reactome_pathwaymatcher: pathwaymatcher.xml annotate

annotate pathwaymatcher.xml @ 1:ee1dfac35bb3 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 7e04827e48352f6b28cf2e2c93a89a270e5bf026

author	galaxyp
date	Wed, 04 Jul 2018 04:27:50 -0400
parents	1e38071ab9d5
children	03487adf8fc2

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>
1 ee1dfac35bb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 7e04827e48352f6b28cf2e2c93a89a270e5bf026 galaxyp parents: 0 diff changeset	6 <token name="@PATHWAYMATCHER_VERSION@">1.8.1</token>
0 1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	7 <token name="@TOOL_SUBVERSION@">0</token>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	8 <xml name="input_fasta">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	9 <param format="fasta" name="input_database" type="data" label="Protein Database"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	10 help="Select FASTA database from history"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	11 </xml>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	12 </macros>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	13 <requirements>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	14 <requirement type="package" version="@PATHWAYMATCHER_VERSION@">pathwaymatcher</requirement>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	15 <requirement type="package" version="3.0">zip</requirement>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	16 </requirements>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	17 <stdio>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	18 <exit_code range="1:" level="fatal" description="Job Failed" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	19 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	20 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	21 </stdio>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	22 <command>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	23 <![CDATA[
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	24 #from datetime import datetime
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	25 #import json
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	26 #import os
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	27 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	28 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	29 #set $temp_stderr = "pathwaym_stderr"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	30 #set $bin_dir = "bin"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	31
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	32 mkdir output;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	33 cwd=`pwd`;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	34 export HOME=\$cwd;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	35
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	36 #####################
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	37 ## Pathway Matcher ##
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	38 #####################
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	39 (pathwaymatcher src.main.java.no.uib.pap.pathwaymatcher.PathwayMatcher
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	40
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	41 #for $i, $s in enumerate($input_types)
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	42
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	43 ## GENETIC VARIANTS
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	44
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	45 #if $s.input_type.input_type_selector == "rsid"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	46 -t rsid -i '${s.input_type.input_rsid}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	47 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	48
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	49 #if $s.input_type.input_type_selector == "chrbp"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	50 -t chrbp -i '${s.input_type.input_chrbp}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	51 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	52
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	53 #if $s.input_type.input_type_selector == "vcf"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	54 -t vcf -i '${s.input_type.input_vcf}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	55 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	56
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	57 ## GENES
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	58
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	59 #if $s.input_type.input_type_selector == "gene"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	60 -t gene -i '${s.input_type.input_gene}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	61 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	62
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	63 ## PEPTIDES
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	64
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	65 #if $s.input_type.input_type_selector == "peptide"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	66 -t peptide -i '${s.input_type.input_peptide}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	67 -f '${s.input_type.input_database}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	68 -r '${s.input_type.ptm_range}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	69 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	70
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	71 #if $s.input_type.input_type_selector == "modifiedpeptide"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	72 -t modifiedpeptide -i '${s.input_type.input_modifiedpeptide}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	73 -f '${s.input_type.input_database}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	74 -r '${s.input_type.ptm_range}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	75 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	76
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	77 ## PROTEINS
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	78
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	79 #if $s.input_type.input_type_selector == "uniprot"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	80 -t uniprot -i '${s.input_type.input_uniprot}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	81 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	82
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	83 #if $s.input_type.input_type_selector == "ensembl"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	84 -t ensembl -i '${s.input_type.input_ensembl}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	85 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	86
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	87 ## PROTEOFORMS
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	88
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	89 #if $s.input_type.input_type_selector == "proteoforms"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	90 #if $s.input_type.proteoform_match_criteria:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	91 -t proteoform -m '${s.input_type.proteoform_match_criteria}' -i '${s.input_type.input_proteoforms}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	92 #else:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	93 -t proteoform -i '${s.input_type.input_proteoforms}'
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	94 #end if
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
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	97 #end for
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	98
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	99 ## OUTPUT OPTIONS
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	100
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	101 #if $output_options.search_top_level_info:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	102 -tlp
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	103 #end if
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 #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	106
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	107 #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	108 -gg
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	109 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	110
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	111 #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	112 -gu
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	113 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	114
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	115 #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	116 -gp
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	117 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	118
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	119 2>> $temp_stderr);
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 ## 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	122 #if $output_options.output_graphs:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	123 mkdir "graphs";
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	124 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	125
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	126 #if '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	127 mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" ;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	128 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	129
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	130 #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	131 mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv";
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	132 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	133
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	134 #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	135 mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv";
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	136 #end if
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	137
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	138 exit_code_for_galaxy=\$?;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	139 cat $temp_stderr 2>&1;
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	140 (exit \$exit_code_for_galaxy)
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	141 ]]>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	142 </command>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	143 <inputs>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	144
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	145 <repeat name="input_types" title="Input" min="1">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	146 <conditional name="input_type">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	147 <param name="input_type_selector" type="select" label="Input type"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	148 help="">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	149 <option value="rsid">Genetic variants - SNP rsId list</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	150 <option value="chrbp">Genetic variants - Chromosomes and base pairs</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	151 <option value="vcf">Genetic variants - Variant Call Format Specification</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	152 <option value="gene">Genes</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	153 <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	154 <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	155 <option value="uniprot">Proteins - UniProt Accession list</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	156 <option value="ensembl">Proteins - Ensembl identifier list</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	157 <option value="proteoforms">Proteoforms</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	158 </param>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	159
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	160 <!-- Genetic variants -->
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	161 <when value="rsid">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	162 <param format="txt" name="input_rsid" type="data" label="SNP rsId list"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	163 help="The file contains one rsid identifier as defined in dbSNP[1] on each row.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	164 The list must be ordered by chromosome and base pair (bp). The list must not have duplicates.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	165 All rsids must appear in the human assembly GRCh37.p13. "/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	166 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	167
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	168 <when value="chrbp">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	169 <param format="txt" name="input_chrbp" type="data" label="Chromosomes and base pairs"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	170 help="Genetic variants can also be represented using the chromosome and the base pair numbers.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	171 The input should be sorted by chromosome number and then by base pair. "/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	172 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	173
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	174 <when value="vcf">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	175 <param format="vcf" name="input_vcf" type="data" label="Variant Call Format Specification"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	176 help="The input follows the Variant Call Format Specification[2] v4.3.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	177 It also allows the possibility to specify only the first 4 columns in the data section of the file:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	178 CHROM, POS, ID, REF. "/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	179 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	180
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	181 <!-- Genes -->
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	182 <when value="gene">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	183 <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	184 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	185 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	186
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	187 <!-- Peptides -->
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	188 <when value="peptide">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	189 <param format="txt" name="input_peptide" type="data" label="Simple list"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	190 help="File with a one peptide sequence in each line."/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	191
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	192 <expand macro="input_fasta" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	193
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	194 <param name="ptm_range" type="integer" value="0" label="PTM position range" optional="true"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	195 help="Plus minus positions for the same PTM site."/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	196 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	197
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	198 <when value="modifiedpeptide">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	199 <param format="txt" name="input_modifiedpeptide" type="data" label="Peptide List with PTM types and sites"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	200 help="Each line of the file corresponds to a single peptide with post-translational modifications."/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	201
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	202 <expand macro="input_fasta" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	203
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	204 <param name="ptm_range" type="integer" value="0" label="PTM position range" optional="true"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	205 help="Plus minus positions for the same PTM site."/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	206 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	207
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	208 <!-- Proteins -->
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	209 <when value="uniprot">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	210 <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	211 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	212 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	213
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	214 <when value="ensembl">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	215 <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	216 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	217 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	218
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	219 <!-- Proteoforms -->
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	220 <when value="proteoforms">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	221 <param format="txt" name="input_proteoforms" type="data" label="Proteoforms"
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	222 help="A proteoform defines a specific state of a protein.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	223 It is composed by the protein UniProt accession, isoform and set of post translational modifications.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	224 The input file contains one line for each proteoform. Each PTM is specified using a modification
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	225 identifier and a site, separated by ':'(semicolon). For example: '00046:133'.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	226 The identifier is a 5 digit id from the PSI-MOD Protein Modification Onthology [6]."/>
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 <param name="proteoform_match_criteria" type="select" label="Proteoform match criteria">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	229 <option value="STRICT">STRICT</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	230 <option value="ONE">ONE</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	231 <option value="SUPERSET" selected="True">SUPERSET</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	232 <option value="SUBSET">SUBSET</option>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	233 </param>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	234 </when>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	235
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	236 </conditional>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	237
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	238 </repeat>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	239
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	240 <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	241
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	242 <param name="search_top_level_info" type="select" label="Add search top level info">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	243 <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	244 <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	245 </param>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	246
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	247 <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	248 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	249 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	250 <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	251 <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	252 <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	253 </param>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	254
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	255 </section>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	256
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	257 </inputs>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	258 <outputs>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	259 <data name="search" format="tsv" from_work_dir="search.tsv" label="${tool.name} - search on ${on_string}" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	260 <data name="analysis" format="tsv" from_work_dir="analysis.tsv" label="${tool.name} - analysis on ${on_string}" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	261 <collection name="graphs_files" type="list" label="${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	262 <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	263 <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	264 </collection>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	265 </outputs>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	266
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	267
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	268 <tests>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	269
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	270 <!-- 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	271 <test>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	272 <repeat name="input_types">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	273 <conditional name="input_type">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	274 <param name="input_type_selector" value="gene"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	275 <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	276 </conditional>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	277 </repeat>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	278 <output name="search" file="genes_search.tsv" ftype="tsv" compare="sim_size" delta="3000" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	279 </test>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	280
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	281 <!-- 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	282 <test>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	283 <repeat name="input_types">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	284 <conditional name="input_type">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	285 <param name="input_type_selector" value="proteoforms"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	286 <param name="input_proteoforms" value="proteoforms.txt" ftype="txt" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	287 </conditional>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	288 </repeat>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	289 <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	290 <output_collection name="graphs_files" type="list">
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	291 <element name="geneExternalEdges" ftype="tsv" file="proteoforms_graphs/geneExternalEdges.tsv" compare="sim_size" delta="1000" />
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	292 <element name="geneInternalEdges" ftype="tsv" file="proteoforms_graphs/geneInternalEdges.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	293 <element name="geneVertices" ftype="tsv" file="proteoforms_graphs/geneVertices.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	294 <element name="proteinExternalEdges" ftype="tsv" file="proteoforms_graphs/proteinExternalEdges.tsv" compare="sim_size" delta="10000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	295 <element name="proteinInternalEdges" ftype="tsv" file="proteoforms_graphs/proteinInternalEdges.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	296 <element name="proteinVertices" ftype="tsv" file="proteoforms_graphs/proteinVertices.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	297 <element name="proteoformExternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformExternalEdges.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	298 <element name="proteoformInternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformInternalEdges.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	299 <element name="proteoformVertices" ftype="tsv" file="proteoforms_graphs/proteoformVertices.tsv" compare="sim_size" delta="1000"/>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	300 </output_collection>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	301 </test>
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 </tests>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	304 <help>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	305
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	306 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	307
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	308 Introduction
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	309
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	310 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	311 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	312 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	313
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	314 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	315
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	316 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	317
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	318 What it does
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	319
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	320 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	321 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	322
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	323 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	324 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	325 researchers and clinicians.
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	326
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	327 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	328
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	329
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	330 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	331
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	332 Inputs and outputs
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	333
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	334 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	335
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	336 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	337
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	338 - Genetic variants
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	339 - Genes
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	340 - Peptides
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	341 - Protein
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	342 - Proteoforms
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	343
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	344 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	345
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	346 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	347
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	348 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	349
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	350 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	351
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	352
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	353 .. class:: infomark
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	354
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	355 References
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	356
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	357 [1] dbSNP_
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	358
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	359 [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	360 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	361
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	362 [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	363 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	364
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	365 [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	366 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	367
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	368 [5] Ensembl:
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	369 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	370
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	371 [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	372 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	373
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	374 .. _dbSNP: https://www.ncbi.nlm.nih.gov/projects/SNP/
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	375 .. _PathwayMatcher: https://github.com/LuisFranciscoHS/PathwayMatcher
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	376 .. _Input: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Input
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	377 .. _Output: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Output
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	378
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	379 </help>
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	380
1e38071ab9d5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	381 </tool>

Mercurial > repos > galaxyp > reactome_pathwaymatcher

annotate pathwaymatcher.xml @ 1:ee1dfac35bb3 draft