annotate percolator.xml @ 3:abed51712ed0 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
author galaxyp
date Sat, 08 Apr 2017 08:23:12 -0400
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1 <tool id="percolator" name="Percolator" version="3.1.0">
0
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2 <description>accurate peptide identification</description>
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3 <requirements>
2
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4 <requirement type="package" version="3.1">percolator</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 <command>
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10 percolator -j '$input'
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11 #if $output_type == "xml"
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12 -X '$percoout' --decoy-xml-output
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13 #else
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14 -J '$percoout'
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15 #end if
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16 $tdmethod
0
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17 #if $cpos
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18 -p $cpos
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19 #end if
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20 #if $cneg
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21 -n $cneg
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22 #end if
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23 #if $testfdr
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24 -t $testfdr
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25 #end if
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26 #if $trainfdr
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27 -F $trainfdr
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28 #end if
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29 #if $maxiter
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30 -i $maxiter
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31 #end if
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32 #if $seed
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33 -S $seed
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34 #end if
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35 #if $default_direction
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36 -V $default_direction
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37 #end if
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38 $quickval $unitnorm $override $onlypsms
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39 </command>
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40 <inputs>
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41 <param name="output_type" label="What to output" type="select" display="radio">
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42 <option value="xml" selected="true">Percolator output (XML)</option>
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43 <option value="tsv">Computed features of input (Tab separated)</option>
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44 </param>
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45 <param name="input" type="data" format="percin" label="Percolator input data" />
2
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46 <param name="tdmethod" type="select" label="Target decoy method">
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47 <option value="-y" selected="true">Mix-max</option>
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48 <option value="-Y">Target-decoy competition (also good when unequal amounts of target/decoy PSMs)</option>
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49 </param>
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50 <param name="cpos" label="Penalty for mistakes on positive examples" type="float" optional="true" />
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51 <param name="cneg" label="Penalty for mistakes on negative examples" type="float" optional="true" />
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52 <param name="trainfdr" label="FDR threshold to define positive examples" type="float" optional="true" help="Set by cross validation if 0."/>
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53 <param name="testfdr" label="FDR threshold for evaluating best cross validation result" type="float" optional="true" />
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54 <param name="maxiter" label="Maximal number of iterations" type="integer" optional="true" />
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55 <param name="quickval" label="Quicker execution by reduced internal cross-validation" type="boolean" truevalue="-x" falsevalue=""/>
2
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56 <param name="default_direction" label="Most informative feature given as feature name." help="Can be negated to indicate lower value=better, e.g -featureName" type="text" optional="true" />
0
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57 <param name="unitnorm" type="boolean" label="Unit normalization instead of standard deviation" truevalue="-u" falsevalue=""/>
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58 <param name="override" label="Override error check?" help="and no fallback on default score vector in case of suspect score vector" type="boolean" truevalue="-O" falsevalue=""/>
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59 <param name="seed" label="Seed of random number generator" type="integer" optional="true" />
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60 <!--<param name="klammer" label="Retention time features calculated as in Klammer et al?" type="boolean" /> TODO: this param goes together with the doc param which I havent figured out how to use yet. -->
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61 <param name="onlypsms" label="Skip all outputs except PSMs" type="boolean" truevalue="-U" falsevalue=""/>
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62 </inputs>
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63 <outputs>
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64 <data format="percout" name="percoout">
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65 <change_format>
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66 <when input="output_type" value="tsv" format="tsv" />
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67 </change_format>
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68 </data>
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="input" value="percolatorTab" />
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73 <param name="output_type" value="xml" />
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74 <output name="percoout" value="percolatorOut.xml" lines_diff="2" />
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75 </test>
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76 <test>
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77 <param name="input" value="percolatorTab" />
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78 <param name="output_type" value="xml" />
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79 <param name="tdmethod" value="-Y" />
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80 <param name="cpos" value="0.00001" />
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81 <param name="cneg" value="0.00001" />
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82 <param name="trainfdr" value="0.1" />
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83 <param name="testfdr" value="0.1" />
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84 <param name="maxiter" value="5" />
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85 <param name="quickval" value="-x" />
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86 <param name="default_direction" value="RawScore" />
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87 <param name="unitnorm" value="-u" />
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88 <param name="override" value="-O" />
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89 <param name="seed" value="2" />
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90 <param name="onlypsms" value="-U" />
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91 <output name="percoout" value="percolatorOut_alloptions.xml" lines_diff="2" />
7a0951d0e13e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
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92 </test>
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93 <test>
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94 <param name="input" value="percolatorTab" />
0
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95 <param name="output_type" value="tsv" />
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96 <output name="percoout" value="percolatorOut.txt" lines_diff="1" />
0
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97 </test>
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98 </tests>
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99 <help>The first step in analyzing an mass spectrometry assay is to match the harvested spectra against a target database using database search engines such as Sequest and Mascot, a process that renders list of peptide-spectrum matches. However, it is not trivial to assess the accuracy of these identifications.
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100
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101 Percolator uses a semi-supervised machine learning to discriminate correct from incorrect peptide-spectrum matches, and calculates accurate statistics such as q-value (FDR) and posterior error probabilities.
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102 </help>
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103 <citations>
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104 <citation type="doi">10.1038/nmeth1113</citation>
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105 <citation type="doi">10.1021/pr700600n</citation>
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106 <citation type="doi">10.1093/bioinformatics/btn294</citation>
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107 </citations>
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108 </tool>