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443 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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444 <conditional name="db_type">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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445 <param name="db_type_selector" value="download" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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446 <param name="db_id" value="gencode:human"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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447 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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448 <conditional name="ms_dataset">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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449 <param name="ms_dataset_type" value="PepQueryDB"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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450 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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451 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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452 <param name="indexType" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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453 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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454 <param name="parameter_set" value=""/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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455 <section name="modifications">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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456 <param name="fixed_mod" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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457 <param name="var_mod" value="2"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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458 <param name="max_mods" value="3"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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459 <param name="unmodified" value="True"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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diff changeset
460 <param name="aa" value="False"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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461 </section>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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462 <section name="digestion">
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diff changeset
463 <param name="enzyme" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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464 <param name="max_missed_cleavages" value="2"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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465 </section>
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466 <section name="ms_params">
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467 <section name="tolerance_params">
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468 <param name="precursor_tolerance" value="10"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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469 <param name="precursor_unit" value="ppm"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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470 <param name="tolerance" value="0.6"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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471 </section>
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472 <section name="search">
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473 <param name="frag_method" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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474 <param name="scoring_method" value="1"/>
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475 <param name="extra_score_validation" value="False"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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476 <param name="min_charge" value="2"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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477 <param name="max_charge" value="3"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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478 <param name="min_peaks" value="10"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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479 <param name="isotope_error" value="0"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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480 <param name="min_score" value="12"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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481 <param name="min_length" value="7"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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482 <param name="max_length" value="45"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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483 <param name="num_random_peptides" value="1000"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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484 </section>
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485 </section>
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486 <output name="psm_txt">
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487 <assert_contents>
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488 <has_text text="LVVVGADGVGK" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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489 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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490 </assert_contents>
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491 </output>
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492 </test>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
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493
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
494 <!-- Test-2 MGF peptide Uniprot.fasta -->
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
495 <test>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
496 <conditional name="validation">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
497 <param name="task_type" value="novel"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
498 </conditional>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
499 <section name="req_inputs">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
500 <conditional name="input_type">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
501 <param name="input_type_selector" value="peptide"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
502 <conditional name="multiple">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
503 <param name="peptide_input_selector" value="single" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
504 <param name="input" value="ELGSSDLTAR"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
505 </conditional>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
506 </conditional>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
507 <conditional name="db_type">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
508 <param name="db_type_selector" value="history" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
509 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
510 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
511 <conditional name="ms_dataset">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
512 <param name="ms_dataset_type" value="history"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
513 <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
514 </conditional>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
515 <param name="indexType" value="1"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
516 </section>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
517 <param name="parameter_set" value=""/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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518 <section name="modifications">
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
519 <!-- 21: iTRAQ 4-plex of K [144.1020624208] -->
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
520 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
521 <param name="fixed_mod" value="1,21,22"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
522 <!-- 2: Oxidation of M [15.99491461956] -->
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
523 <param name="var_mod" value="2"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
524 <param name="max_mods" value="3"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
525 <param name="unmodified" value="True"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
526 <param name="aa" value="False"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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diff changeset
527 </section>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
528 <section name="digestion">
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
529 <param name="enzyme" value="1"/>
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
530 <param name="max_missed_cleavages" value="2"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
531 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
532 <section name="ms_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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diff changeset
533 <section name="tolerance_params">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
534 <param name="precursor_tolerance" value="10"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
535 <param name="precursor_unit" value="ppm"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
536 <param name="tolerance" value="0.6"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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537 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
538 <section name="search">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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diff changeset
539 <param name="frag_method" value="1"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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diff changeset
540 <param name="scoring_method" value="1"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
541 <param name="extra_score_validation" value="False"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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diff changeset
542 <param name="min_charge" value="2"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
543 <param name="max_charge" value="3"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
544 <param name="min_peaks" value="10"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
545 <param name="isotope_error" value="0"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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546 <param name="min_score" value="12"/>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
547 <param name="min_length" value="7"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
548 <param name="max_length" value="45"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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549 <param name="num_random_peptides" value="1000"/>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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550 </section>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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551 </section>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
552 <output name="psm_txt">
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
553 <assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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554 <has_text text="ELGSSDLTAR" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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555 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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556 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
557 <output name="psm_rank_txt">
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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558 <assert_contents>
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
559 <has_text text="ELGSSDLTAR" />
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
560 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t0\t1\t995\t0.002\d+\t1\t0\tYes\t24.1\d+\t24.1\d+"/>
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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561 </assert_contents>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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562 </output>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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563 </test>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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564
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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565 </tests>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
566 <help><![CDATA[
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
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diff changeset
567 **PepQuery2**
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
568
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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diff changeset
569 PepQuery_ is a universal targeted peptide search engine for identifying or validating known and novel peptides of interest in any local or publicly available mass spectrometry-based proteomics datasets.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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diff changeset
570
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
571
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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572 PepQuery_ is a peptide-centric search engine for novel peptide identification and validation. Cancer genomics studies have identified a large number of genomic alterations that may lead to novel, cancer-specific protein sequences. Proteins resulted from these genomic alterations are attractive candidates for cancer biomarkers and therapeutic targets. The leading approach to proteomic validation of genomic alterations is to analyze tandem mass spectrometry (MS/MS) data using customized proteomics databases created from genomics data. Such analysis is time-consuming and requires thorough training and detailed knowledge in proteomics data analysis, leading to a gap between MS/MS data and the cancer genomics community. PepQuery does not require customized databases and allows quick and easy proteomic validation of genomic alterations.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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diff changeset
573
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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diff changeset
574 PepQuery2 leverages a new MS/MS indexing approach and cloud storage to enable ultrafast, targeted identification of both novel and known peptides. PepQuery2 allows users to search more than one billion MS/MS data indexed in the PepQueryDB from any computers with internet access. It also supports direct analysis of user provided MS/MS data, any public datasets in PRIDE, MassIVE, jPOSTrepo and iProX, or Universal Spectrum Identifiers (USIs) from ProteomeXchange.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
575
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
576 **Inputs**
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
577 - A sequence to match, one of the following:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
578
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
579 - A peptide string (or strings separated by commas)
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
580 - A history dataset with a list of peptides
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
581 - A protein string or a history dataset with a protein fasta
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
582 - A DNA string that is at least 60 base pairs in length
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
parents:
diff changeset
583
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
584
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
585 - MS/MS data used for identification, one of the following:
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
586
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
587 - Mass Spectrometry history datasets in MGF, mzML, or mzXML format
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
588 - An Indexed MS/MS dataset (from previous PepQuery2 run or from **PepQuery2 index** tool.)
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
589 - PepQueryDB dataset IDs
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
590
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
591 ..
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
592
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
593 Multiple datasets from PepQueryDB must be separated by comma. A pattern to match datasets in PepQueryDB is also supported, for example, use 'CPTAC' to search all datasets contain 'CPTAC'. In addition, dataset selection from PepQueryDB based on data type (w:global proteome, p:phosphorylation, a:acetylation, u:ubiquitination, g:glycosylation) is also supported. For example, use 'p' to search all phosphoproteomics datasets in PepQueryDB. The **PepQuery2 Show Sets** tool will list available PepQueryDB datasets.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
594
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
595
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
596 - Dataset IDs from public proteomics data repositories: PRIDE, MassIVE, jPOSTrepo and iProX
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
597
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
598 ..
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
599
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
600 Dataset ID from public proteomics data repositories, one dataset is supported for each analysis. For example, use 'PXD000529' to use all MS/MS data from dataset PXD000529 or use 'PXD000529:LM3' to use data files containing LM3 from dataset PXD000529
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
601
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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diff changeset
602 - A reference protein fasta database, novel peptides matching a reference sequence will be excluded.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
603
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
604 - A protein fasta file
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
605 - The ID for a public reference protein database from RefSeq, GENCODE, Ensembl or UniProt.
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
606
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
607
1
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
608 **Options**
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
609
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
610 - MS/MS searching parameter set name
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
611
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
612 ..
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
613
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
614 Setting a *parameter set name* will change defaults for various options, These may be overridden by manually setting the option.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
615 The **PepQuery2 Show Sets** tool *PepQuery Predefined Parameter Sets* will list those available along with the option values that will be set.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
616 The **PepQuery2 Show Sets** tool *PepQuery Datasets* column *parameter_set* column for each PepQueryDB dataset.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
617
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
618
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
parents: 0
diff changeset
619 - Override default options
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
620
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
621 ..
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
622
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
623 Values for modifications are provided in a select list.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
624 The **PepQuery2 Show Sets** tool *PepQuery Modifications* lists all available modifications.
6b5ce9e2b0d0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 3f50a508dbb9050be48de5685cec9a82683d8457
galaxyp
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diff changeset
625
0
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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626 **Outputs**
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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627 - Parameters:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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628
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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629 - parameters used in the search
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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630
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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631 - PSM - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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632
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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633 - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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634
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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635 - PSM Rank - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
636
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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637 - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank *n_ptm*
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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638
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
639 - An MGF with the best matching spectrums
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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640
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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641 - Detail - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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642
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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643 - spectrum_title peptide modification pep_mass score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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644
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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645 - PSM annotation - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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646
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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647 - peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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diff changeset
648
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
649 - PTM - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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650
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
651 - spectrum_title peptide charge exp_mass pep_mass tol_ppm tol_da isotope_error modification score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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652
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
653 - PTM Detail - tabular with columns:
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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654
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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655 - peptide modification n spectrum_title charge exp_mass tol_ppm tol_da isotope_error pep_mass mz score n_db total_db n_random total_random pvalue rank ptm_spectrum_title ptm_peptide ptm_charge ptm_exp_mass ptm_pep_mass ptm_tol_ppm ptm_tol_da ptm_isotope_error ptm_modification ptm_score
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
656
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
galaxyp
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diff changeset
657 - An Indexed MS/MS dataset *when MS/MS data is MGF, mzML, or mzXML history datasets*
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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658
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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659 The *n_ptm* field is added when using unrestricted modification searching (-um).
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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660
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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661 .. _PepQuery: http://pepquery.org/document.html
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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662
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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663 ]]></help>
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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664 <expand macro="citations" />
3c45645197f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 05525c46f05b74566fc162f5ad9c792f3e28811d
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665 </tool>