reactome_pathwaymatcher: pathwaymatcher.xml annotate

annotate pathwaymatcher.xml @ 6:b43dec819c48 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967"

author	galaxyp
date	Mon, 06 Apr 2020 23:18:10 +0000
parents	00ee806dd5ff
children

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>
6 b43dec819c48 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967" galaxyp parents: 5 diff changeset	7 <token name="@TOOL_SUBVERSION@">4</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>
6 b43dec819c48 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967" galaxyp parents: 5 diff changeset	16 <requirement type="package" version="8.31">coreutils</requirement>
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	17 </requirements>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	18 <stdio>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	19 <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	20 <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	21 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	22 <regex match="filename not matched: reports/proteins_proteoforms.txt" level="fatal" description="PeptideShaker archive does not contain the proteoforms file. It may have been created by a 1.x PeptideShaker version."/>
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	23 </stdio>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	24 <command>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	25 <![CDATA[
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	26 #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	27 #import json
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	28 #import os
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	29 #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	30 #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	31 #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	32 #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	33
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	34 mkdir output;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	35 cwd=`pwd`;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	36 export HOME=\$cwd;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	37
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	38 ## If we use peptideshaker 2.x files as inputs, firstly we need to uncompress their proteoforms files.
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	39 #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	40 #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms"
6 b43dec819c48 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967" galaxyp parents: 5 diff changeset	41 unzip -j '${$s.match_type.input_peptideshakerzip_proteoforms}' 'reports/proteins_proteoforms.txt' -d './' &&
b43dec819c48 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967" galaxyp parents: 5 diff changeset	42 mv proteins_proteoforms.txt ps_proteoforms_'${$i}'.txt &&
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	43 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	44 #end for
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	45
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	46 #####################
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	47 ## Pathway Matcher ##
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	48 #####################
6 b43dec819c48 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967" galaxyp parents: 5 diff changeset	49 pathwaymatcher
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	50
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	51 #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	52 ## PROTEOFORMS
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	53
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	54 #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	55 #if $s.match_type.proteoform_match_criteria:
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	56 match-proteoforms -m '${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	57 #else:
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	58 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	59 #end if
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
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	62 ## 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	63
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	64 #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	65 #if $s.match_type.proteoform_peptideshakerzip_match_criteria:
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	66 match-proteoforms -m '${s.match_type.proteoform_peptideshakerzip_match_criteria}' -i ps_proteoforms_'${$i}'.txt -r '${s.match_type.proteoform_peptideshakerzip_range}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	67 #else:
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	68 match-proteoforms -i ps_proteoforms_'${$i}'.txt -r '${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	69 #end if
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
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 ## GENES
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	74
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	75 #if $s.match_type.match_type_selector == "gene"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	76 match-genes -i '${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	77 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	78
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 ## PROTEINS
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	81
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	82 #if $s.match_type.match_type_selector == "uniprot"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	83 match-uniprot -i '${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	84 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	85
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	86 #if $s.match_type.match_type_selector == "ensembl"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	87 match-ensembl -i '${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	88 #end if
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	89
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	90
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	91 ## GENETIC VARIANTS
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	92
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	93 #if $s.match_type.match_type_selector == "vcf"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	94 match-vcf -i '${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	95 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	96
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	97 #if $s.match_type.match_type_selector == "chrbp"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	98 match-chrbp -i '${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	99 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	100
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	101 #if $s.match_type.match_type_selector == "rsid"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	102 match-rsids -i '${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	103 #end if
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	104
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 ## PEPTIDES
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	107
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	108 #if $s.match_type.match_type_selector == "peptide"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	109 match-peptides -i '${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	110 -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	111 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	112
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	113 #if $s.match_type.match_type_selector == "modifiedpeptide"
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	114 match-modified-peptides -i '${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	115 -f '${s.match_type.input_database}'
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	116 -m '${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	117 -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	118 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	119 #end for
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 ## OUTPUT OPTIONS
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	122
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	123 #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	124 -T
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	125 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	126
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	127 #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	128
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	129 #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	130 -gg
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	131 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	132
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	133 #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	134 -gu
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	135 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	136
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	137 #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	138 -gp
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	139 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	140
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	141 ## 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	142 #if $output_options.output_graphs:
6 b43dec819c48 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967" galaxyp parents: 5 diff changeset	143 && mkdir "graphs"
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	144 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	145 #if 'gg' in $output_graphs_list:
6 b43dec819c48 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967" galaxyp parents: 5 diff changeset	146 && mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv"
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	147 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	148 #if 'gu' in $output_graphs_list:
6 b43dec819c48 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967" galaxyp parents: 5 diff changeset	149 && mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv"
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	150 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	151 #if 'gp' in $output_graphs_list:
6 b43dec819c48 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967" galaxyp parents: 5 diff changeset	152 && mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv"
0 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 </command>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	156 <inputs>
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	157 <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	158 <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	159 <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	160 help="">
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	161 <option value="proteoforms">Proteoforms</option>
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	162 <option value="peptideshakerzip_proteoforms">Proteoforms from Peptideshaker 2.x Archive</option>
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	163 <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	164 <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	165 <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	166 <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	167 <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	168 <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	169 <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	170 <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	171 </param>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	172
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	173 <!-- Proteoforms -->
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	174 <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	175 <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	176 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	177 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	178 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	179 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	180 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	181
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	182 <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	183 <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	184 <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	185 <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	186 <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	187 <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	188 <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	189 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	190 <option value="ACCESSION">ACCESSION</option>
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	191 </param>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	192
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	193 <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	194 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	195 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	196
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	197 <when value="peptideshakerzip_proteoforms">
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	198 <param format="zip" name="input_peptideshakerzip_proteoforms" type="data" label="Proteoforms from Peptideshaker 2.x Archive"
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	199 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	200 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	201 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	202 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	203 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	204
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	205 <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	206 <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	207 <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	208 <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	209 <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	210 <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	211 <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	212 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	213 <option value="ACCESSION">ACCESSION</option>
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	214 </param>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	215
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	216 <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	217 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	218 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	219
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	220
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	221 <!-- Genes -->
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	222 <when value="gene">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	223 <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	224 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	225 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	226
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	227
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	228 <!-- Proteins -->
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	229 <when value="uniprot">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	230 <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	231 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	232 </when>
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 <when value="ensembl">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	235 <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	236 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	237 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	238
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	239 <!-- Genetic variants -->
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	240
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	241 <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	242 <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	243 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	244 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	245 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	246 </when>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	247
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	248 <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	249 <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	250 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	251 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	252 </when>
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="rsid">
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="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	256 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	257 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	258 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	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
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	261
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	262 <!-- Peptides -->
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	263 <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	264 <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	265 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	266
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	267 <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	268
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	269 </when>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	270
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	271 <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	272 <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	273 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	274
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	275 <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	276
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	277 <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	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	285 <option value="ACCESSION">ACCESSION</option>
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	286 </param>
3 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 <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	289 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	290 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	291
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	292 </conditional>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	293
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	294 </repeat>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	295
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	296 <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	297
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	298 <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	299 <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	300 <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	301 </param>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	302
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	303 <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	304 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	305 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	306 <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	307 <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	308 <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	309 </param>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	310
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	311 </section>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	312
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	313 </inputs>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	314 <outputs>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	315 <data name="search" format="tsv" from_work_dir="search.tsv" label="${tool.name} - search on ${on_string}" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	316 <data name="analysis" format="tsv" from_work_dir="analysis.tsv" label="${tool.name} - analysis on ${on_string}" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	317 <collection name="graphs_files" type="list" label="${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	318 <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	319 <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	320 </collection>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	321 </outputs>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	322
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	323
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	324 <tests>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	325
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	326 <!-- 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	327 <test>
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	328 <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	329 <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	330 <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	331 <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	332 </conditional>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	333 </repeat>
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	334 <output name="search" ftype="tsv" >
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	335 <assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	336 <has_line_matching expression="CFTR\tP13569\tR-HSA-383190\tHCO3- transport through ion channel\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	337 <has_line_matching expression="TGFB1\tP01137\tR-HSA-170850\tPhosphorylated SMAD2/3 dissociates from TGFBR\tR-HSA-170834\tSignaling by TGF-beta Receptor Complex\tR-HSA-162582\tSignal Transduction"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	338 <has_line_matching expression="SCNN1B\tP51168\tR-HSA-2682349\tRAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	339 <has_line_matching expression="TNFRSF1A\tP19438\tR-HSA-5626988\tTNF-alpha:TNFR1 binds NSMAF\tR-HSA-75893\tTNF signaling\tR-HSA-162582\tSignal Transduction"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	340 <has_n_columns n="8" />
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	341 </assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	342 </output>
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	343 </test>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	344
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	345 <!-- 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	346 <test>
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	347 <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	348 <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	349 <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	350 <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	351 <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	352 </conditional>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	353 </repeat>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	354 <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	355 <output_collection name="graphs_files" type="list">
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	356 <element name="geneExternalEdges" ftype="tsv">
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	357 <assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	358 <has_line_matching expression="ERBB4\tSRC\tReaction\tR-HSA-1963586\tcatalyst\tcatalyst"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	359 <has_line_matching expression="RNF85\tSRC1\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	360 <has_line_matching expression="CBL2\tUNQ2500/PRO5800\tReaction\tR-HSA-5654677\tinput\tinput"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	361 <has_line_matching expression="FN1\tPRKM3\tReaction\tR-HSA-5672973\tcatalyst\toutput"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	362 <has_line_matching expression="MAPK11\tMAPK12\tSet\tR-HSA-448855\tmember/candidate\tmember/candidate"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	363 <has_line_matching expression="SAPK2B\tSAPK3\tSet\tR-HSA-448855\tmember/candidate\tmember/candidate"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	364 <has_n_columns n="6" />
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	365 </assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	366 </element>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	367 <element name="geneInternalEdges" ftype="tsv" file="proteoforms_graphs/geneInternalEdges.tsv" compare="sim_size" delta="10"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	368 <element name="geneVertices" ftype="tsv">
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	369 <assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	370 <has_line_matching expression="ERK1\tMitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	371 <has_line_matching expression="CREB1\tCyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ]"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	372 <has_line_matching expression="SAPK2\tMitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	373 <has_line_matching expression="STAT5\tSignal transducer and activator of transcription 5A ]"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	374 <has_n_columns n="2" />
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	375 </assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	376 </element>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	377 <element name="proteinExternalEdges" ftype="tsv">
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	378 <assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	379 <has_line_matching expression="P12931\tP56975\tReaction\tR-HSA-1963586\tcatalyst\toutput"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	380 <has_line_matching expression="P12931\tP51617\tReaction\tR-HSA-2316434\tcatalyst\tregulator"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	381 <has_line_matching expression="P12931\tQ8N302\tReaction\tR-HSA-6802933\tcatalyst\tinput"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	382 <has_line_matching expression="O95352\tP12931\tComplex\tR-HSA-6802695\tcomponent\tcomponent"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	383 <has_line_matching expression="Q15759\tQ16539\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	384 <has_n_columns n="6" />
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	385 </assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	386 </element>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	387 <element name="proteinInternalEdges" ftype="tsv">
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	388 <assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	389 <has_line_matching expression="P00519\tP12931\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	390 <has_line_matching expression="P12931\tQ9UQC2\tReaction\tR-HSA-205234\toutput\toutput"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	391 <has_line_matching expression="P12931\tP27361\tReaction\tR-HSA-6802933\tinput\toutput"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	392 <has_line_matching expression="P12931\tP27361\tReaction\tR-HSA-6802910\tinput\tinput"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	393 <has_line_matching expression="P00519\tP12931\tSet\tR-HSA-8942611\tmember/candidate\tmember/candidate"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	394 <has_line_matching expression="P12931\tP42229\tComplex\tR-HSA-1469999\tcomponent\tcomponent"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	395 <has_n_columns n="6" />
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	396 </assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	397 </element>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	398 <element name="proteinVertices" ftype="tsv">
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	399 <assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	400 <has_line_matching expression="P16220\tCyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ]"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	401 <has_line_matching expression="P27361\tMitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	402 <has_line_matching expression="P42229\tSignal transducer and activator of transcription 5A ]"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	403 <has_n_columns n="2" />
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	404 </assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	405 </element>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	406 <element name="proteoformExternalEdges" ftype="tsv">
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	407 <assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	408 <has_line_matching expression="O43597;00048:55,00048:227\tP22681;\tComplex\tR-HSA-934576\tcomponent\tcomponent"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	409 <has_line_matching expression="P00533;00048:992,00048:1045,00048:1068,00048:1086,00048:1148,00048:1173\tP22681;\tComplex\tR-HSA-182935\tcomponent\tcomponent"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	410 <has_line_matching expression="P27361;00047:202,00048:204\tP28482;00047:185,00048:187\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	411 <has_line_matching expression="P12931;00048:419\tQ01196;\tComplex\tR-HSA-8937687\tcomponent\tcomponent"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	412 <has_line_matching expression="P15509;\tP42229;00048:694\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	413 <has_n_columns n="6" />
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	414 </assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	415 </element>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	416 <element name="proteoformInternalEdges" ftype="tsv">
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	417 <assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	418 <has_line_matching expression="P27361;00047:202,00048:204\tQ15759;00047:180,00048:182\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	419 <has_line_matching expression="P27361;00047:202,00048:204\tQ15759;00047:180,00048:182\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	420 <has_n_columns n="6" />
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	421 </assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	422 </element>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	423 <element name="proteoformVertices" ftype="tsv">
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	424 <assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	425 <has_line_matching expression="P16220;00046:133\tCyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ]"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	426 <has_line_matching expression="Q15759;00047:180,00048:182\tMitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	427 <has_line_matching expression="P42229;00048:694\tSignal transducer and activator of transcription 5A ]"/>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	428 <has_n_columns n="2" />
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	429 </assert_contents>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	430 </element>
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	431
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	432 </output_collection>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	433 </test>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	434
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	435 </tests>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	436 <help>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	437
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	438 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	439
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	440 Introduction
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	441
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	442 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	443 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	444 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	445
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	446 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	447
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	448 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	449
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	450 What it does
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 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	453 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	454
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	455 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	456 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	457 researchers and clinicians.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	458
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	459 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	460
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	461
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	462 .. class:: infomark
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 Inputs and outputs
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	465
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	466 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	467
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	468 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	469
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	470 - Genetic variants
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	471 - Genes
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	472 - Peptides
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	473 - Protein
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	474 - Proteoforms
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	475
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	476 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	477
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	478 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	479
2 03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9 galaxyp parents: 1 diff changeset	480 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	481
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	482 You can easily test PathwayMatcher functionality creating text files with the example data we provide with proteoforms and proteins information of Cystic Fibrosis:
2 03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9 galaxyp parents: 1 diff changeset	483
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	484 Proteoforms:
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	485
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	486 ::
2 03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9 galaxyp parents: 1 diff changeset	487
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	488 P01137;
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	489 P10145;
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	490 P12318;
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	491 P12318;00048:288,00048:304
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	492 P13569;
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	493 P13569;01148:null
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	494 P19438;
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	495 P37088;
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	496 P37088;01148:null
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	497 P51168;
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	498 P51170;
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	499 P51170;01148:null
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	500 Q14CN2;
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	501 Q16623;
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	502 Q9UJW0;
2 03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9 galaxyp parents: 1 diff changeset	503
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	504 Proteins:
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	505 ::
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	506
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	507 P13569
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	508 P01137
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	509 P12318
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	510 Q9UJW0
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	511 P51168
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	512 P51170
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	513 P37088
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	514 P19438
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	515 Q14CN2
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	516 Q16623
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	517 P10145
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	518
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	519 After copying and pasting this data into new text files, you can upload them to Galaxy by directly using the Galaxy upload dialog (the button with the arrow pointing up in the top-left area, and then choosing Choose local file).
2 03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9 galaxyp parents: 1 diff changeset	520
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9 galaxyp parents: 1 diff changeset	521 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	522
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9 galaxyp parents: 1 diff changeset	523 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	524
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9 galaxyp parents: 1 diff changeset	525 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	526
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9 galaxyp parents: 1 diff changeset	527 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	528
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9 galaxyp parents: 1 diff changeset	529 .. class:: infomark
03487adf8fc2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 069a6264f2c44e1374fdd9d2be0a41527ec5fed9 galaxyp parents: 1 diff changeset	530
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	531 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	532
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	533 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	534
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	535 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	536
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	537 References
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	538
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	539 [1] dbSNP_
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	540
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	541 [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	542 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	543
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	544 [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	545 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	546
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	547 [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	548 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	549
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	550 [5] Ensembl:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	551 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	552
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	553 [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	554 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	555
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	556 .. _dbSNP: https://www.ncbi.nlm.nih.gov/projects/SNP/
4 36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	557 .. _PathwayMatcher: https://github.com/PathwayAnalysisPlatform/PathwayMatcher
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	558 .. _Input: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/wiki/Input
36cc1538f775 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa galaxyp parents: 3 diff changeset	559 .. _Output: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/wiki/Output
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	560
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	561 </help>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	562
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	563 <citations>
5 00ee806dd5ff planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit e86212821a8621c4e99150c6fd7e4c4a1437a110 galaxyp parents: 4 diff changeset	564 <citation type="doi">doi:10.1093/gigascience/giz088</citation>
3 f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	565 </citations>
f3be3f08dcfa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b galaxyp parents: 2 diff changeset	566
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	567 </tool>

Mercurial > repos > galaxyp > reactome_pathwaymatcher

annotate pathwaymatcher.xml @ 6:b43dec819c48 draft default tip