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annotate pecan.xml @ 0:69274b068a48 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pecan commit 21855dec2949420d3bccfd6c9912578e9aacecf0
author jjohnson
date Fri, 25 Aug 2017 14:25:21 -0400
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69274b068a48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pecan commit 21855dec2949420d3bccfd6c9912578e9aacecf0
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1 <tool id="pecan" name="PECAN" version="0.1.0">
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2 <description>detect peptides directly from DIA Mass Spec</description>
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3 <requirements>
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4 <requirement type="package" version="0.9.9.3">pecan</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <version_command>pecan --VERSION</version_command>
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10 <command><![CDATA[
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11 ## ln mzML file
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12 #if $isolation.isolationsrc == 'entered':
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13 #set $isolationfile = $isolationSheme
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14 #else
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15 #set $isolationfile = $isolation.isolation_windows
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16 #end if
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17 #set $outputRoot = 'test'
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18 awk 'NF>1 && $1 ~ /^[0-9]+(\.[0-9]*)?$/{print \$1; print \$2; print "$outputRoot"}' $isolationfile |
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19 xargs -n3 -P\${GALAXY_SLOTS}
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20 pecan
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21 #if $backgroundProteome:
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22 --backgroundProteome='$backgroundProteome'
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23 #end if
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24 --bgDecoyNumber=$bgDecoyNumber
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25 #if $decoyTag and str($decoyTag):
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26 --decoyTag=$decoyTag
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27 #end if
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28 --ionTypes=$--ionTypes
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29 --minElution=$minElution
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30 --maxElution=$maxElution
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31 --overlap=$advanced_options.overlap
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32 #if $advanced_options.ms1.ms1Unit == 'ppm':
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33 --ms1Unit=ppm
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34 --ms1Tolerance=$advanced_options.ms1.ms1Tolerance
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35 #elif $advanced_options.ms1.ms1Unit == 'mz':
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36 --ms1Unit=mz
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37 --ms1Tolerance=$advanced_options.ms1.ms1Tolerance
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38 #end if
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39 #if $advanced_options.ms2.ms2Unit == 'ppm':
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40 --ms2Unit=ppm
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41 --ms2Tolerance=$advanced_options.ms2.ms2Tolerance
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42 #elif $advanced_options.ms2.ms2Unit == 'mz':
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43 --ms2Unit=mz
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44 --ms2Tolerance=$advanced_options.ms2.ms2Tolerance
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45 #end if
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46 --minCharge=$advanced_options.minCharge
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47 --maxCharge=$advanced_options.maxCharge
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48 #if $advanced_options.ms2Boundaries.specify == 'specify':
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49 --ms2Boundaries="$advanced_options.ms2Boundaries.ms2BoundariesMin,$advanced_options.ms2Boundaries.ms2BoundariesMax"
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50 #end if
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51 --alpha=$advanced_options.alpha
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52 --beta=$advanced_options.beta
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53 --idotp=$advanced_options.idotp
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54 --topX=$advanced_options.topX
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55 #if $advanced_options.fixedMod and str($advanced_options.fixedMod):
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56 --fixedMod='$advanced_options.fixedMod'
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57 #end if
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58 $input $peptides 2>1 > run.log
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59 && cat "$outputRoot"*.log > '$log_file'
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60 && cat "$outputRoot"*.td.feature | awk 'NR==1{print $0};!/peakCalibratedScore/{print $0}' > '$feature_file'
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61 ]]></command>
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62
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63 <configfiles>
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64 <configfile name="isolationSheme">#slurp
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65 #import re
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66 #if $isolation.isolationsrc == 'entered':
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67 #echo $re.sub(r'(\d+[.]\d+)\s+(\d+[.]\d)\s*',r'\1\t\2\n',$isolation.isolation_windows.strip())
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68 #end if
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69 #slurp</configfile>
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70 </configfiles>
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71 <inputs>
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72 <param name="input" type="data" format="mzml" label="centroided mzML file"/>
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73 <param name="sciex" type="boolean" truevalue="--sciex" falsevalue="" checked="false"
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74 label="mzML files were generated from AB SCIEX MS Data Converter"/>
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75 <param name="peptides" type="data" format="tabular" multiple="true" label="target peptides"/>
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76
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77 <conditional name="isolation">
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78 <param name="isolationsrc" type="select" label="isolation windows">
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79 <option value="entered">Enter isolation windows</option>
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80 <option value="history">Read isolation windows from a history dataset</option>
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81 </param>
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82 <when value="entered">
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83 <param name="isolation_windows" type="text" area="true" size="20x20" value="" label="isolation windows">
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84 <validator type="regex" message="enter pairs of window boudaries, e.g.:400.0 420.0">^(?ms)(\d+[.]\d+\s\d+[.]\d)(\s\d+[.]\d+\s\d+[.]\d)*$</validator>
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85 </param>
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86 </when>
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87 <when value="history">
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88 <param name="isolation_windows" type="data" format="tabular" label="isolation windows"/>
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89 </when>
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90 </conditional>
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91
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92 <!-- species - default proteomes for (ecoli/yeast/mouse/human) -->
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93 <param name="backgroundProteome" type="data" format="tabular" optional="true" label="BackgroundProteome"
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94 help="Peptide list file name of background proteome. Recommended if querying for a small number of peptides."/>
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95 <param name="bgDecoyNumber" type="integer" value="2000" min="0" label="Number of decoys used for background estimation"
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96 optional="True" help="(-n) Default= 2000" />
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97 <param name="decoyTag" type="text" value="decoy" optional="true" label="Tag for decoy sequences in the database"/>
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98
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99 <param name="ionTypes" type="select" label="Fragment ion types" help="suggested HCD: y, reCID: by">
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100 <option value="by">by</option>
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101 <option value="y">y</option>
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102 <option value="b">b</option>
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103 </param>
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104
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105 <param name="minElution" type="integer" value="12" min="1" label="Minimum time in seconds a peptide is expected to elute"
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106 optional="True" help="(-m) Default= 12 seconds" />
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107 <param name="maxElution" type="integer" value="30" min="1" label="Maximum time in seconds a peptide is expected to elute"
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108 optional="True" help="(-x) Default= 30 seconds" />
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109
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110 <section name="advanced_options" expanded="false" title="Advanced Options">
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111 <param name="overlap" type="integer" value="0" min="0" max="100" label="Overlap percentage of isolation window"/>
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112 <conditional name="ms1">
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113 <param name="ms1Unit" type="select" label="Unit for precursor ion extraction tolerance">
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114 <option value="ppm">ppm</option>
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115 <option value="mz">mz</option>
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116 </param>
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117 <when value="ppm">
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118 <param name="ms1Tolerance" type="integer" value="10" min="0" label="ms1Tolerance"
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119 help="Mass error for precursor ion extracting"/>
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120 </when>
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121 <when value="mz">
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122 <param name="ms1Tolerance" type="float" value="10" min="0" label="ms1Tolerance"
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123 help="Mass error for precursor ion extracting"/>
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124 </when>
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125 </conditional>
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126 <conditional name="ms2">
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127 <param name="ms2Unit" type="select" label="Unit for fragment ion extraction tolerance">
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128 <option value="ppm">ppm</option>
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129 <option value="mz">mz</option>
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130 </param>
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131 <when value="ppm">
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132 <param name="ms2Tolerance" type="integer" value="10" min="0" label="ms2Tolerance"
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133 help="Mass error for precursor ion extracting"/>
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134 </when>
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135 <when value="mz">
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136 <param name="ms2Tolerance" type="float" value="10" min="0" label="ms2Tolerance"
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137 help="Mass error for precursor ion extracting"/>
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138 </when>
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139 </conditional>
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140 <param name="minCharge" type="integer" value="2" min="1" label="Minimum charge state searched"/>
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141 <param name="maxCharge" type="integer" value="3" min="1" label="Maximum charge state searched"/>
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142 <conditional name="ms2Boundaries">
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143 <param name="specify" type="select" label="Unit for fragment ion extraction tolerance">
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144 <option value="calculate">Let PECAN calculate MS2 Boundaries</option>
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145 <option value="specify">Specify MS2 Boundaries</option>
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146 </param>
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147 <when value="calculate"/>
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148 <when value="specify">
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149 <param name="ms2BoundariesMin" type="float" value="" label="Specify the MS2 scan lower m/z limit for the target window"/>
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150 <param name="ms2BoundariesMax" type="float" value="" label="Specify the MS2 scan upper m/z limit for the target window"/>
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151 </when>
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152 </conditional>
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153 <param name="alpha" type="float" value="1.8" min="0.0" label="Alpha hyperparameter to set score threshold for cIons" />
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154 <param name="beta" type="float" value="0.4" min="0.0" max="1.0" label="Beta hyperparameter to set score threshold for cIons" />
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155 <param name="idotp" type="float" value="0.0" min="0.0" label="MS1 idotp threshold used for peak picking" />
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156 <param name="topX" type="integer" value="1" min="1" label="Reporting top x peaks per charged peptide"/>
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157
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158 <param name="fixedMod" type="text" value="" optional="true" label="Fixed modifications in the sample">
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159 <help><![CDATA[
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160 Fixed modifications in the sample. For example, default C[+57.021] will treat every Cys
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161 in the query sequences and background proteome as C[+57.021] while overwriting any
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162 specific modifications on individual Cys
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163 If multiple fixed modifications are desired use "," to separate each fixedMod tag
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164 (e.g. C[+57.021],M[+15.995])
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165 ]]></help>
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166 <validator type="regex" message="C[+57.021],M[+15.995]">^([A-Z]\[[+-]\d+[.]\d+\](,[A-Z]\[[+-]\d+[.]\d+\])*)*$</validator>
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167 <sanitizer sanitize="False"/>
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168 </param>
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169 </section>
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170 <!--
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171 verbosity#Verbosity level for file logging (WARNING/INFO/DEBUG) Default=INFO
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172 -->
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173 </inputs>
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174 <outputs>
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175 <data name="log_file" format="txt" label="" />
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176 <data name="feature_file" format="percin" label="" />
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177 </outputs>
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178 <help><![CDATA[
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179 **PECAN**
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180
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181 PECAN (PEptide-Centric ANalysis) is a tool for peptide detection directly from DIA data without the need of a spectral library. PECAN takes a list of peptide sequences and query each peptide against the DIA data (in centroid mzML format) and reports the best evidence of detection for each peptide. The PECAN report is designed for Percolator to separate correct from incorrect matches with false discovery rate (FDR) control.
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182
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183 usage: pecan [-h] [-d DECOYTAG] [--ms1Unit MS1UNIT] [--ms2Unit MS2UNIT]
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184 [-p MS1TOLERANCE] [-q MS2TOLERANCE] [-m MINELUTION]
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185 [-x MAXELUTION] [-b BACKGROUNDPROTEOME] [-n BGDECOYNUMBER]
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186 [-i IDOTP] [-v VERBOSITY] [-t TOPX] [--minCharge MINCHARGE]
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187 [--maxCharge MAXCHARGE] [-s IONTYPES] [--overlap OVERLAP]
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188 [--SCIEX] [--VERSION] [--ms2Boundaries MS2BOUNDARIES]
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189 [--alpha ALPHA] [--beta BETA] [--fixedMod FIXEDMOD]
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190 mzMLFileName peptideListFileName isolationStart isolationEnd
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191 outputRoot
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192
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193
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194
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195 positional arguments:
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196 mzMLFileName path to the centroid .mzML file
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197 peptideListFileName path to the query peptide list
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198 isolationStart precursor m/z of isolation start
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199 isolationEnd precursor m/z of isolation end
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200 outputRoot name base of the output files
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201
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202 optional arguments:
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203 -h, --help show this help message and exit
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204 -d DECOYTAG, --decoyTag DECOYTAG
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205 Tag for decoy sequences in the database
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206 Default= decoy
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207
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208 --ms1Unit MS1UNIT Unit (ppm/mz) for precursor ion extraction tolerance
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209 Used with -p
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210 Default=ppm
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211
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212 --ms2Unit MS2UNIT Unit (ppm/mz) for fragment ion extraction tolerance
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213 Used with -q
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214 Default=ppm
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215
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216 -p MS1TOLERANCE, --ms1Tolerance MS1TOLERANCE
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217 Mass error for precursor ion extracting
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218 Default=10
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219
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220 -q MS2TOLERANCE, --ms2Tolerance MS2TOLERANCE
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221 Mass error for fragment ion extracting
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222 Default=10
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223
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224 -m MINELUTION, --minElution MINELUTION
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225 Minimum time in seconds a peptide is expected to elute
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226 Default= 12 seconds
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227
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228 -x MAXELUTION, --maxElution MAXELUTION
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229 Maximum time in seconds a peptide is expected to elute
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230 Default= 30 seconds
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231
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232 -b BACKGROUNDPROTEOME, --backgroundProteome BACKGROUNDPROTEOME
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233 Peptide list file name of background proteome
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234 Recommended if querying for a small number of peptides
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235 Default=None
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236
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237 -n BGDECOYNUMBER, --bgDecoyNumber BGDECOYNUMBER
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238 Number of decoys used for background estimation
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239 Default=2000
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240
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241 -i IDOTP, --idotp IDOTP
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242 MS1 idotp threshold used for peak picking
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243 Default=0.000000
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244
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245 -v VERBOSITY, --verbosity VERBOSITY
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246 Verbosity level for file logging (WARNING/INFO/DEBUG)
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247 Default=INFO
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248
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249 -t TOPX, --topX TOPX Reporting top x peaks per charged peptide
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250 Default=1
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251
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252 --minCharge MINCHARGE
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253 Minimum charge state searched
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254 Default=2
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255
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256 --maxCharge MAXCHARGE
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257 Maximum charge state searched
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258 Default=3
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259
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260 -s IONTYPES, --ionTypes IONTYPES
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261 == To be added == Fragment ion types (b, y, or by)
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262 Default=by
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263
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264 --overlap OVERLAP Overlap percentage of isolation window
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265 Default=0
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266
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267 --SCIEX Flag if mzML is generated from AB Sciex converter
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268 --VERSION Show current PECAN version
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269
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270 --ms2Boundaries MS2BOUNDARIES
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271 Specify the MS2 scan lower and upper m/z limit such as 200,2000 for the target window
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272 If not specify pecan will determine it with a function
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273
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274 --alpha ALPHA Alpha hyperparameter to set score threshold for cIons
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275
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276 --beta BETA Beta hyperparameter to set cutoff for number of cIons
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277
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278 --fixedMod FIXEDMOD Fixed modifications in the sample. For example, default C[+57.021] will treat every Cys
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279 in the query sequences and background proteome as C[+57.021] while overwriting any
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280 specific modifications on individual Cys
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281 If multiple fixed modifications are desired use "," to separate each fixedMod tag
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282 (e.g. C[+57.021],M[+15.995])
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283
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69274b068a48 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pecan commit 21855dec2949420d3bccfd6c9912578e9aacecf0
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286 </tool>