Mercurial > repos > galaxyp > pyprophet_export

annotate pyprophet_export.xml @ 4:3cf580bf28e2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
author galaxyp
date Fri, 05 Jun 2020 12:38:25 -0400
parents 102d940d365c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
1 <tool id="pyprophet_export" name="PyProphet export" version="@VERSION@.1">
0
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
2 <description>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
3 Export tabular files, optional swath2stats export
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
4 </description>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
5 <macros>
2bc6bbf651b9 "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>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
7 </macros>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
8 <expand macro="requirements">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
9 <requirement type="package" version="1.16.0">bioconductor-swath2stats</requirement>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
10 <requirement type="package" version="0.8.4">r-dplyr</requirement>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
11 <requirement type="package" version="1.12.8">r-data.table</requirement>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
12 <requirement type="package" version="2.3">r-gridextra</requirement>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
13 </expand>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
14 <command detect_errors="aggressive">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
15 <![CDATA[
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
16 ln -s '$input' ./input.osw &&
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
17 pyprophet export
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
18 --in=./input.osw
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
19 --format=$conditional_output.format
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
20
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
21 #if $conditional_output.format=='legacy_split':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
22 $conditional_output.transition_quant
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
23 --max_transition_pep=$conditional_output.max_transition_pep
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
24 --ipf=$conditional_output.ipf
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
25 --ipf_max_peptidoform_pep=$conditional_output.ipf_max_peptidoform_pep
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
26 --max_rs_peakgroup_qvalue=$conditional_output.max_rs_peakgroup_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
27 --max_global_peptide_qvalue=$conditional_output.max_global_peptide_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
28 --max_global_protein_qvalue=$conditional_output.max_global_protein_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
29
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
30 #elif $conditional_output.format=='legacy_merged':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
31 $conditional_output.transition_quant
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
32 --max_transition_pep=$conditional_output.max_transition_pep
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
33 --ipf=$conditional_output.ipf
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
34 --ipf_max_peptidoform_pep=$conditional_output.ipf_max_peptidoform_pep
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
35 --max_rs_peakgroup_qvalue=$conditional_output.max_rs_peakgroup_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
36 --max_global_peptide_qvalue=$conditional_output.max_global_peptide_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
37 --max_global_protein_qvalue=$conditional_output.max_global_protein_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
38
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
39 #elif $conditional_output.format=='matrix':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
40 --ipf=$conditional_output.ipf
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
41 --ipf_max_peptidoform_pep=$conditional_output.ipf_max_peptidoform_pep
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
42 --max_rs_peakgroup_qvalue=$conditional_output.max_rs_peakgroup_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
43 --max_global_peptide_qvalue=$conditional_output.max_global_peptide_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
44 --max_global_protein_qvalue=$conditional_output.max_global_protein_qvalue
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
45 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
46 $peptide_error
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
47 $protein_error
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
48 --out=./output.tsv
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
49
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
50 #if $conditional_swath2stats.swath2stats=='yes_swath2stats':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
51 && cat '${swath2stats}'
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
52 && Rscript '${swath2stats}'
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
53 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
54
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
55 #if $conditional_output.format=='score_plots':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
56 && mv *score_plots.pdf '$score_plots'
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
57 #else:
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
58 && mv output.tsv '$export_file'
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
59 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
60
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
61
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
62 ]]>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
63 </command>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
64 <configfiles>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
65 <configfile name="swath2stats"><![CDATA[
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
66
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
67 #if $conditional_swath2stats.swath2stats=='yes_swath2stats':
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
68
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
69 library("SWATH2stats")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
70 library("data.table")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
71 library("dplyr")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
72 library(gridExtra)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
73
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
74 ########################### Input ##############################################
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
75
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
76 ## read in pyprophet export file
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
77 data_me <- data.frame(fread('output.tsv', sep='\t', header=TRUE))
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
78
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
79 ## read in study design template
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
80 study_design <- data.frame(fread('$conditional_swath2stats.study_design', sep='\t', header=TRUE))
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
81
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
82 ## merge both files on filename column
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
83 data.annotated <- sample_annotation(data_me, study_design, column.file = "filename")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
84
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
85
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
86 ########################### QC plots and tabular files #########################
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
87
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
88 ## remove decoys when generating plots
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
89 data.annotated.nodecoy <- subset(data.annotated, decoy==FALSE)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
90
4
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
91 pdf("summary.pdf", fonts = "Times", pointsize = 8)
0
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
92 plot(0,type='n',axes=FALSE,ann=FALSE)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
93 title(main="Summarized plots and tables from pyprophet export file")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
94
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
95 ## Look at Numbers of peptides and proteins per run
4
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
96 ## for many runs table needs to be split over several pages
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
97 number_samples = nrow(count_analytes(data.annotated.nodecoy))
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
98
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
99 ### for more than 20 annotation groups print only 20 samples per page:
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
100 if (number_samples <= 20){
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
101 grid.table(count_analytes(data.annotated.nodecoy), rows= NULL)
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
102 }else{
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
103 grid.table(count_analytes(data.annotated.nodecoy)[1:20,], rows= NULL)
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
104 mincount = 21
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
105 maxcount = 40
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
106 for (count15 in 1:(ceiling(number_samples/20)-1)){
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
107 plot(0,type='n',axes=FALSE,ann=FALSE)
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
108 if (maxcount <= number_samples){
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
109 grid.table(count_analytes(data.annotated.nodecoy)[mincount:maxcount,], rows= NULL)
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
110 mincount = mincount+20
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
111 maxcount = maxcount+20
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
112 }else{### stop last page with last sample otherwise NA in table
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
113 grid.table(count_analytes(data.annotated.nodecoy)[mincount:number_samples,], rows= NULL)}
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
114 }
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
115 }
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
116
0
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
117
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
118 ## Correlation of the intensities
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
119 correlation_int <- plot_correlation_between_samples(data.annotated.nodecoy, column.values = 'Intensity')
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
120
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
121 ## Plot the correlation of the delta_rt, which is the deviation of the retention time from the expected retention time
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
122 correlation_rt <- plot_correlation_between_samples(data.annotated.nodecoy, column.values = 'delta_rt')
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
123
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
124 ## Plot the variation of the signal across replicates
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
125 variation <- plot_variation(data.annotated.nodecoy)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
126 plot(0,type='n',axes=FALSE,ann=FALSE)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
127 grid.table(variation[[2]])
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
128
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
129 ## Plot the total variation versus variation within replicates
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
130 variation_total <- plot_variation_vs_total(data.annotated.nodecoy)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
131
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
132 ## Calculate the summed signal per peptide and protein across samples
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
133 peptide_signal <- write_matrix_peptides(data.annotated.nodecoy)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
134 protein_signal <- write_matrix_proteins(data.annotated.nodecoy)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
135
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
136
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
137 #if str($conditional_swath2stats.conditional_fdr_replica.calc_fdr_replica) =="calc_fdr_replica_yes":
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
138
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
139 ## Estimate the overall FDR across runs using a target decoy strategy
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
140 fdr_target_decoy <- assess_fdr_overall(data.annotated, n.range = $conditional_swath2stats.conditional_fdr_replica.n_range, FFT = $conditional_swath2stats.conditional_fdr_replica.fft, output = 'Rconsole')
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
141 print(fdr_target_decoy)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
142 dev.off()
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
143 #else
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
144 dev.off()
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
145 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
146
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
147 ############################# Filtering ########################################
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
148
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
149 data.filtered = data.annotated
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
150
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
151 #if str($conditional_swath2stats.conditional_fdr_replica.calc_fdr_replica) =="calc_fdr_replica_yes":
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
152
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
153 ## According to this FDR estimation one can filter the data with a higher mscore threshold to reach an overall protein FDR of 5%.
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
154 ## Check what m-score cut-off is requiered for Protein FDR of 5 %
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
155 cutoff_mscore = mscore4protfdr(data_me, FFT = $conditional_swath2stats.conditional_fdr_replica.fft, fdr_target = $conditional_swath2stats.conditional_fdr_replica.fdr_target)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
156 print(cutoff_mscore)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
157 ## Filter data for values that pass the 0.001 mscore criteria in at least two replicates of one condition
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
158 data.filtered <- filter_mscore_condition(data.filtered, cutoff_mscore, n.replica = $conditional_swath2stats.conditional_fdr_replica.n_replica)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
159 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
160
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
161 #if str($conditional_swath2stats.conditional_max_pep.filter_max_pep) == "filter_max_pep_yes":
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
162 ## Select only the 10 peptides showing strongest signal per protein
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
163 data.filtered <- filter_on_max_peptides(data.filtered, n_peptides = $conditional_swath2stats.conditional_max_pep.n_peptides_max)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
164 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
165
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
166
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
167 #if str($conditional_swath2stats.conditional_min_pep.filter_min_pep) == "filter_min_pep_yes":
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
168 ## Filter for proteins that are supported by at least two peptides
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
169 data.filtered <- filter_on_min_peptides(data.filtered, n_peptides = $conditional_swath2stats.conditional_min_pep.n_peptides_min)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
170 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
171
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
172 ########################### Output ############################################
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
173 ## Convert the data into a transition-level format (one row per transition measured).
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
174 data.transition <- disaggregate(data.filtered)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
175
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
176 ## Convert the data into the format required by MSstats.
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
177 MSstats.input <- convert4MSstats(data.transition)
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
178
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
179 ### Transitions which were found at different RT / multiple scans are combined by summarizing the Intensities
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
180 Test = MSstats.input %>% group_by(ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, BioReplicate, Condition, Run) %>% summarise(Intensity = sum(Intensity))
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
181
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
182 Test = Test[, c("ProteinName", "PeptideSequence", "PrecursorCharge", "FragmentIon", "ProductCharge", "IsotopeLabelType", "Intensity", "BioReplicate", "Condition", "Run")]
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
183
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
184 write.table(Test, file="$msstats_input", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
185 write.table(peptide_signal, file="$peptide_signal", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
186 write.table(protein_signal, file="$protein_signal", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
187
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
188 #end if
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
189
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
190 ]]></configfile>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
191 </configfiles>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
192 <inputs>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
193 <param name="input" type="data" format="osw" label="Input file" help="This file needs to be in OSW format (--in)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
194 <conditional name="conditional_output">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
195 <param argument="format" type="select" label="Export format, either matrix, legacy_split, legacy_merged (mProphet/PyProphet) or score_plots format" >
4
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
196 <option value="legacy_split" selected="True">legacy_split</option>
0
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
197 <option value="legacy_merged">legacy_merged</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
198 <option value="matrix">matrix</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
199 <option value="score_plots">score_plots</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
200 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
201 <when value="legacy_split">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
202
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
203 <param name="transition_quant" type="boolean" truevalue="--transition_quantification" falsevalue="--no-transition_quantification" checked="True" label="Report aggregated transition-level quantification" help="(--transition_quantification / --no-transition_quantification)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
204 <param argument="max_transition_pep" type="float" value="0.7" label="Maximum PEP to retain scored transitions for quantification (requires transition-level scoring)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
205 <param argument="ipf" type="select" display="radio" label="Should IPF results be reported if present? 'peptidoform': Report results on peptidoform-level, 'augmented': Augment OpenSWATH results with IPF scores, 'disable': Ignore IPF results" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
206 <option value="peptidoform" selected="True" >peptidoform </option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
207 <option value="augmented">augmented</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
208 <option value="disable">disable</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
209 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
210 <param argument="ipf_max_peptidoform_pep" type="float" value="0.4" label="IPF: Filter results to maximum run-specific peptidoform-level PEP" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
211 <param argument="max_rs_peakgroup_qvalue" type="float" value="0.05" label="Filter results to maximum run-specific peak group-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
212 <param argument="max_global_peptide_qvalue" type="float" value="0.01" label="Filter results to maximum global peptide-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
213 <param argument="max_global_protein_qvalue" type="float" value="0.01" label="ilter results to maximum global protein-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
214 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
215 <when value="legacy_merged">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
216
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
217 <param name="transition_quant" type="boolean" truevalue="--transition_quantification" falsevalue="--no-transition_quantification" checked="True" label="Report aggregated transition-level quantification" help="(--transition_quantification / --no-transition_quantification)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
218 <param argument="max_transition_pep" type="float" value="0.7" label="Maximum PEP to retain scored transitions for quantification (requires transition-level scoring)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
219 <param argument="ipf" type="select" display="radio" label="Should IPF results be reported if present? 'peptidoform': Report results on peptidoform-level, 'augmented': Augment OpenSWATH results with IPF scores, 'disable': Ignore IPF results" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
220 <option value="peptidoform" selected="True">peptidoform </option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
221 <option value="augmented">augmented</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
222 <option value="disable">disable</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
223 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
224 <param argument="ipf_max_peptidoform_pep" type="float" value="0.4" label="IPF: Filter results to maximum run-specific peptidoform-level PEP" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
225 <param argument="max_rs_peakgroup_qvalue" type="float" value="0.05" label="Filter results to maximum run-specific peak group-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
226 <param argument="max_global_peptide_qvalue" type="float" value="0.01" label="Filter results to maximum global peptide-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
227 <param argument="max_global_protein_qvalue" type="float" value="0.01" label="ilter results to maximum global protein-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
228 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
229 <when value="matrix">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
230
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
231 <param argument="ipf" type="select" display="radio" label="Should IPF results be reported if present? 'peptidoform': Report results on peptidoform-level, 'augmented': Augment OpenSWATH results with IPF scores, 'disable': Ignore IPF results" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
232 <option value="peptidoform" selected="True">peptidoform </option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
233 <option value="augmented">augmented</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
234 <option value="disable">disable</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
235 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
236 <param argument="ipf_max_peptidoform_pep" type="float" value="0.4" label="IPF: Filter results to maximum run-specific peptidoform-level PEP" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
237 <param argument="max_rs_peakgroup_qvalue" type="float" value="0.05" label="Filter results to maximum run-specific peak group-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
238 <param argument="max_global_peptide_qvalue" type="float" value="0.01" label="Filter results to maximum global peptide-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
239 <param argument="max_global_protein_qvalue" type="float" value="0.01" label="ilter results to maximum global protein-level q-value" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
240 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
241 <when value="score_plots"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
242 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
243 <param name="peptide_error" type="boolean" truevalue="--peptide" falsevalue="--no-peptide" checked="True" label="Append peptide-level error-rate estimates if available" help="(--peptide / --no-peptide)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
244 <param name="protein_error" type="boolean" truevalue="--protein" falsevalue="--no-protein" checked="True" label="Append protein-level error-rate estimates if available" help="(--protein / --no-protein)" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
245 <conditional name="conditional_swath2stats">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
246 <param name="swath2stats" type="select" label="Use swath2stats to export file for statsics" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
247 <option value="yes_swath2stats" selected="True">yes</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
248 <option value="no_swath2stats">no</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
249 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
250 <when value="yes_swath2stats">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
251 <param name="study_design" type="data" format="tabular" label="Study design tabular file" help="Needs to have columns with Filename, Condition, BioReplicate, Run" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
252 <conditional name="conditional_fdr_replica">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
253 <param name="calc_fdr_replica" type="select" label="Filter for fdr and number of replicates" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
254 <option value="calc_fdr_replica_yes" selected="True">Yes</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
255 <option value="calc_fdr_replica_no">No</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
256 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
257 <when value="calc_fdr_replica_yes">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
258 <param name="fft" type="float" value="0.5" label="FFT. Ratio of false positives to true negatives, q-values from pyProphet stats output" help="As an approximation, the q-values of multiple runs are averaged and supplied as argument FFT. Numeric from 0 to 1."/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
259 <param name="n_range" type="float" value="10" label="Option to set the number of magnitude for which the m_score threshold is decreased" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
260 <param name="fdr_target" type="float" value="0.05" label="FDR target." help="An m_score cutoff achieving and FDR smaller fdr_target will be selected. Calculated as FDR = decoys*FFT/targets" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
261 <param name="n_replica" type="integer" value="2" label="Number Replicates." help="Number of measurements within at least one condition that have to pass the mscore threshold for this transition." />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
262 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
263 <when value="calc_fdr_replica_no"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
264 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
265 <conditional name="conditional_max_pep">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
266 <param name="filter_max_pep" type="select" label="Filter for a maximum number of peptides per protein" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
267 <option value="filter_max_pep_yes" selected="True">Yes</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
268 <option value="filter_max_pep_no">No</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
269 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
270 <when value="filter_max_pep_yes">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
271 <param name="n_peptides_max" type="integer" value="10" label="Maximum number of peptides per protein." help="Maximum number of highest intense peptides to filter the data on." />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
272 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
273 <when value="filter_max_pep_no"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
274 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
275 <conditional name="conditional_min_pep">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
276 <param name="filter_min_pep" type="select" label="Filter for a proteins that are supported by a minimum number of peptides" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
277 <option value="filter_min_pep_yes" selected="True">Yes</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
278 <option value="filter_min_pep_no">No</option>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
279 </param>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
280 <when value="filter_min_pep_yes">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
281 <param name="n_peptides_min" type="integer" value="2" label="Minimum number of peptides per protein" help="Number of minimal number of peptide IDs associated with a protein ID in order to be kept in the dataset." />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
282 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
283 <when value="filter_min_pep_no"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
284 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
285 </when>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
286 <when value="no_swath2stats"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
287 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
288 </inputs>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
289 <outputs>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
290 <data name="export_file" format="tabular" label="${tool.name} on ${on_string}: export.tabular" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
291 <filter>conditional_output['format'] != 'score_plots'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
292 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
293 <data name="score_plots" format="pdf" label="${tool.name} on ${on_string}: score_plots.pdf" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
294 <filter>conditional_output['format'] == 'score_plots'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
295 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
296 <data name="summary" format="pdf" from_work_dir="summary.pdf" label = "${tool.name} on ${on_string}: summary.pdf">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
297 <filter>conditional_swath2stats['swath2stats'] == 'yes_swath2stats'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
298 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
299 <data name="peptide_signal" format="tabular" label="${tool.name} on ${on_string}: peptide_signal.tabular" from_work_dir="peptide_signal.tabular" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
300 <filter>conditional_swath2stats['swath2stats'] == 'yes_swath2stats'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
301 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
302 <data name="protein_signal" format="tabular" label="${tool.name} on ${on_string}: protein_signal.tabular" from_work_dir="protein_signal.tabular" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
303 <filter>conditional_swath2stats['swath2stats'] == 'yes_swath2stats'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
304 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
305 <data name="msstats_input" format="tabular" label="${tool.name} on ${on_string}: msstats_input.tabular" from_work_dir="msstats_input.tabular" >
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
306 <filter>conditional_swath2stats['swath2stats'] == 'yes_swath2stats'</filter>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
307 </data>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
308 </outputs>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
309 <tests>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
310 <test expect_num_outputs="1">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
311 <param name="input" value="protein2.osw" ftype="osw" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
312 <param name="format" value="legacy_merged" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
313 <param name="max_global_peptide_qvalue" value="0.2" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
314 <conditional name="conditional_swath2stats">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
315 <param name="swath2stats" value="no_swath2stats"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
316 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
317 <output name="export_file" file="output.tabular" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
318 </test>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
319 <test expect_num_outputs="1">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
320 <param name="input" value="protein2.osw" ftype="osw" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
321 <param name="format" value="score_plots" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
322 <conditional name="conditional_swath2stats">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
323 <param name="swath2stats" value="no_swath2stats"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
324 </conditional>
2
102d940d365c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
galaxyp
parents: 0
diff changeset
325 <output name="score_plots" file="score_plots.pdf" compare="sim_size" />
0
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
326 </test>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
327 <test expect_failure="true">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
328 <param name="input" value="protein2.osw" ftype="osw" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
329 <param name="format" value="legacy_merged" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
330 <conditional name="conditional_swath2stats">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
331 <param name="study_design" value="study_design.tabular" ftype="tabular" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
332 <conditional name="conditional_fdr_replica">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
333 <param name="calc_fdr_replica" value="calc_fdr_replica_no"/>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
334 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
335 <conditional name="conditional_max_pep">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
336 <param name="filter_max_pep" value="filter_max_pep_no" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
337 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
338 <conditional name="conditional_min_pep">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
339 <param name="filter_min_pep" value="filter_min_pep_no" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
340 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
341 </conditional>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
342 <assert_stderr>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
343 <has_text text="replacement has 1 row, data has 0" />
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
344 </assert_stderr>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
345 </test>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
346 </tests>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
347 <help>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
348 <![CDATA[
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
349 **What it does**
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
350
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
351 PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
352
4
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
353 Export tabular (tsv) tables. By default, both peptide- and transition-level quantification is reported, which is necessary for requantification or SWATH2stats. If peptide and protein inference in the global context was conducted, the results will be filtered to 1% FDR by default.
0
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
354
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
355 Optional SWATH2stats output. SWATH2stats is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
356
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
357 **Study desing file for SWATH2stats**
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
358
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
359 - Tabular file with columns that are named: Filename, Condition, BioReplicate, Run.
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
360 - The Filename should be part or the same as the original filenames used in OpenSWATH workflow
4
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
361 - The Condition will be used for statistical analysis. In case multiple conditions are of interest for statistical analysis (e.g. diagnosis and age), this tool has to be run multiple times as SWATH2stats can only handle one condition at a time
0
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
362 - The BioReplicate is corresponds to the biological replicate
4
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
363 - The Run is the number of the MS run in which the sample was measured
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
364
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
365 - **Example for one replicate per patient**
0
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
366
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
367 ::
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
368
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
369 Filename Condition BioReplicate Run
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
370 healthy1.mzml healthy 1 1
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
371 healthy2.mzml healthy 2 2
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
372 diseased1.mzml diseased 3 3
4
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
373 diseased2.mzml diseased 4 4
0
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
374 ...
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
375 ...
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
376
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
377
4
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
378 - **Example for two replicates per patient**
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
379
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
380 ::
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
381
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
382 Filename Condition BioReplicate Run
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
383 healthy1.mzml healthy 1 1
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
384 healthy2.mzml healthy 1 2
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
385 diseased1.mzml diseased 2 3
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
386 diseased2.mzml diseased 2 4
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
387 ...
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
388 ...
3cf580bf28e2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit 8b9f6963836c6ccb227343ce952e7b9a015d0483"
galaxyp
parents: 2
diff changeset
389
0
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
390 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).
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
391
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
392 For more information, visit @link@
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
393
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
394 ]]>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
395 </help>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
396 <expand macro="citations">
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
397 <citation type="doi">10.1371/journal.pone.0153160</citation>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
398 </expand>
2bc6bbf651b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit a83d231286a8df67483df46e76b4b3a2ef90b251"
galaxyp
parents:
diff changeset
399 </tool>