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annotate percolator.xml @ 1:86770eea5b09 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
author galaxyp
date Sat, 04 Mar 2017 20:36:03 -0500
parents 3a49065a05d6
children 7a0951d0e13e
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1 <tool id="percolator" name="Percolator" version="3.0.1">
0
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2 <description>accurate peptide identification</description>
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3 <requirements>
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4 <requirement type="package" version="3.0">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 #if $cpos
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17 -p $cpos
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18 #end if
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19 #if $cneg
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20 -n $cneg
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21 #end if
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22 #if $testfdr
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23 -t $testfdr
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24 #end if
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25 #if $trainfdr
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26 -F $trainfdr
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27 #end if
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28 #if $maxiter
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29 -i $maxiter
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30 #end if
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31 #if $seed
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32 -S $seed
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33 #end if
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34 #if $default_direction
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35 -V $default_direction
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36 #end if
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37 $quickval $unitnorm $override $onlypsms
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38 </command>
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39 <inputs>
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40 <param name="output_type" label="What filetype to output" type="select" display="radio">
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41 <option value="xml" selected="true">percolator XML (for further processing)</option>
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42 <option value="tsv">Tab-separated</option>
0
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43 </param>
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44 <param name="input" type="data" format="percin" label="Percolator input data" />
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45 <param name="cpos" label="Penalty for mistakes on positive examples" type="float" optional="true" />
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46 <param name="cneg" label="Penalty for mistakes on negative examples" type="float" optional="true" />
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47 <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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48 <param name="testfdr" label="FDR threshold for evaluating best cross validation result" type="float" optional="true" />
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49 <param name="maxiter" label="Maximal number of iterations" type="integer" optional="true" />
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50 <param name="quickval" label="Quicker execution by reduced internal cross-validation" type="boolean" truevalue="-x" falsevalue=""/>
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51 <param name="default_direction" label="Most informative feature given as feature number" type="integer" optional="true" />
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52 <param name="unitnorm" type="boolean" label="Unit normalization instead of standard deviation" truevalue="-u" falsevalue=""/>
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53 <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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54 <param name="seed" label="Seed of random number generator" type="integer" optional="true" />
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55 <!--<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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56 <param name="onlypsms" label="Skip all outputs except PSMs" type="boolean" truevalue="-U" falsevalue=""/>
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57 </inputs>
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58 <outputs>
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59 <data format="percout" name="percoout">
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60 <change_format>
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61 <when input="output_type" value="tsv" format="tsv" />
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62 </change_format>
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63 </data>
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="input" value="percolatorTab" />
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68 <param name="output_type" value="xml" />
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69 <output name="percoout" value="percolatorOut.xml" lines_diff="2" />
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70 </test>
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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="tsv" />
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74 <output name="percoout" value="percolatorOut.txt" />
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75 </test>
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76 </tests>
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77 <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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78
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79 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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80 </help>
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81 <citations>
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82 <citation type="doi">10.1038/nmeth1113</citation>
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83 <citation type="doi">10.1021/pr700600n</citation>
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84 <citation type="doi">10.1093/bioinformatics/btn294</citation>
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85 </citations>
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86 </tool>