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annotate pepquery2.xml @ 2:c32806a80862 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 22916ed24dfb8452c8142e5d6b282d0e931af91f
author galaxyp
date Wed, 08 May 2024 17:12:21 +0000
parents b5489f81c2fa
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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@">
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2 <description>Peptide-centric search engine for novel peptide identification and validation.</description>
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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"
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13 level="fatal"
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14 description="java Exception" />
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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' &&
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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
1
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36 #if $digestion.enzyme == '0'
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37 -XX:ThreadStackSize=2048
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38 #end if
0
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39 #if $validation.task_type == "known"
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40 -s 2 $validation.decoy
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41 #else
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42 -s 1
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43 #end if
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44 #if $req_inputs.ms_dataset.ms_dataset_type in ['history', 'indexed']
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45 -ms '$index_dir'
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46 #elif $req_inputs.ms_dataset.ms_dataset_type in ['PepQueryDB', 'public']
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47 -b '$req_inputs.ms_dataset.dataset'
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48 #end if
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49
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50 #if $req_inputs.db_type.db_type_selector == 'history'
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51 -db '$db_file'
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52 #else
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53 -db '$req_inputs.db_type.db_id'
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54 #end if
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55 #if $req_inputs.input_type.input_type_selector == 'peptide'
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56 -t $req_inputs.input_type.input_type_selector
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57 -i '$req_inputs.input_type.multiple.input'
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58 #else
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59 -t $req_inputs.input_type.input_type_selector
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60 #if $req_inputs.input_type.input_type_selector == 'protein'
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61 #if $req_inputs.input_type.multiple.protein_input_selector == 'identifier'
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62 #set $prot_id = str($req_inputs.input_type.multiple.input).replace('|','\|')
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63 -i '"$prot_id"'
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64 #else
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65 -i '$req_inputs.input_type.multiple.input'
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66 #end if
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67 #else
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68 -i '$req_inputs.input_type.input'
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69 #if $req_inputs.input_type.input_type_selector == 'DNA'
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70 #if $req_inputs.input_type.frame == 'None'
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71 -frame '0'
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72 #else
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73 -frame '$req_inputs.input_type.frame'
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74 #end if
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75 #else
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76 -anno '$req_inputs.input_type.anno'
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77 #end if
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78 #end if
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79 #end if
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80 #if $req_inputs.indexType
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81 -indexType $req_inputs.indexType
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82 #end if
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83
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84 #if $modifications.fixed_mod
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85 -fixMod '$modifications.fixed_mod'
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86 #end if
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87 #if $modifications.var_mod
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88 -varMod '$modifications.var_mod'
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89 #end if
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90 #if $digestion.enzyme
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91 -e '$digestion.enzyme'
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92 #end if
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93 #if $digestion.max_missed_cleavages
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94 -c '$digestion.max_missed_cleavages'
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95 #end if
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96
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97 #if $modifications.max_mods
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98 -maxVar '$modifications.max_mods'
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99 #end if
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100 $modifications.unmodified
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101 $modifications.aa
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102 #if $ms_params.tolerance_params.precursor_tolerance
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103 -tol '$ms_params.tolerance_params.precursor_tolerance'
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104 #end if
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105
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106 #if $ms_params.tolerance_params.precursor_unit
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107 -tolu '$ms_params.tolerance_params.precursor_unit'
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108 #end if
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109 #if $ms_params.tolerance_params.tolerance
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110 -itol '$ms_params.tolerance_params.tolerance'
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111 #end if
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112 #if $ms_params.search.frag_method
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113 -fragmentMethod '$ms_params.search.frag_method'
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114 #end if
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115 #if $ms_params.search.scoring_method
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116 -m '$ms_params.search.scoring_method'
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117 #end if
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118 $ms_params.search.extra_score_validation
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119 #if $ms_params.search.max_charge
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120 -maxCharge '$ms_params.search.max_charge'
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121 #end if
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122 #if $ms_params.search.min_charge
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123 -minCharge '$ms_params.search.min_charge'
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124 #end if
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125 #if $ms_params.search.min_peaks
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126 -minPeaks '$ms_params.search.min_peaks'
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127 #end if
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128 #if $ms_params.search.isotope_error
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129 -ti '$ms_params.search.isotope_error'
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130 #end if
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131 #if $ms_params.search.min_score
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132 -minScore '$ms_params.search.min_score'
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133 #end if
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134 #if $ms_params.search.min_length
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135 -minLength '$ms_params.search.min_length'
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136 #end if
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137 #if $ms_params.search.max_length
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138 -maxLength '$ms_params.search.max_length'
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139 #end if
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140 #if $ms_params.search.num_random_peptides
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141 -n '$ms_params.search.num_random_peptides'
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142 #end if
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143 #if 'psm_annotation.txt' in $outputs_selected
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144 -plot
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145 #end if
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146 $fast
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147 -o pepquery_output
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148 | tee >(sed "s/\x1b[^m]*m//g" > log.txt)
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149 #set $flist = str($outputs_selected).replace(',',' ').replace('ms_index','')
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150 && 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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151 && for f in `find pepquery_output/*/ -name parameter.txt`; do cp \$f pepquery_output/parameter.txt; done
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152 ]]>
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153 </command>
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154 <inputs>
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155 <conditional name="validation">
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156 <param name="task_type" argument="-s" type="select" label="Validation Task Type">
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157 <option value="novel" selected="true">novel peptide/protein validation</option>
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158 <option value="known">known peptide/protein validation</option>
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159 </param>
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160 <when value="novel"/>
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161 <when value="known">
2
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162 <param argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
0
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163 </when>
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164 </conditional>
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165 <section name="req_inputs" title="Input Data" expanded="true">
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166 <conditional name="input_type">
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167 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >
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168 <option value="peptide">peptide</option>
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169 <option value="protein">protein</option>
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170 <option value="DNA">DNA (translate to protein sequences)</option>
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171 <!-- VCF,BED,GTF input options have not been implemented in this tool -->
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172 </param>
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173 <when value="peptide">
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174 <conditional name="multiple">
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175 <param name="peptide_input_selector" type="select" label="Peptides?">
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176 <option value="multiple">Peptide list from your history</option>
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177 <option value="single">Single peptide entered as text</option>
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178 </param>
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179 <when value="multiple">
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180 <param name="input" argument="-i" type="data" format="tabular" label="Peptide Sequences (.txt)">
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181 <help>Peptide sequence file containing peptides which you want to search (no column headers).
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182 First column is am peptide sequence. Optional second column is spectrum title.
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183 </help>
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184 </param>
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185 </when>
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186 <when value="single">
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187 <param name="input" argument="-i" type="text" label="Peptide Sequence" help="Peptide sequence(s) which you want to search">
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188 <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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189 </param>
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190 </when>
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191 </conditional>
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192 </when>
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193 <when value="protein">
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194 <conditional name="multiple">
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195 <param name="protein_input_selector" type="select" label="Proteins?">
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196 <option value="multiple">Protein fasta from your history</option>
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197 <option value="single">Single protein entered as text</option>
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198 <option value="identifier">Protein Identifier from selected Protein Reference Database</option>
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199 </param>
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200 <when value="multiple">
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201 <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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202 </when>
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203 <when value="single">
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204 <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search">
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205 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator>
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206 </param>
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207 </when>
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208 <when value="identifier">
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209 <param name="input" argument="-i" type="text" label="Protein Identifier" help="Protein ID from the selected Protein Reference Database. E.g. sp|P07205|PGK2_HUMAN from swissprot:human">
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210 <sanitizer invalid_char="">
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211 <valid initial="string.ascii_letters,string.digits">
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212 <add value="|" />
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213 </valid>
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214 </sanitizer>
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215 <validator type="regex" message="Spaces not allowed in ID">^[^ ]+$</validator>
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216 </param>
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217 </when>
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218 </conditional>
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219 </when>
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220 <when value="DNA">
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221 <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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222 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator>
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223 </param>
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224 <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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225 <option value="1">1</option>
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226 <option value="2">2</option>
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227 <option value="3">3</option>
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228 <option value="4">4</option>
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229 <option value="5">5</option>
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230 <option value="6">6</option>
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231 </param>
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232 </when>
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233 </conditional>
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234 <conditional name="db_type">
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235 <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" >
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236 <option value="history">history</option>
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237 <option value="download">download</option>
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238 </param>
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239 <when value="history">
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240 <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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241 </when>
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242 <when value="download">
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243 <param name="db_id" type="text" value="" label="Public protein sequence database">
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244 <help>Currently supported dowloads: gencode:human, swissprot:human, refseq:human</help>
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245 <option value="gencode:human">gencode:human</option>
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246 <option value="swissprot:human">swissprot:human</option>
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247 <option value="refseq:human">refseq:human</option>
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248 <validator type="regex" message="">^(swissprot|refseq|gencode):(human)$</validator>
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249 </param>
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250 </when>
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251 </conditional>
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252 <conditional name="ms_dataset">
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253 <param name="ms_dataset_type" type="select" label="MS/MS dataset to search" help="" >
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254 <option value="history"> Spectrum Datasets from history</option>
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255 <option value="indexed">Indexed MS/MS spectrums</option>
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256 <option value="PepQueryDB">PepQueryDB</option>
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257 <option value="public">public proteomics data repositories</option>
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258 </param>
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259 <when value="history">
2
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260 <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML" />
0
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261 </when>
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262 <when value="indexed">
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263 <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
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264 </when>
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265 <when value="PepQueryDB">
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266 <param name="dataset" argument="-b" type="text" value="" label="PepQueryDB dataset">
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267 <help>PepQueryDB dataset IDs (separated by commas).</help>
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268 <expand macro="pepquerydb_options" />
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269 <validator type="regex" message="PepQueryDB dataset_name(,dataset_name)">^[a-zA-Z][^,]*(,[a-zA-Z][^,]*)*$</validator>
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270 </param>
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271 </when>
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272 <when value="public">
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273 <param name="dataset" type="text" value="" label="Public dataset">
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274 <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD|MSV|JPST).*$</validator>
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275 </param>
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276 </when>
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277 </conditional>
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278
2
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279 <param argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
0
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280 <option value="1">index (1-based) in MGF</option>
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281 <option value="2">spectrum title in MGF</option>
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282 </param>
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283 </section>
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284
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285 <param name="parameter_set" argument="-p" type="text" value="" optional="true" label="MS/MS searching parameter set name">
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286 <help>Currently supported set names start with: MS1 or TMT</help>
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287 <option value="MS1_H_MS2_H_LF">MS1_H_MS2_H_LF</option>
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288 <option value="MS1_H_MS2_L_LF">MS1_H_MS2_L_LF</option>
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289 <option value="TMT10_11">TMT10_11</option>
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290 <option value="TMT10_11_MS2_L">TMT10_11_MS2_L</option>
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291 <option value="TMT10_11_MS2_L_phosphorylation">TMT10_11_MS2_L_phosphorylation</option>
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292 <option value="TMT10_11_acetylation">TMT10_11_acetylation</option>
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293 <option value="TMT10_11_glycosylation">TMT10_11_glycosylation</option>
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294 <option value="TMT10_11_phosphorylation">TMT10_11_phosphorylation</option>
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295 <option value="TMT10_11_ubiquitination">TMT10_11_ubiquitination</option>
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296 </param>
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297
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298 <section name="modifications" title="Modifications" expanded="false">
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299 <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" optional="true">
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300 <help>Default: 1: Carbamidomethylation of C [57.02146372057]</help>
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301 <expand macro="modifications" />
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302 </param>
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303 <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" optional="true">
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304 <help>Default: 2: Oxidation of M [15.99491461956]</help>
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305 <expand macro="modifications" />
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306 </param>
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307
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308 <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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309 <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)" />
2
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310 <param 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." />
0
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311 </section>
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312
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313 <section name="digestion" title="Digestion" expanded="false">
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314 <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion. Default: Trypsin" >
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315 <option value="0">Non enzyme</option>
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316 <option value="1">Trypsin</option>
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317 <option value="2">Trypsin (no P rule)</option>
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318 <option value="3">Arg-C</option>
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319 <option value="4">Arg-C (no P rule)</option>
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320 <option value="5">Arg-N</option>
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321 <option value="6">Glu-C</option>
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322 <option value="7">Lys-C</option>
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323 </param>
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324 <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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325 </section>
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326
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327 <section name="ms_params" title="Mass spectrometer" expanded="false">
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328 <section name="tolerance_params" title="Tolerance" expanded="true">
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329 <param name="precursor_tolerance" argument="-tol" type="integer" value="" optional="true" label="Precursor Tolerance" help="The error window on experimental peptide mass values. This parameter is usually set according to the mass spectrometer which was used to generate the MS/MS data. Default: 10" />
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330 <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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331 <option value="ppm">ppm</option>
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332 <option value="Da">Da</option>
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333 </param>
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334 <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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335 </section>
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336
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337 <section name="search" title="PSM" expanded="false">
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338 <param name="frag_method" argument="-fragmentMethod" type="select" optional="true" label="Fragmentation Method" help="Default: CID/HCD">
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339 <option value="1">CID/HCD</option>
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340 <option value="2">ETD</option>
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341 </param>
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342 <param name="scoring_method" argument="-m" type="select" optional="true" label="Scoring Method" help="Default: HyperScore">
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343 <option value="1">HyperScore</option>
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344 <option value="2">MVH</option>
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345 </param>
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346 <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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347 <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"/>
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348 <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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349 <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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350 <param name="isotope_error" argument="-ti" type="text" value="" optional="true" label="Isotope peak error range">
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351 <help>A comma-sepated range of integers from -2 to 2, e.g. '-1,0,1,2' Default: 0</help>
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352 <validator type="regex" message="">^((-2,)?-1,)?0(,1(,2)?)?$</validator>
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353 </param>
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354 <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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355 <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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356 <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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357 <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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358 </section>
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359 </section>
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360
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361 <param name="outputs_selected" type="select" multiple="true" optional="false" label="Select outputs">
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362 <option value="psm.txt">psm.txt</option>
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363 <option value="psm_rank.txt" selected="true">psm_rank.txt</option>
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364 <option value="psm_rank.mgf">psm_rank.mgf</option>
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365 <option value="psm_annotation.txt">psm_annotation.txt</option>
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366 <option value="psm_type.txt">psm_type.txt</option>
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367 <option value="detail.txt">detail.txt</option>
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368 <option value="ptm.txt">ptm.txt</option>
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369 <option value="ptm_detail.txt">ptm_detail.txt</option>
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370 <option value="ms_index">MS/MS Index</option>
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371 </param>
2
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372 <param 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." />
0
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373 </inputs>
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374 <outputs>
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375 <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
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376 </data>
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377 <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">
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378 <filter>'parameter.txt' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
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379 </data>
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380 <data name="ms_index" format="txt" label="${tool.name} on ${on_string}: index summary.txt" from_work_dir="index_dir/summary.txt">
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381 <filter>'ms_index' in outputs_selected and req_inputs['ms_dataset']['ms_dataset_type'] == 'history'</filter>
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382 </data>
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383 <data name="psm_txt" format="tabular" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: psm.txt">
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384 <filter>'psm.txt' in outputs_selected</filter>
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385 <actions>
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386 <action name="comment_lines" type="metadata" default="1" />
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387 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue" />
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388 </actions>
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389 </data>
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390
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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391 <data name="psm_rank_txt" format="tabular" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: psm_rank.txt">
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392 <filter>'psm_rank.txt' in outputs_selected</filter>
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393 <actions>
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394 <action name="comment_lines" type="metadata" default="1" />
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395 <action name="column_names" type="metadata" default="peptide,modification,n,spectrum_title,charge,exp_mass,tol_ppm,tol_da,isotope_error,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,n_ptm,confident,ref_delta_score,mod_delta_score" />
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396 </actions>
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397 </data>
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398
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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399 <data name="psm_rank_mgf" format="mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: psm_rank.mgf">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
400 <filter>'psm_rank.mgf' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
401 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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402 <data name="psm_type_txt" format="tabular" from_work_dir="pepquery_output/psmi_type.txt" label="${tool.name} on ${on_string}: psm_type.txt">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
403 <filter>'psm_type.txt' in outputs_selected</filter>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
404 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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405 <action name="comment_lines" type="metadata" default="1" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
406 <action name="column_names" type="metadata" default="peptide,spectrum_title,type" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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407 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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408 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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409 <data name="psm_annotation_txt" format="tabular" from_work_dir="pepquery_output/psm_annotation.txt" label="${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
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410 <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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411 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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412 <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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413 <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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414 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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415 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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416 <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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417 <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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418 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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419 <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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420 <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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421 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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422 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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423
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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424 <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
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425 <filter>'ptm.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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426 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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427 <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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428 <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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429 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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430 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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431 <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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432 <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
galaxyp
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433 <actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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434 <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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435 <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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436 </actions>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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437 </data>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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438
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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439 </outputs>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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440 <tests>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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441 <!-- 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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442 <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:
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443 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
444 <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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445 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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446 <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
447 <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
448 <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:
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449 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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450 <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
451 <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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452 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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453 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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454 <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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455 <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:
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456 <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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457 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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458 <conditional name="ms_dataset">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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459 <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
460 <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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461 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
462 <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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463 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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464 <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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465 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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466 <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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parents:
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467 <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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468 <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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parents:
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469 <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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parents:
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470 <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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diff changeset
471 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
472 <section name="digestion">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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473 <param name="enzyme" value="1"/>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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474 <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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475 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
476 <section name="ms_params">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
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477 <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
478 <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
479 <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
480 <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
481 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
482 <section name="search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
483 <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
484 <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
485 <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
486 <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
487 <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
488 <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
489 <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
490 <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
491 <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
492 <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
493 <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
494 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
495 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
496 <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
497 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
498 <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
499 <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
500 <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
501 <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
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 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
504 <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
505 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
506 <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
507 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
508 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
509 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
510
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
511 <!-- 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
512 <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
513 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
514 <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
515 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
516 <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
517 <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
518 <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
519 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
520 <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
521 <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
522 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
523 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
524 <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
525 <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
526 <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
527 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
528 <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
529 <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
530 <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
531 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
532 <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
533 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
534 <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
535 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
536 <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
537 <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
538 <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
539 <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
540 <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
541 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
542 <section name="digestion">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
543 <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
544 <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
545 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
546 <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
547 <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
548 <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
549 <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
550 <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
551 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
552 <section name="search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
553 <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
554 <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
555 <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
556 <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
557 <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
558 <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
559 <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
560 <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
561 <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
562 <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
563 <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
564 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
565 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
566 <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
567 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
568 <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
569 <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
570 <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
571 <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
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 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
574 <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
575 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
576 <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
577 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
578 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
579 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
580
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
581 <!-- 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
582 <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
583 <conditional name="validation">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
584 <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
585 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
586 <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
587 <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
588 <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
589 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
590 <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
591 <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
592 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
593 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
594 <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
595 <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
596 <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
597 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
598 <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
599 <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
600 <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
601 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
602 <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
603 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
604 <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
605 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
606 <!-- 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
607 <!-- 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
608 <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
609 <!-- 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
610 <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
611 <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
612 <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
613 <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
614 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
615 <section name="digestion">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
616 <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
617 <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
618 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
619 <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
620 <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
621 <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
622 <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
623 <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
624 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
625 <section name="search">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
626 <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
627 <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
628 <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
629 <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
630 <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
631 <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
632 <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
633 <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
634 <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
635 <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
636 <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
637 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
638 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
639 <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
640 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
parents:
diff changeset
641 <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
642 <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
643 <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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644 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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645 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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646 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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647
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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648 <!-- 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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parents:
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649 <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
650 <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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651 <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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652 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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653 <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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654 <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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655 <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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656 <conditional name="multiple">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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657 <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
658 <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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659 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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660 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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661 <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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662 <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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663 <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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664 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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665 <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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666 <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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667 <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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668 </conditional>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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669 <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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670 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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671 <section name="modifications">
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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672 <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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673 </section>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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674 <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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675 <assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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676 <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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677 <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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678 <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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679 </assert_contents>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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680 </output>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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681 </test>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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682
1
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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683 <!-- Test-5 Non-enzyme search -->
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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684 <test expect_num_outputs="2">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
685 <conditional name="validation">
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diff changeset
686 <param name="task_type" value="novel"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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687 </conditional>
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688 <section name="req_inputs">
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galaxyp
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689 <conditional name="input_type">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
690 <param name="input_type_selector" value="peptide"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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691 <conditional name="multiple">
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galaxyp
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692 <param name="peptide_input_selector" value="single" />
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
693 <param name="input" value="ELGSSDLTAR"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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694 </conditional>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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695 </conditional>
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galaxyp
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diff changeset
696 <conditional name="db_type">
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diff changeset
697 <param name="db_type_selector" value="history" />
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
698 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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699 </conditional>
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galaxyp
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diff changeset
700 <conditional name="ms_dataset">
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galaxyp
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diff changeset
701 <param name="ms_dataset_type" value="history"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
702 <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
703 </conditional>
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galaxyp
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diff changeset
704 <param name="indexType" value="1"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
705 </section>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
706 <param name="parameter_set" value=""/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
707 <section name="modifications">
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diff changeset
708 <!-- 21: iTRAQ 4-plex of K [144.1020624208] -->
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
709 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
710 <param name="fixed_mod" value="1,21,22"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
711 <!-- 2: Oxidation of M [15.99491461956] -->
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
712 <param name="var_mod" value="2"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
713 <param name="max_mods" value="3"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
714 <param name="unmodified" value="True"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
715 <param name="aa" value="False"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
716 </section>
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galaxyp
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diff changeset
717 <section name="digestion">
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galaxyp
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diff changeset
718 <param name="enzyme" value="0"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
719 </section>
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galaxyp
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720 <section name="ms_params">
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galaxyp
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diff changeset
721 <section name="tolerance_params">
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diff changeset
722 <param name="precursor_tolerance" value="10"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
723 <param name="precursor_unit" value="ppm"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
724 <param name="tolerance" value="0.6"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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725 </section>
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galaxyp
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diff changeset
726 <section name="search">
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diff changeset
727 <param name="frag_method" value="1"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
728 <param name="scoring_method" value="1"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
729 <param name="extra_score_validation" value="False"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
730 <param name="min_charge" value="2"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
731 <param name="max_charge" value="3"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
732 <param name="min_peaks" value="10"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
733 <param name="isotope_error" value="0"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
734 <param name="min_score" value="12"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
735 <param name="min_length" value="7"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
736 <param name="max_length" value="45"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
737 <param name="num_random_peptides" value="1000"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
738 </section>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
739 </section>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
740 <output name="psm_rank_txt">
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
741 <assert_contents>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
742 <has_text text="ELGSSDLTAR" />
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
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diff changeset
743 <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\t13\t1\t995\t0.002\d+\t1\t0\tYes\t10.3\d+\t8.23\d+"/>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
galaxyp
parents: 0
diff changeset
744 <has_n_columns n="22" />
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
745 </assert_contents>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
746 </output>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
747 </test>
b5489f81c2fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit fb66172091bb840e4cb673975fd1ebbfd8dcf3f7
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diff changeset
748
0
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
749 </tests>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
750 <help><![CDATA[
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
751 **PepQuery2**
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
752
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
753 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
754
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
755
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
756 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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757
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
758 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
759
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
760 **Inputs**
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
761 - 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
762
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
763 - 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
764 - 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
765 - 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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766 - 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
767
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
768
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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parents:
diff changeset
769 - 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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parents:
diff changeset
770
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
771 - 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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parents:
diff changeset
772 - 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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parents:
diff changeset
773 - 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
774
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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775 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
776
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
777 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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diff changeset
778
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
779
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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780 - 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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781
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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782 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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783
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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784 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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diff changeset
785
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
786 - 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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diff changeset
787
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
788 - 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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789 - 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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790
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
791
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
792 **Options**
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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793
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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794 - MS/MS searching parameter set name
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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795
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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796 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
797
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
798 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
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diff changeset
799 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
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800 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
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diff changeset
801
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
802
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
803 - Override default options
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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804
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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805 ..
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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806
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
807 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
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808 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
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diff changeset
809
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
810 **Outputs**
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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diff changeset
811 - Log.txt:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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diff changeset
812
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
galaxyp
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diff changeset
813 - Logging output from PepQuery2
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
814 - 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
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diff changeset
815
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
816 - 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
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diff changeset
817
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
818 - 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
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diff changeset
819
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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820 - 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
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diff changeset
821
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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822 - Parameters:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
823
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
824 - parameters used in the search
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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825
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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diff changeset
826 - PSM - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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827
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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828 - 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
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829
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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830 - PSM Rank - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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831
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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832 - 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
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833
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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834 - An MGF with the best matching spectrums
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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835
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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836 - Detail - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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837
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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838 - spectrum_title peptide modification pep_mass score
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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839
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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840 - PSM annotation - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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841
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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842 - 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
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843
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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844 - PTM - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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845
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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846 - 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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847
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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848 - PTM Detail - tabular with columns:
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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849
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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850 - 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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851
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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852 - 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
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853
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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854
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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855 .. _PepQuery: http://pepquery.org/document.html
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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856
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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857 ]]></help>
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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858 <expand macro="citations" />
a07976bbc4d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
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859 </tool>