annotate pyprophet_peptide.xml @ 0:611120fd1717 draft

"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
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
2 <description>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
3 Peptide error-rate estimation
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
4 </description>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
5 <macros>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
6 <import>macros.xml</import>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
7 </macros>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
8 <expand macro="requirements"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
9 <command detect_errors="aggressive">
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
10 <![CDATA[
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
11 pyprophet peptide
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
12 --in='$input'
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
13 --context=$context
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
14 $parametric
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
15 $pfdr
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
16 --pi0_lambda=$pi0_lambda_start $pi0_lambda_end $pi0_lambda_steps
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
17 --pi0_method=$pi0_method
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
18 --pi0_smooth_df=$pi0_smooth_df
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
19 $pi0_smooth_log
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
20 $lfdr_truncate
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
21 $lfdr_monotone
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
22 --lfdr_transformation=$lfdr_transformation
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
23 --lfdr_adj=$lfdr_adj
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
24 --lfdr_eps=$lfdr_eps
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
26
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
27
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
28 ]]>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
29 </command>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
30 <inputs>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
35 <option value="global">global</option>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
36 </param>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
37 <!-- sollte peptide-level FDR heißen?-->
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
42 <param name="pi0_lambda_steps" type="float" value="0.05" label="Use non-parametric estimation of p-values. Steps value" help="(--pi0_lambda)"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
45 <option value="smoother">smoother</option>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
46 </param>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
52 <option value="probit" selected="True" >probit</option>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
53 <option value="logit">logit</option>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
54 </param>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
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" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
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" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
57 </inputs>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
58 <outputs>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
59 <data name="peptide_plots" format="pdf" label="${tool.name} on ${on_string}: peptides.pdf" from_work_dir="peptide.pdf" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
60 <data name="output" format="osw" label="${tool.name} on ${on_string}: peptide.osw" from_work_dir="output.osw" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
61 </outputs>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
62 <tests>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
63 <test expect_num_outputs="2">
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
64 <param name="input" value="score.osw" ftype="osw" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
65 <param name="context" value="experiment-wide" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
66 <output name="output" file="peptide1.osw" compare="sim_size" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
67 <output name="peptide_plots" file="peptide1.pdf" compare="sim_size" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
68 </test>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
69 <test expect_num_outputs="2">
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
70 <param name="input" value="peptide1.osw" ftype="osw" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
71 <param name="context" value="global" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
72 <output name="output" file="peptide2.osw" compare="sim_size" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
73 <output name="peptide_plots" file="peptide2.pdf" compare="sim_size" />
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
74 </test>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
75 </tests>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
76 <help>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
77 <![CDATA[
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
78 **What it does**
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
79
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
81
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
83
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
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"
galaxyp
parents:
diff changeset
85
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
86 For more information, visit @link@
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
87
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
88 ]]>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
89 </help>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
90 <expand macro="citations"/>
611120fd1717 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
91 </tool>