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annotate pepquery2.xml @ 0:a07976bbc4d9 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
author galaxyp
date Sun, 06 Nov 2022 16:25:25 +0000
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a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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1 <tool id="pepquery2" name="PepQuery2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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2 <description>Peptide-centric search engine for novel peptide identification and validation.</description>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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3 <macros>
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4 <import>macros.xml</import>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" description="Failed" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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11 <regex match="Exception"
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12 source="stderr"
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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13 level="fatal"
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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14 description="java Exception" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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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"
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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20 ln -s '$req_inputs.db_type.db_file' '$db_file' &&
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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21 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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22 #if $req_inputs.ms_dataset.ms_dataset_type == 'history'
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23 @INDEX_SPECTRUM_FILES@
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24 $index_spectrum_files($ms_index.files_path, $req_inputs.ms_dataset.spectrum_files) &&
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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25 #elif $req_inputs.ms_dataset.ms_dataset_type == 'indexed'
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26 #if $os.path.exists($os.path.join($req_inputs.ms_dataset.index.extra_files_path, 'summary.txt'))
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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27 #set $index_dir = 'index_dir'
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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28 ln -s '$req_inputs.ms_dataset.index.extra_files_path' index_dir &&
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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29 #else
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30 #raise ValueError
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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31 #end if
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32 #end if
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33 ## PepQuery command
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34 pepquery
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35 -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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36 #if $validation.task_type == "known"
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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37 -s 2 $validation.decoy
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38 #else
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39 -s 1
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40 #end if
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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41 #if $req_inputs.ms_dataset.ms_dataset_type in ['history', 'indexed']
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42 -ms '$index_dir'
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43 #elif $req_inputs.ms_dataset.ms_dataset_type in ['PepQueryDB', 'public']
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44 -b '$req_inputs.ms_dataset.dataset'
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45 #end if
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46
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47 #if $req_inputs.db_type.db_type_selector == 'history'
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48 -db '$db_file'
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49 #else
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50 -db '$req_inputs.db_type.db_id'
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51 #end if
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52 #if $req_inputs.input_type.input_type_selector == 'peptide'
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53 -t $req_inputs.input_type.input_type_selector
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54 -i '$req_inputs.input_type.multiple.input'
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55 #else
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56 -t $req_inputs.input_type.input_type_selector
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57 #if $req_inputs.input_type.input_type_selector == 'protein'
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58 #if $req_inputs.input_type.multiple.protein_input_selector == 'identifier'
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59 #set $prot_id = str($req_inputs.input_type.multiple.input).replace('|','\|')
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60 -i '"$prot_id"'
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61 #else
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62 -i '$req_inputs.input_type.multiple.input'
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63 #end if
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64 #else
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65 -i '$req_inputs.input_type.input'
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66 #if $req_inputs.input_type.input_type_selector == 'DNA'
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67 #if $req_inputs.input_type.frame == 'None'
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68 -frame '0'
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69 #else
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70 -frame '$req_inputs.input_type.frame'
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71 #end if
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72 #else
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73 -anno '$req_inputs.input_type.anno'
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74 #end if
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75 #end if
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76 #end if
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77 #if $req_inputs.indexType
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78 -indexType $req_inputs.indexType
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79 #end if
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80
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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81 #if $modifications.fixed_mod
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82 -fixMod '$modifications.fixed_mod'
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83 #end if
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84 #if $modifications.var_mod
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85 -varMod '$modifications.var_mod'
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86 #end if
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87 #if $digestion.enzyme
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88 -e '$digestion.enzyme'
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89 #end if
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90 #if $digestion.max_missed_cleavages
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91 -c '$digestion.max_missed_cleavages'
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92 #end if
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93
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94 #if $modifications.max_mods
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95 -maxVar '$modifications.max_mods'
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96 #end if
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97 $modifications.unmodified
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98 $modifications.aa
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99 #if $ms_params.tolerance_params.precursor_tolerance
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100 -tol '$ms_params.tolerance_params.precursor_tolerance'
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101 #end if
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102
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103 #if $ms_params.tolerance_params.precursor_unit
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104 -tolu '$ms_params.tolerance_params.precursor_unit'
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105 #end if
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106 #if $ms_params.tolerance_params.tolerance
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107 -itol '$ms_params.tolerance_params.tolerance'
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108 #end if
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109 #if $ms_params.search.frag_method
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110 -fragmentMethod '$ms_params.search.frag_method'
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111 #end if
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112 #if $ms_params.search.scoring_method
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113 -m '$ms_params.search.scoring_method'
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114 #end if
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115 $ms_params.search.extra_score_validation
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116 #if $ms_params.search.max_charge
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117 -maxCharge '$ms_params.search.max_charge'
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118 #end if
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119 #if $ms_params.search.min_charge
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120 -minCharge '$ms_params.search.min_charge'
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121 #end if
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122 #if $ms_params.search.min_peaks
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123 -minPeaks '$ms_params.search.min_peaks'
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124 #end if
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125 #if $ms_params.search.isotope_error
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126 -ti '$ms_params.search.isotope_error'
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127 #end if
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128 #if $ms_params.search.min_score
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129 -minScore '$ms_params.search.min_score'
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130 #end if
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131 #if $ms_params.search.min_length
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132 -minLength '$ms_params.search.min_length'
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133 #end if
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134 #if $ms_params.search.max_length
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135 -maxLength '$ms_params.search.max_length'
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136 #end if
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137 #if $ms_params.search.num_random_peptides
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138 -n '$ms_params.search.num_random_peptides'
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139 #end if
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140 #if 'psm_annotation.txt' in $outputs_selected
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141 -plot
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142 #end if
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143 $fast
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144 -o pepquery_output
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145 | tee >(sed "s/\x1b[^m]*m//g" > log.txt)
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146 #set $flist = str($outputs_selected).replace(',',' ').replace('ms_index','')
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147 && for i in $flist; do for f in `find pepquery_output/*/* -name \$i`; do cat \$f >> pepquery_output/\${i}; done; done
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148 && for f in `find pepquery_output/*/ -name parameter.txt`; do cp \$f pepquery_output/parameter.txt; done
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149 ]]>
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150 </command>
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151 <inputs>
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152 <conditional name="validation">
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153 <param name="task_type" argument="-s" type="select" label="Validation Task Type">
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154 <option value="novel" selected="true">novel peptide/protein validation</option>
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155 <option value="known">known peptide/protein validation</option>
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156 </param>
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157 <when value="novel"/>
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158 <when value="known">
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159 <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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160 </when>
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161 </conditional>
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162 <section name="req_inputs" title="Input Data" expanded="true">
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163 <conditional name="input_type">
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164 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
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165 <option value="peptide">peptide</option>
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166 <option value="protein">protein</option>
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167 <option value="DNA">DNA (translate to protein sequences)</option>
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168 <!-- VCF,BED,GTF input options have not been implemented in this tool -->
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169 </param>
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170 <when value="peptide">
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171 <conditional name="multiple">
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172 <param name="peptide_input_selector" type="select" label="Peptides?">
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173 <option value="multiple">Peptide list from your history</option>
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174 <option value="single">Single peptide entered as text</option>
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175 </param>
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176 <when value="multiple">
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177 <param name="input" argument="-i" type="data" format="tabular" label="Peptide Sequences (.txt)">
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178 <help>Peptide sequence file containing peptides which you want to search (no column headers).
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179 First column is am peptide sequence. Optional second column is spectrum title.
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180 </help>
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181 </param>
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182 </when>
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183 <when value="single">
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184 <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search">
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185 <validator type="regex" message="Must be AA letters, multiple peptides separated by commas">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+(,[AC-IK-NP-TV-Yac-ik-np-tv-y]+)*$</validator>
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186 </param>
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187 </when>
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188 </conditional>
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189 </when>
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190 <when value="protein">
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191 <conditional name="multiple">
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192 <param name="protein_input_selector" type="select" label="Proteins?">
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193 <option value="multiple">Protein fasta from your history</option>
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194 <option value="single">Single protein entered as text</option>
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195 <option value="identifier">Protein Identifier from selected Protein Reference Database</option>
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196 </param>
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197 <when value="multiple">
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198 <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." />
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199 </when>
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200 <when value="single">
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201 <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search">
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202 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
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203 </param>
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204 </when>
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205 <when value="identifier">
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206 <param name="input" argument="-i" type="text" label="Protein Identifier" help="Protein ID from the selected Protein Reference Database. E.g. sp|P07205|PGK2_HUMAN from swissprot:human">
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207 <sanitizer invalid_char="">
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208 <valid initial="string.ascii_letters,string.digits">
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209 <add value="|" />
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210 </valid>
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211 </sanitizer>
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212 <validator type="regex" message="Spaces not allowed in ID">^[^ ]+$</validator>
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213 </param>
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214 </when>
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215 </conditional>
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216 </when>
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217 <when value="DNA">
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218 <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search">
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219 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator>
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220 </param>
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221 <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">
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222 <option value="1">1</option>
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223 <option value="2">2</option>
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224 <option value="3">3</option>
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225 <option value="4">4</option>
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226 <option value="5">5</option>
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227 <option value="6">6</option>
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228 </param>
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229 </when>
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230 </conditional>
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231 <conditional name="db_type">
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232 <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" >
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233 <option value="history">history</option>
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234 <option value="download">download</option>
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235 </param>
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236 <when value="history">
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237 <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." />
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238 </when>
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239 <when value="download">
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240 <param name="db_id" type="text" value="" label="Public protein sequence database">
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241 <help>Currently supported dowloads: gencode:human, swissprot:human, refseq:human</help>
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242 <option value="gencode:human">gencode:human</option>
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243 <option value="swissprot:human">swissprot:human</option>
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244 <option value="refseq:human">refseq:human</option>
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245 <validator type="regex" message="">^(swissprot|refseq|gencode):(human)$</validator>
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246 </param>
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247 </when>
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248 </conditional>
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249 <conditional name="ms_dataset">
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250 <param name="ms_dataset_type" type="select" label="MS/MS dataset to search" help="" >
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251 <option value="history"> Spectrum Datasets from history</option>
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252 <option value="indexed">Indexed MS/MS spectrums</option>
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253 <option value="PepQueryDB">PepQueryDB</option>
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254 <option value="public">public proteomics data repositories</option>
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255 </param>
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256 <when value="history">
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257 <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" />
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258 </when>
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259 <when value="indexed">
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260 <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
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261 </when>
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262 <when value="PepQueryDB">
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263 <param name="dataset" argument="-b" type="text" value="" label="PepQueryDB dataset">
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264 <help>PepQueryDB dataset IDs (separated by commas).</help>
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265 <expand macro="pepquerydb_options" />
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266 <validator type="regex" message="PepQueryDB dataset_name(,dataset_name)">^[a-zA-Z][^,]*(,[a-zA-Z][^,]*)*$</validator>
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267 </param>
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268 </when>
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269 <when value="public">
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270 <param name="dataset" type="text" value="" label="Public dataset">
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271 <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD|MSV|JPST).*$</validator>
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272 </param>
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273 </when>
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274 </conditional>
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275
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276 <param name="indexType" argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
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277 <option value="1">index (1-based) in MGF</option>
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278 <option value="2">spectrum title in MGF</option>
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279 </param>
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280 </section>
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281
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282 <param name="parameter_set" argument="-p" type="text" value="" optional="true" label="MS/MS searching parameter set name">
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283 <help>Currently supported set names start with: MS1 or TMT</help>
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284 <option value="MS1_H_MS2_H_LF">MS1_H_MS2_H_LF</option>
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285 <option value="MS1_H_MS2_L_LF">MS1_H_MS2_L_LF</option>
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286 <option value="TMT10_11">TMT10_11</option>
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287 <option value="TMT10_11_MS2_L">TMT10_11_MS2_L</option>
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288 <option value="TMT10_11_MS2_L_phosphorylation">TMT10_11_MS2_L_phosphorylation</option>
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289 <option value="TMT10_11_acetylation">TMT10_11_acetylation</option>
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290 <option value="TMT10_11_glycosylation">TMT10_11_glycosylation</option>
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291 <option value="TMT10_11_phosphorylation">TMT10_11_phosphorylation</option>
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292 <option value="TMT10_11_ubiquitination">TMT10_11_ubiquitination</option>
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293 </param>
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294
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295 <section name="modifications" title="Modifications" expanded="false">
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296 <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" optional="true">
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297 <help>Default: 1: Carbamidomethylation of C [57.02146372057]</help>
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298 <expand macro="modifications" />
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299 </param>
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300 <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" optional="true">
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301 <help>Default: 2: Oxidation of M [15.99491461956]</help>
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302 <expand macro="modifications" />
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303 </param>
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304
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305 <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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306 <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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307 <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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308 </section>
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309
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310 <section name="digestion" title="Digestion" expanded="false">
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311 <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion. Default: Trypsin" >
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312 <option value="0">Non enzyme</option>
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313 <option value="1">Trypsin</option>
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314 <option value="2">Trypsin (no P rule)</option>
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315 <option value="3">Arg-C</option>
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316 <option value="4">Arg-C (no P rule)</option>
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317 <option value="5">Arg-N</option>
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318 <option value="6">Glu-C</option>
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319 <option value="7">Lys-C</option>
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320 </param>
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321 <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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322 </section>
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323
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324 <section name="ms_params" title="Mass spectrometer" expanded="false">
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325 <section name="tolerance_params" title="Tolerance" expanded="true">
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326 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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327 <param name="precursor_unit" argument="-tolu" type="select" optional="true" label="Precursor Unit" help="The unit of precursor ion m/z tolerance. Default: ppm">
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328 <option value="ppm">ppm</option>
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329 <option value="Da">Da</option>
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330 </param>
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331 <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" />
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332 </section>
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333
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334 <section name="search" title="PSM" expanded="false">
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335 <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method" help="Default: CID/HCD">
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336 <option value="1">CID/HCD</option>
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337 <option value="2">ETD</option>
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338 </param>
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339 <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method" help="Default: HyperScore">
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340 <option value="1">HyperScore</option>
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341 <option value="2">MVH</option>
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342 </param>
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343 <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" />
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344 <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"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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345 <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" />
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346 <param name="min_peaks" argument="-minPeaks" type="integer" value="" optional="true" label="Minimum Peaks" help="Min peaks in spectrum. Default: 10" />
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347 <param name="isotope_error" argument="-ti" type="text" value="" optional="true" label="Isotope peak error range">
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348 <help>A comma-sepated range of integers from -2 to 2, e.g. '-1,0,1,2' Default: 0</help>
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349 <validator type="regex" message="">^((-2,)?-1,)?0(,1(,2)?)?$</validator>
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350 </param>
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351 <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" />
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352 <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" />
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353 <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" />
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354 <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" />
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355 </section>
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356 </section>
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357
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358 <param name="outputs_selected" type="select" multiple="true" optional="false" label="Select outputs">
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359 <option value="psm.txt">psm.txt</option>
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360 <option value="psm_rank.txt" selected="true">psm_rank.txt</option>
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361 <option value="psm_rank.mgf">psm_rank.mgf</option>
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362 <option value="psm_annotation.txt">psm_annotation.txt</option>
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363 <option value="psm_type.txt">psm_type.txt</option>
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364 <option value="detail.txt">detail.txt</option>
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365 <option value="ptm.txt">ptm.txt</option>
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366 <option value="ptm_detail.txt">ptm_detail.txt</option>
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367 <option value="ms_index">MS/MS Index</option>
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368 </param>
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369 <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." />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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370 </inputs>
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371 <outputs>
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372 <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
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373 </data>
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374 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">
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375 <filter>'parameter.txt' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
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376 </data>
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377 <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt">
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378 <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
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379 </data>
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380 <data name="psm_txt" format="tabular" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: psm.txt">
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381 <filter>'psm.txt' in outputs_selected</filter>
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382 <actions>
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383 <action name="comment_lines" type="metadata" default="1" />
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384 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue" />
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385 </actions>
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386 </data>
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387
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388 <data name="psm_rank_txt" format="tabular" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: psm_rank.txt">
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389 <filter>'psm_rank.txt' in outputs_selected</filter>
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390 <actions>
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391 <action name="comment_lines" type="metadata" default="1" />
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392 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,n_ptm,confident,ref_delta_score,mod_delta_score" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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393 </actions>
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394 </data>
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395
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396 <data name="psm_rank_mgf" format="mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: psm_rank.mgf">
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diff changeset
397 <filter>'psm_rank.mgf' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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398 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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399 <data name="psm_type_txt" format="tabular" from_work_dir="pepquery_output/psmi_type.txt" label="${tool.name} on ${on_string}: psm_type.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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400 <filter>'psm_type.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
401 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
402 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
403 <action name="column_names" type="metadata" default="peptide,spectrum_title,type" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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404 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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405 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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406 <data name="psm_annotation_txt" format="tabular" from_work_dir="pepquery_output/psm_annotation.txt" label="${tool.name} on ${on_string}: psm_annotation.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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407 <filter>'psm_annotation.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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408 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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409 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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410 <action name="column_names" type="metadata" default="peptide,modification,Query,calc_mr,observed_mz,charge,pepSeq,m_label,m_mz,m_intensity,mz,intensity" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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411 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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412 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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413 <data name="detail_txt" format="tabular" from_work_dir="pepquery_output/detail.txt" label="${tool.name} on ${on_string}: detail.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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414 <filter>'detail.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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415 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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416 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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417 <action name="column_names" type="metadata" default="spectrum_title,peptide,modification,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,score" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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418 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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419 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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420
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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421 <data name="ptm_txt" format="tabular" from_work_dir="pepquery_output/ptm.txt" label="${tool.name} on ${on_string}: ptm.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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422 <filter>'ptm.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
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423 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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424 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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425 <action name="column_names" type="metadata" default="spectrum_title,peptide,charge,exp_mass,pep_mass,tol_ppm,tol_da,isotope_error,modification,score" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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426 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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427 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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428 <data name="ptm_detail_txt" format="tabular" from_work_dir="pepquery_output/ptm_detail.txt" label="${tool.name} on ${on_string}: ptm_detail.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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429 <filter>'ptm_detail.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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430 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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431 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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432 <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" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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433 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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434 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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435
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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436 </outputs>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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437 <tests>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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438 <!-- Test-1 PepQueryDB peptide gencode:human -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
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439 <test expect_num_outputs="2">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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440 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
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441 <param name="task_type" value="novel"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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442 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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443 <section name="req_inputs">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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444 <conditional name="input_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
445 <param name="input_type_selector" value="peptide"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
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446 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
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447 <param name="peptide_input_selector" value="single" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
448 <param name="input" value="LVVVGADGVGK,AHSSMVGVNLPQK"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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449 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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450 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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451 <conditional name="db_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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452 <param name="db_type_selector" value="download" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
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453 <param name="db_id" value="gencode:human"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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454 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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455 <conditional name="ms_dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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456 <param name="ms_dataset_type" value="PepQueryDB"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
457 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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458 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
459 <param name="indexType" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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460 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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461 <param name="parameter_set" value=""/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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462 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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463 <param name="fixed_mod" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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464 <param name="var_mod" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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465 <param name="max_mods" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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466 <param name="unmodified" value="True"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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467 <param name="aa" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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468 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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469 <section name="digestion">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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470 <param name="enzyme" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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471 <param name="max_missed_cleavages" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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472 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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473 <section name="ms_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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474 <section name="tolerance_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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475 <param name="precursor_tolerance" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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476 <param name="precursor_unit" value="ppm"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
477 <param name="tolerance" value="0.6"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
478 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
479 <section name="search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
480 <param name="frag_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
481 <param name="scoring_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
482 <param name="extra_score_validation" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
483 <param name="min_charge" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
484 <param name="max_charge" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
485 <param name="min_peaks" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
486 <param name="isotope_error" value="0"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
487 <param name="min_score" value="12"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
488 <param name="min_length" value="7"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
489 <param name="max_length" value="45"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
490 <param name="num_random_peptides" value="1000"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
491 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
492 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
493 <output name="psm_rank_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
494 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
495 <has_text text="LVVVGADGVGK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
496 <not_has_text text="AHSSMVGVNLPQK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
497 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
498 <has_n_columns n="22" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
499 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
500 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
501 <output name="log_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
502 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
503 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
504 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
505 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
506 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
507
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
508 <!-- Test-2 PepQueryDB peptide gencode:human pep.txt -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
509 <test expect_num_outputs="2">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
510 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
511 <param name="task_type" value="novel"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
512 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
513 <section name="req_inputs">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
514 <conditional name="input_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
515 <param name="input_type_selector" value="peptide"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
516 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
517 <param name="peptide_input_selector" value="multiple" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
518 <param name="input" ftype="tabular" value="pep.txt"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
519 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
520 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
521 <conditional name="db_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
522 <param name="db_type_selector" value="download" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
523 <param name="db_id" value="gencode:human"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
524 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
525 <conditional name="ms_dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
526 <param name="ms_dataset_type" value="PepQueryDB"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
527 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
528 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
529 <param name="indexType" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
530 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
531 <param name="parameter_set" value=""/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
532 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
533 <param name="fixed_mod" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
534 <param name="var_mod" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
535 <param name="max_mods" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
536 <param name="unmodified" value="True"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
537 <param name="aa" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
538 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
539 <section name="digestion">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
540 <param name="enzyme" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
541 <param name="max_missed_cleavages" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
542 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
543 <section name="ms_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
544 <section name="tolerance_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
545 <param name="precursor_tolerance" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
546 <param name="precursor_unit" value="ppm"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
547 <param name="tolerance" value="0.6"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
548 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
549 <section name="search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
550 <param name="frag_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
551 <param name="scoring_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
552 <param name="extra_score_validation" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
553 <param name="min_charge" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
554 <param name="max_charge" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
555 <param name="min_peaks" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
556 <param name="isotope_error" value="0"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
557 <param name="min_score" value="12"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
558 <param name="min_length" value="7"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
559 <param name="max_length" value="45"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
560 <param name="num_random_peptides" value="1000"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
561 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
562 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
563 <output name="psm_rank_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
564 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
565 <has_text text="LVVVGADGVGK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
566 <not_has_text text="AHSSMVGVNLPQK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
567 <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
568 <has_n_columns n="22" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
569 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
570 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
571 <output name="log_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
572 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
573 <has_text text="Ignore peptide (reason: exist in reference database): AHSSMVGVNLPQK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
574 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
575 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
576 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
577
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
578 <!-- Test-3 MGF peptide Uniprot.fasta -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
579 <test expect_num_outputs="2">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
580 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
581 <param name="task_type" value="novel"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
582 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
583 <section name="req_inputs">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
584 <conditional name="input_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
585 <param name="input_type_selector" value="peptide"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
586 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
587 <param name="peptide_input_selector" value="single" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
588 <param name="input" value="ELGSSDLTAR"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
589 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
590 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
591 <conditional name="db_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
592 <param name="db_type_selector" value="history" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
593 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
594 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
595 <conditional name="ms_dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
596 <param name="ms_dataset_type" value="history"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
597 <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
598 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
599 <param name="indexType" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
600 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
601 <param name="parameter_set" value=""/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
602 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
603 <!-- 21: iTRAQ 4-plex of K [144.1020624208] -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
604 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
605 <param name="fixed_mod" value="1,21,22"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
606 <!-- 2: Oxidation of M [15.99491461956] -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
607 <param name="var_mod" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
608 <param name="max_mods" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
609 <param name="unmodified" value="True"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
610 <param name="aa" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
611 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
612 <section name="digestion">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
613 <param name="enzyme" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
614 <param name="max_missed_cleavages" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
615 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
616 <section name="ms_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
617 <section name="tolerance_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
618 <param name="precursor_tolerance" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
619 <param name="precursor_unit" value="ppm"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
620 <param name="tolerance" value="0.6"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
621 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
622 <section name="search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
623 <param name="frag_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
624 <param name="scoring_method" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
625 <param name="extra_score_validation" value="False"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
626 <param name="min_charge" value="2"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
627 <param name="max_charge" value="3"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
628 <param name="min_peaks" value="10"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
629 <param name="isotope_error" value="0"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
630 <param name="min_score" value="12"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
631 <param name="min_length" value="7"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
632 <param name="max_length" value="45"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
633 <param name="num_random_peptides" value="1000"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
634 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
635 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
636 <output name="psm_rank_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
637 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
638 <has_text text="ELGSSDLTAR" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
639 <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+"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
640 <has_n_columns n="22" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
641 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
642 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
643 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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644
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
645 <!-- Test-4 PepQueryDB known peptide gencode:human pep.txt -->
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
646 <test expect_num_outputs="2">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
647 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
648 <param name="task_type" value="known"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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649 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
650 <section name="req_inputs">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
651 <conditional name="input_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
652 <param name="input_type_selector" value="peptide"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
653 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
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654 <param name="peptide_input_selector" value="single" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
655 <param name="input" value="AHSSMVGVNLPQK"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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656 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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657 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
658 <conditional name="db_type">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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659 <param name="db_type_selector" value="download" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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660 <param name="db_id" value="gencode:human"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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661 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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662 <conditional name="ms_dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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663 <param name="ms_dataset_type" value="PepQueryDB"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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664 <param name="dataset" value="CPTAC_LUAD_Discovery_Study_Proteome_PDC000153" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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665 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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666 <param name="indexType" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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667 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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668 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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669 <param name="unmodified" value="True"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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670 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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671 <output name="psm_rank_txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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672 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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673 <has_text text="AHSSMVGVNLPQK" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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674 <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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675 <has_n_columns n="22" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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676 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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677 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
678 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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679
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
680 </tests>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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681 <help><![CDATA[
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
682 **PepQuery2**
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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683
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
684 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.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
685
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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686
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
687 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.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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688
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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689 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.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
690
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
691 **Inputs**
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
692 - A sequence to match, one of the following:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
693
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
694 - A peptide string (or strings separated by commas)
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
695 - A history dataset with a list of peptides
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
696 - A protein string or a history dataset with a protein fasta
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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697 - A DNA string that is at least 60 base pairs in length
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
698
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
699
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
700 - MS/MS data used for identification, one of the following:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
701
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
702 - Mass Spectrometry history datasets in MGF, mzML, or mzXML format
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
703 - An Indexed MS/MS dataset (from previous PepQuery2 run or from **PepQuery2 index** tool.)
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
704 - PepQueryDB dataset IDs
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
705
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
706 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
707
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
708 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.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
709
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
710
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
711 - Dataset IDs from public proteomics data repositories: PRIDE, MassIVE, jPOSTrepo and iProX
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
712
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
713 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
714
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
715 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
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
716
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
717 - A reference protein fasta database, novel peptides matching a reference sequence will be excluded.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
718
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
719 - A protein fasta file
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
720 - The ID for a public reference protein database from RefSeq, GENCODE, Ensembl or UniProt.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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721
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
722
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
723 **Options**
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
724
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
725 - MS/MS searching parameter set name
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
726
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
727 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
728
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
729 Setting a *parameter set name* will change defaults for various options, These may be overridden by manually setting the option.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
730 The **PepQuery2 Show Sets** tool *PepQuery Predefined Parameter Sets* will list those available along with the option values that will be set.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
731 The **PepQuery2 Show Sets** tool *PepQuery Datasets* column *parameter_set* column for each PepQueryDB dataset.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
732
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
733
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
734 - Override default options
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
735
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
736 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
737
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
738 Values for modifications are provided in a select list.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
739 The **PepQuery2 Show Sets** tool *PepQuery Modifications* lists all available modifications.
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
740
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
741 **Outputs**
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
742 - Log.txt:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
743
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
744 - Logging output from PepQuery2
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
745 - When searching for *novel* peptides ignored peptide have a log message similar to:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
746
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
747 - Ignore peptide (reason: exist in reference database): *PEPTIDE*
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
748
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
749 - When searching for *known* proteins, ignored protein have a log message similar to:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
750
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
751 - Target protein is not present in database *DATABASE_NAME*: *PROTEIN_NAME*, ignored!
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
752
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
753 - Parameters:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
754
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
755 - parameters used in the search
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
756
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
757 - PSM - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
758
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
759 - peptide modification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
760
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
761 - PSM Rank - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
762
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
763 - peptide mo/dification n spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank n_ptm
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
764
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
765 - An MGF with the best matching spectrums
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
766
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
767 - Detail - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
768
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
769 - spectrum_title peptide modification pep_mass score
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
770
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
771 - PSM annotation - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
772
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
773 - peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
774
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
775 - PTM - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
776
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
777 - spectrum_title peptide charge exp_mass pep_mass tol_ppm tol_da isotope_error modification score
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
778
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
779 - PTM Detail - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
780
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
781 - 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
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
782
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
783 - An Indexed MS/MS dataset *when MS/MS data is MGF, mzML, or mzXML history datasets*
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
784
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
785
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
786 .. _PepQuery: http://pepquery.org/document.html
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
787
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
788 ]]></help>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
789 <expand macro="citations" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
790 </tool>