Mercurial > repos > galaxyp > reactome_pathwaymatcher

annotate pathwaymatcher.xml @ 3:f3be3f08dcfa draft

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/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
author galaxyp
date Wed, 08 May 2019 13:40:59 -0400
parents 03487adf8fc2
children 36cc1538f775
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
1 <tool id="reactome_pathwaymatcher" name="Pathway Matcher" version="@PATHWAYMATCHER_VERSION@.@TOOL_SUBVERSION@">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
2 <description>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
3 PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
4 </description>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
5 <macros>
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
6 <token name="@PATHWAYMATCHER_VERSION@">1.9.1</token>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
7 <token name="@TOOL_SUBVERSION@">1</token>
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
8 <xml name="input_fasta">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
9 <param format="fasta" name="input_database" type="data" label="Protein Database"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
10 help="Select FASTA database from history"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
11 </xml>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
12 </macros>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
13 <requirements>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
14 <requirement type="package" version="@PATHWAYMATCHER_VERSION@">pathwaymatcher</requirement>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
15 <requirement type="package" version="3.0">zip</requirement>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
16 </requirements>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
17 <stdio>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
18 <exit_code range="1:" level="fatal" description="Job Failed" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
19 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
20 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
21 </stdio>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
22 <command>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
23 <![CDATA[
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
24 #from datetime import datetime
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
25 #import json
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
26 #import os
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
27 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
28 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
29 #set $temp_stderr = "pathwaym_stderr"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
30 #set $bin_dir = "bin"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
31
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
32 mkdir output;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
33 cwd=`pwd`;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
34 export HOME=\$cwd;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
35
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
36 ## If we use peptideshaker files as inputs, firstly we need to uncompress their proteoforms files.
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
37 #for $i, $s in enumerate($match_types)
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
38 #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
39 ##unzip -l $s.match_type.input_peptideshakerzip_proteoforms;
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
40 unzip -j '${$s.match_type.input_peptideshakerzip_proteoforms}' 'output_reports/proteoforms.txt' -d './';
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
41 mv proteoforms.txt ps_proteoforms_'${$i}'.txt;
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
42 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
43 #end for
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
44
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
45 #####################
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
46 ## Pathway Matcher ##
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
47 #####################
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
48 (pathwaymatcher
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
49
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
50 #for $i, $s in enumerate($match_types)
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
51
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
52
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
53 ## PROTEOFORMS
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
54
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
55 #if $s.match_type.match_type_selector == "proteoforms"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
56 #if $s.match_type.proteoform_match_criteria:
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
57 match-proteoforms -m '${s.match_type.proteoform_match_criteria}' -i '${s.match_type.input_proteoforms}' -r '${s.match_type.proteoform_range}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
58 #else:
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
59 match-proteoforms -i '${s.match_type.input_proteoforms}' -r '${s.match_type.proteoform_range}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
60 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
61 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
62
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
63 ## PROTEOFORMS FROM PEPTIDESHAKER FILE
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
64
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
65 #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
66 #if $s.match_type.proteoform_peptideshakerzip_match_criteria:
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
67 match-proteoforms -m '${s.match_type.proteoform_peptideshakerzip_match_criteria}' -i ps_proteoforms_'${$i}'.txt -r '${s.match_type.proteoform_peptideshakerzip_range}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
68 #else:
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
69 match-proteoforms -i ps_proteoforms_'${$i}'.txt -r '${s.match_type.proteoform_peptideshakerzip_range}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
70 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
71 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
72
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
73
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
74 ## GENES
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
75
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
76 #if $s.match_type.match_type_selector == "gene"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
77 match-genes -i '${s.match_type.input_gene}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
78 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
79
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
80
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
81 ## PROTEINS
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
82
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
83 #if $s.match_type.match_type_selector == "uniprot"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
84 match-uniprot -i '${s.match_type.input_uniprot}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
85 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
86
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
87 #if $s.match_type.match_type_selector == "ensembl"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
88 match-ensembl -i '${s.match_type.input_ensembl}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
89 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
90
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
91
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
92 ## GENETIC VARIANTS
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
93
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
94 #if $s.match_type.match_type_selector == "vcf"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
95 match-vcf -i '${s.match_type.input_vcf}'
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
96 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
97
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
98 #if $s.match_type.match_type_selector == "chrbp"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
99 match-chrbp -i '${s.match_type.input_chrbp}'
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
100 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
101
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
102 #if $s.match_type.match_type_selector == "rsid"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
103 match-rsids -i '${s.match_type.input_rsid}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
104 #end if
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
105
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
106
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
107 ## PEPTIDES
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
108
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
109 #if $s.match_type.match_type_selector == "peptide"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
110 match-peptides -i '${s.match_type.input_peptide}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
111 -f '${s.match_type.input_database}'
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
112 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
113
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
114 #if $s.match_type.match_type_selector == "modifiedpeptide"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
115 match-modified-peptides -i '${s.match_type.input_modifiedpeptide}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
116 -f '${s.match_type.input_database}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
117 -m '${s.match_type.modifiedpeptide_match_criteria}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
118 -r '${s.match_type.modifiedpeptide_ptm_range}'
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
119 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
120
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
121
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
122 #end for
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
123
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
124 ## OUTPUT OPTIONS
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
125
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
126 #if $output_options.search_top_level_info:
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
127 -T
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
128 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
129
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
130 #set $output_graphs_list = str($output_options.output_graphs).split(',')
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
131
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
132 #if 'gg' in $output_graphs_list:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
133 -gg
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
134 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
135
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
136 #if 'gu' in $output_graphs_list:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
137 -gu
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
138 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
139
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
140 #if 'gp' in $output_graphs_list:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
141 -gp
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
142 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
143
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
144 2>> $temp_stderr);
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
145
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
146 ## We create a folder to contain graphs files.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
147 #if $output_options.output_graphs:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
148 mkdir "graphs";
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
149 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
150
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
151 #if 'gg' in $output_graphs_list:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
152 mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" ;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
153 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
154
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
155 #if 'gu' in $output_graphs_list:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
156 mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv";
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
157 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
158
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
159 #if 'gp' in $output_graphs_list:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
160 mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv";
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
161 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
162
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
163 exit_code_for_galaxy=\$?;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
164 cat $temp_stderr 2>&1;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
165 (exit \$exit_code_for_galaxy)
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
166 ]]>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
167 </command>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
168 <inputs>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
169
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
170 <repeat name="match_types" title="Match" min="1">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
171 <conditional name="match_type">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
172 <param name="match_type_selector" type="select" label="Match type"
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
173 help="">
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
174 <option value="proteoforms">Proteoforms</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
175 <option value="peptideshakerzip_proteoforms">Proteoforms from Peptideshaker Archive</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
176 <option value="gene">Genes</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
177 <option value="uniprot">Proteins - UniProt Accession list</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
178 <option value="ensembl">Proteins - Ensembl identifier list</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
179 <option value="vcf">Genetic variants - Variant Call Format Specification</option>
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
180 <option value="chrbp">Genetic variants - Chromosomes and base pairs</option>
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
181 <option value="rsid">Genetic variants - SNP rsId list</option>
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
182 <option value="peptide">Peptides - Simple list</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
183 <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option>
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
184
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
185 </param>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
186
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
187
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
188 <!-- Proteoforms -->
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
189 <when value="proteoforms">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
190 <param format="txt" name="input_proteoforms" type="data" label="Proteoforms"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
191 help="A proteoform defines a specific state of a protein.
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
192 It is composed by the protein UniProt accession, isoform and set of post translational modifications.
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
193 The input file contains one line for each proteoform. Each PTM is specified using a modification
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
194 identifier and a site, separated by ':'(semicolon). For example: '00046:133'.
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
195 The identifier is a 5 digit id from the PSI-MOD Protein Modification Onthology [6]."/>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
196
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
197 <param name="proteoform_match_criteria" type="select" label="Proteoform match criteria">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
198 <option value="STRICT">STRICT</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
199 <option value="SUPERSET">SUPERSET</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
200 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
201 <option value="SUBSET" selected="True">SUBSET</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
202 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
203 <option value="ONE">ONE</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
204 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
205 </param>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
206
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
207 <param name="proteoform_range" type="integer" value="0" label="Integer range of error for PTM sites" optional="true"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
208 help="Plus minus positions for the same PTM site"/>
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
209 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
210
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
211 <when value="peptideshakerzip_proteoforms">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
212 <param format="zip" name="input_peptideshakerzip_proteoforms" type="data" label="Proteoforms from Peptideshaker Archive"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
213 help="A proteoform defines a specific state of a protein.
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
214 It is composed by the protein UniProt accession, isoform and set of post translational modifications.
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
215 The input file contains one line for each proteoform. Each PTM is specified using a modification
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
216 identifier and a site, separated by ':'(semicolon). For example: '00046:133'.
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
217 The identifier is a 5 digit id from the PSI-MOD Protein Modification Onthology [6]."/>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
218
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
219 <param name="proteoform_peptideshakerzip_match_criteria" type="select" label="Proteoform match criteria">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
220 <option value="STRICT">STRICT</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
221 <option value="SUPERSET">SUPERSET</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
222 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
223 <option value="SUBSET" selected="True">SUBSET</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
224 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
225 <option value="ONE">ONE</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
226 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
227 </param>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
228
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
229 <param name="proteoform_peptideshakerzip_range" type="integer" value="0" label="Integer range of error for PTM sites" optional="true"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
230 help="Plus minus positions for the same PTM site"/>
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
231 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
232
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
233
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
234 <!-- Genes -->
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
235 <when value="gene">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
236 <param format="txt" name="input_gene" type="data" label="Genes"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
237 help="File with a one gene name in each line. Genes follow the HUGO gene nomenclature[3]."/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
238 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
239
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
240
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
241 <!-- Proteins -->
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
242 <when value="uniprot">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
243 <param format="txt" name="input_uniprot" type="data" label="UniProt Accession list"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
244 help="File with a one Uniprot Accession [4] in each line."/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
245 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
246
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
247 <when value="ensembl">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
248 <param format="txt" name="input_ensembl" type="data" label="Ensembl identifier list"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
249 help="File with a one Ensembl identifier [5] in each line."/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
250 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
251
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
252 <!-- Genetic variants -->
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
253
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
254 <when value="vcf">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
255 <param format="vcf" name="input_vcf" type="data" label="Variant Call Format Specification"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
256 help="The input follows the Variant Call Format Specification[2] v4.3.
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
257 It also allows the possibility to specify only the first 4 columns in the data section of the file:
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
258 CHROM, POS, ID, REF. "/>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
259 </when>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
260
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
261 <when value="chrbp">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
262 <param format="txt" name="input_chrbp" type="data" label="Chromosomes and base pairs"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
263 help="Genetic variants can also be represented using the chromosome and the base pair numbers.
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
264 The input should be sorted by chromosome number and then by base pair. "/>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
265 </when>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
266
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
267 <when value="rsid">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
268 <param format="txt" name="input_rsid" type="data" label="SNP rsId list"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
269 help="The file contains one rsid identifier as defined in dbSNP[1] on each row.
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
270 The list must be ordered by chromosome and base pair (bp). The list must not have duplicates.
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
271 All rsids must appear in the human assembly GRCh37.p13. "/>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
272 </when>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
273
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
274
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
275 <!-- Peptides -->
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
276 <when value="peptide">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
277 <param format="txt" name="input_peptide" type="data" label="Simple list"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
278 help="File with a one peptide sequence in each line."/>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
279
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
280 <expand macro="input_fasta" />
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
281
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
282 </when>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
283
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
284 <when value="modifiedpeptide">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
285 <param format="txt" name="input_modifiedpeptide" type="data" label="Peptide List with PTM types and sites"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
286 help="Each line of the file corresponds to a single peptide with post-translational modifications."/>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
287
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
288 <expand macro="input_fasta" />
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
289
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
290 <param name="modifiedpeptide_match_criteria" type="select" label="Proteoform match criteria. Only modified peptides.">
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
291 <option value="STRICT">STRICT</option>
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
292 <option value="SUPERSET">SUPERSET</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
293 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
294 <option value="SUBSET" selected="True">SUBSET</option>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
295 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option>
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
296 <option value="ONE">ONE</option>
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
297 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
298 </param>
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
299
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
300 <param name="modifiedpeptide_ptm_range" type="integer" value="0" label="PTM position range" optional="true"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
301 help="Integer number margin error for sites of PTMs. Only for modified peptides."/>
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
302 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
303
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
304
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
305
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
306 </conditional>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
307
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
308 </repeat>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
309
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
310 <section name="output_options" expanded="true" title="Output options">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
311
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
312 <param name="search_top_level_info" type="select" label="Add Top Level Pathways in the search result.">
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
313 <option value="0" selected="True">False</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
314 <option value="1">True</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
315 </param>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
316
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
317 <param name="output_graphs" type="select" display="checkboxes" multiple="True" label="Connection graphs"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
318 help="Generates a zipped file with connection graphs as an additional output when executing the pathway search and analysis.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
319 The graph can use genes, proteins or proteoforms as vertices.">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
320 <option value="gg">Genes</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
321 <option value="gu">Proteins</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
322 <option value="gp">Proteoforms</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
323 </param>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
324
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
325 </section>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
326
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
327 </inputs>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
328 <outputs>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
329 <data name="search" format="tsv" from_work_dir="search.tsv" label="${tool.name} - search on ${on_string}" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
330 <data name="analysis" format="tsv" from_work_dir="analysis.tsv" label="${tool.name} - analysis on ${on_string}" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
331 <collection name="graphs_files" type="list" label="${tool.name} - graphs on ${on_string}" >
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
332 <filter>output_options['output_graphs'] != None</filter>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
333 <discover_datasets pattern="__name_and_ext__" directory="graphs" ext="tsv"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
334 </collection>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
335 </outputs>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
336
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
337
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
338 <tests>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
339
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
340 <!-- Test that genes search works -->
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
341 <test>
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
342 <repeat name="match_types">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
343 <conditional name="match_type">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
344 <param name="match_type_selector" value="gene"/>
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
345 <param name="input_gene" value="genes.txt" ftype="txt" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
346 </conditional>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
347 </repeat>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
348 <output name="search" file="genes_search.tsv" ftype="tsv" compare="sim_size" delta="3000" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
349 </test>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
350
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
351 <!-- Test graphs from proteoforms -->
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
352 <test>
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
353 <repeat name="match_types">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
354 <conditional name="match_type">
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
355 <param name="match_type_selector" value="proteoforms"/>
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
356 <param name="input_proteoforms" value="proteoforms.txt" ftype="txt" />
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
357 <param name="proteoform_match_criteria" value="SUBSET"/>
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
358 </conditional>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
359 </repeat>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
360 <param name="output_graphs" value="gg,gu,gp" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
361 <output_collection name="graphs_files" type="list">
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
362 <!-- <element name="geneExternalEdges" ftype="tsv" file="proteoforms_graphs/geneExternalEdges.tsv" compare="sim_size" delta="1000" /> -->
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
363 <element name="geneInternalEdges" ftype="tsv" file="proteoforms_graphs/geneInternalEdges.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
364 <element name="geneVertices" ftype="tsv" file="proteoforms_graphs/geneVertices.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
365 <element name="proteinExternalEdges" ftype="tsv" file="proteoforms_graphs/proteinExternalEdges.tsv" compare="sim_size" delta="10000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
366 <element name="proteinInternalEdges" ftype="tsv" file="proteoforms_graphs/proteinInternalEdges.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
367 <element name="proteinVertices" ftype="tsv" file="proteoforms_graphs/proteinVertices.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
368 <element name="proteoformExternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformExternalEdges.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
369 <element name="proteoformInternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformInternalEdges.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
370 <element name="proteoformVertices" ftype="tsv" file="proteoforms_graphs/proteoformVertices.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
371 </output_collection>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
372 </test>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
373
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
374 </tests>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
375 <help>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
376
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
377 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
378
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
379 **Introduction**
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
380
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
381 Biological pathways are an excellent resource to analyze the causes and consequences of certain phenotypes.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
382 Most of the components of the pathways are proteins. When searching for relevant pathways to perform analysis
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
383 of a patient sample proteins, it is very common to lose information due to lack of precision in the search.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
384
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
385 This leads to result sets with many extra selected pathways that are not really related to the input sample.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
386
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
387 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
388
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
389 **What it does**
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
390
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
391 We present more fine grained approach to search, not only with the gene names, but also with post translational
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
392 modifications of the proteins, such as phosphorylation.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
393
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
394 Ultimately, any omics dataset with its mutations and
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
395 modifications will be mapped directly to the functional knowledgebases allowing the functional interpretation by
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
396 researchers and clinicians.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
397
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
398 The reference database used is Reactome, a free, open source, curated and peer reviewed database of biological reactions, that contains the quality data needed for this type of fine grained search. database of biological reactions. It can be readily queried with omics datasets, and we are improving its features by extending the matching the clinical data to the biological pathways. Not only will the gene names be used, but also mutations or post translational modifications such as phosphorylation.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
399
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
400
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
401 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
402
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
403 **Inputs and outputs**
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
404
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
405 PathwayMatcher can search for reactions and pathways with various input types, and generates mapping files to the database.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
406
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
407 The input can be:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
408
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
409 - Genetic variants
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
410 - Genes
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
411 - Peptides
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
412 - Protein
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
413 - Proteoforms
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
414
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
415 The output of PathwayMatcher is composed of two files, the Reaction and Pathway mapping and the statistical analysis of the relevant pathways.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
416
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
417 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
418
2
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
419 **Try it now**
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
420
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
421 You can easily test PathwayMatcher functionality using the example files we provide with proteoforms and proteins information of Cystic Fibrosis:
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
422
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
423 https://media.githubusercontent.com/media/PathwayAnalysisPlatform/PathwayMatcher/master/src/test/resources/Proteoforms/Simple/CysticFibrosis.txt
2
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
424
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
425 https://media.githubusercontent.com/media/PathwayAnalysisPlatform/PathwayMatcher/master/src/test/resources/Proteins/UniProt/CysticFibrosis.txt
2
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
426
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
427 You can upload them to Galaxy by directly copying and pasting their URL into the Galaxy upload dialog (the button with the arrow pointing up in the top-left area, and then choosing *Pasta/Fetch data*).
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
428
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
429 Once they appear in green in your history, they have been uploaded and you can use them as inputs in PathwayMatcher.
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
430
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
431 Now, select *Proteoforms* as input type and, in the next drop-down list, the entry of your history corresponding to the proteoforms file you uploaded.
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
432
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
433 Then, click on *insert input* to add a new PathwayMatcher input for the proteins. Select *Proteins - Uniprot accession list* as input type and, in the next drop-down list, the entry in your history corresponding to this proteins file.
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
434
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
435 **Everything is ready**. By clicking on *Execute* PathwayMatcher will run with your chosen inputs and, after a short time, it will show in your history two more files with the search results and its analysis.
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
436
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
437 .. class:: infomark
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9
galaxyp
parents: 1
diff changeset
438
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
439 Information included with this tool is a brief summary of the main one included in PathwayMatcher_.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
440
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
441 Specific information about PathwayMatcher's Input_ and Output_ may also be found there.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
442
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
443 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
444
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
445 **References**
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
446
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
447 [1] dbSNP_
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
448
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
449 [2] VCF v4.3:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
450 http://samtools.github.io/hts-specs/VCFv4.3.pdf
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
451
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
452 [3] genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2015 Jan;43(Database issue):D1079-85. doi: 10.1093/nar/gku1071. :
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
453 https://www.ncbi.nlm.nih.gov/pubmed/25361968
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
454
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
455 [4] UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45: D158-D169 (2017):
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
456 http://dx.doi.org/doi:10.1093/nar/gkw1099
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
457
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
458 [5] Ensembl:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
459 https://www.ensembl.org/info/genome/stable_ids/index.html
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
460
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
461 [6] The PSI-MOD community standard for representation of protein modification data. Nature Biotechnology 26, 864 - 866 (2008):
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
462 http://www.nature.com/nbt/journal/v26/n8/full/nbt0808-864.html
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
463
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
464 .. _dbSNP: https://www.ncbi.nlm.nih.gov/projects/SNP/
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
465 .. _PathwayMatcher: https://github.com/LuisFranciscoHS/PathwayMatcher
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
466 .. _Input: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Input
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
467 .. _Output: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Output
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
468
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
469 </help>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
470
3
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
471 <citations>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
472 <citation type="doi">doi:10.1101/375097</citation>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
473 </citations>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
parents: 2
diff changeset
474
0
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
parents:
diff changeset
475 </tool>