Mercurial > repos > galaxyp > pyprophet_peptide

annotate pyprophet_peptide.xml @ 0:611120fd1717 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
author galaxyp
date Tue, 25 Feb 2020 18:28:24 -0500
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611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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1 <tool id="pyprophet_peptide" name="PyProphet peptide" version="@VERSION@.0">
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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2 <description>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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3 Peptide error-rate estimation
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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4 </description>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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5 <macros>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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6 <import>macros.xml</import>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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7 </macros>
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8 <expand macro="requirements"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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9 <command detect_errors="aggressive">
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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10 <![CDATA[
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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11 pyprophet peptide
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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12 --in='$input'
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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13 --context=$context
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14 $parametric
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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15 $pfdr
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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16 --pi0_lambda=$pi0_lambda_start $pi0_lambda_end $pi0_lambda_steps
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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17 --pi0_method=$pi0_method
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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18 --pi0_smooth_df=$pi0_smooth_df
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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19 $pi0_smooth_log
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20 $lfdr_truncate
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21 $lfdr_monotone
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22 --lfdr_transformation=$lfdr_transformation
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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23 --lfdr_adj=$lfdr_adj
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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24 --lfdr_eps=$lfdr_eps
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25 --out='./output.osw' && mv *_peptide.pdf peptide.pdf
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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26
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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27
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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28 ]]>
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29 </command>
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30 <inputs>
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31 <param name="input" type="data" format="osw" label="Input file" help="This file needs to be in OSW format (--in)" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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32 <param argument="--context" type="select" display="radio" label="Context to estimate protein-level FDR control" >
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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33 <option value="run-specific" selected="True" >run-specific</option>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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34 <option value="experiment-wide">experiment-wide</option>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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35 <option value="global">global</option>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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36 </param>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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37 <!-- sollte peptide-level FDR heißen?-->
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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38 <param name="parametric" type="boolean" truevalue="--parametric" falsevalue="--no-parametric" label="Do parametric estimation of p-values" help="(--parametric / --no-parametric)"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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39 <param name="pfdr" type="boolean" truevalue="--pfdr" falsevalue="--no-pfdr" label="Compute positive false discovery rate (pFDR) instead of FDR" help="(--pfdr / --no-pfdr)"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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40 <param name="pi0_lambda_start" type="float" value="0.1" label="Use non-parametric estimation of p-values. Start value" help="(--pi0_lambda)"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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41 <param name="pi0_lambda_end" type="float" value="0.5" label="Use non-parametric estimation of p-values. End value" help="(--pi0_lambda)"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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42 <param name="pi0_lambda_steps" type="float" value="0.05" label="Use non-parametric estimation of p-values. Steps value" help="(--pi0_lambda)"/>
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43 <param argument="pi0_method" type="select" display="radio" label="Either 'smoother' or 'bootstrap'; the method for automatically choosing tuning parameter in the estimation of pi_0, the proportion of true null hypotheses" >
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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44 <option value="bootstrap" selected="True" >bootstrap</option>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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45 <option value="smoother">smoother</option>
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46 </param>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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47 <param argument="--pi0_smooth_df" type="integer" value="3" label="Number of degrees-of-freedom to use when estimating pi_0 with a smoother" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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48 <param name="pi0_smooth_log" type="boolean" truevalue="--pi0_smooth_log_pi0" falsevalue="--no-pi0_smooth_log_pi0" label="If True and pi0_method = 'smoother', pi0 will be estimated by applying a smoother to a scatterplot of log(pi0) estimates against the tuning parameter lambda" help="(--pi0_smooth_log_pi0 / --no-pi0_smooth_log_pi0)"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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49 <param name="lfdr_truncate" type="boolean" truevalue="--lfdr_truncate" falsevalue="--no-lfdr_truncate" checked="True" label="If True, local FDR values >1 are set to 1" help="(--lfdr_truncate / --no-lfdr_truncate)"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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50 <param name="lfdr_monotone" type="boolean" truevalue="--lfdr_monotone" falsevalue="--no-lfdr_monotone" checked="True" label="If True, local FDR values are non-decreasing with increasing p-values" help="(--lfdr_monotone / --no-lfdr_monotone)"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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51 <param argument="--lfdr_transformation" type="select" display="radio" label="Either a 'probit' or 'logit' transformation is applied to the p-values so that a local FDR estimate can be formed that does not involve edge effects of the [0,1] interval in which the p-values lie" >
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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52 <option value="probit" selected="True" >probit</option>
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53 <option value="logit">logit</option>
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54 </param>
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55 <param argument="--lfdr_adj" type="float" value="1.5" label="Numeric value that is applied as a multiple of the smoothing bandwidth used in the density estimation" />
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56 <param argument="--lfdr_eps" type="float" value="1e-08" label="Numeric value that is threshold for the tails of the empirical p-value distribution" />
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57 </inputs>
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58 <outputs>
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59 <data name="peptide_plots" format="pdf" label="${tool.name} on ${on_string}: peptides.pdf" from_work_dir="peptide.pdf" />
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60 <data name="output" format="osw" label="${tool.name} on ${on_string}: peptide.osw" from_work_dir="output.osw" />
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61 </outputs>
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62 <tests>
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63 <test expect_num_outputs="2">
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64 <param name="input" value="score.osw" ftype="osw" />
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65 <param name="context" value="experiment-wide" />
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66 <output name="output" file="peptide1.osw" compare="sim_size" />
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67 <output name="peptide_plots" file="peptide1.pdf" compare="sim_size" />
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68 </test>
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69 <test expect_num_outputs="2">
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70 <param name="input" value="peptide1.osw" ftype="osw" />
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71 <param name="context" value="global" />
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72 <output name="output" file="peptide2.osw" compare="sim_size" />
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73 <output name="peptide_plots" file="peptide2.pdf" compare="sim_size" />
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74 </test>
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75 </tests>
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76 <help>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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77 <![CDATA[
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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78 **What it does**
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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79
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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80 PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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81
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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82 Infer peptides and conduct error-rate estimation in different contexts.
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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83
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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84 PyProphet is a Python re-implementation of the mProphet algorithm (Reiter 2010 Nature Methods) optimized for SWATH-MS data acquired by data-independent acquisition (DIA). The algorithm was originally published in (Telemann 2014 Bioinformatics) and has since been extended to support new data types and analysis modes (Rosenberger 2017, Nature biotechnology and Nature methods).
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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85
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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86 For more information, visit @link@
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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87
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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88 ]]>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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89 </help>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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90 <expand macro="citations"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
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91 </tool>