reactome_pathwaymatcher: pathwaymatcher.xml annotate

annotate pathwaymatcher.xml @ 0:f66af2b04a98 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a

author	galaxyp
date	Wed, 20 Jun 2018 14:21:10 -0400
parents
children	5d0c44bc354d

rev	line source
0 f66af2b04a98 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@">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	2 <description>
f66af2b04a98 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.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	4 </description>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	5 <macros>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	6 <token name="@PATHWAYMATCHER_VERSION@">1.8</token>
f66af2b04a98 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>
f66af2b04a98 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">
f66af2b04a98 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"
f66af2b04a98 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"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	11 </xml>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	12 </macros>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	13 <requirements>
f66af2b04a98 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>
f66af2b04a98 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>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	16 </requirements>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	17 <stdio>
f66af2b04a98 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" />
f66af2b04a98 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"/>
f66af2b04a98 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"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	21 </stdio>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	22 <command>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	23 <![CDATA[
f66af2b04a98 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
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	25 #import json
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	26 #import os
f66af2b04a98 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")
f66af2b04a98 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")
f66af2b04a98 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"
f66af2b04a98 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"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	31
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	32 mkdir output;
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	33 cwd=`pwd`;
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	34 export HOME=\$cwd;
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	35
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	36 #####################
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	37 ## Pathway Matcher ##
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	38 #####################
f66af2b04a98 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
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	40
f66af2b04a98 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)
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	42
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	43 ## GENETIC VARIANTS
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	44
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	45 #if $s.input_type.input_type_selector == "rsid"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	46 -t rsid -i '${s.input_type.input_rsid}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	47 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	48
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	49 #if $s.input_type.input_type_selector == "chrbp"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	50 -t chrbp -i '${s.input_type.input_chrbp}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	51 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	52
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	53 #if $s.input_type.input_type_selector == "vcf"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	54 -t vcf -i '${s.input_type.input_vcf}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	55 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	56
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	57 ## GENES
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	58
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	59 #if $s.input_type.input_type_selector == "gene"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	60 -t gene -i '${s.input_type.input_gene}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	61 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	62
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	63 ## PEPTIDES
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	64
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	65 #if $s.input_type.input_type_selector == "peptide"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	66 -t peptide -i '${s.input_type.input_peptide}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	67 -f '${s.input_type.input_database}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	68 -r '${s.input_type.ptm_range}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	69 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	70
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	71 #if $s.input_type.input_type_selector == "modifiedpeptide"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	72 -t modifiedpeptide -i '${s.input_type.input_modifiedpeptide}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	73 -f '${s.input_type.input_database}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	74 -r '${s.input_type.ptm_range}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	75 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	76
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	77 ## PROTEINS
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	78
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	79 #if $s.input_type.input_type_selector == "uniprot"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	80 -t uniprot -i '${s.input_type.input_uniprot}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	81 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	82
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	83 #if $s.input_type.input_type_selector == "ensembl"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	84 -t ensembl -i '${s.input_type.input_ensembl}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	85 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	86
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	87 ## PROTEOFORMS
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	88
f66af2b04a98 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"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	90
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	91 #if $s.input_type.proteoform_match_criteria:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	92 -t proteoform -m '${s.input_type.proteoform_match_criteria}' -i '${s.input_type.input_proteoforms}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	93 #else:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	94 -t proteoform -i '${s.input_type.input_proteoforms}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	95 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	96
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	97 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	98
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	99 #end for
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	100
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	101 ## OUTPUT OPTIONS
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	102
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	103 #if $output_options.search_top_level_info:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	104 -tlp
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	105 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	106
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	107 #set $output_graphs_list = str($output_options.output_graphs).split(',')
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	108
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	109 #if 'gg' in $output_graphs_list:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	110 -gg
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	111 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	112
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	113 #if 'gu' in $output_graphs_list:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	114 -gu
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	115 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	116
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	117 #if 'gp' in $output_graphs_list:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	118 -gp
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	119 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	120
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	121 2>> $temp_stderr);
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	122
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	123 ## We create a folder to contain graphs files.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	124 #if $output_options.output_graphs:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	125 mkdir "graphs";
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	126 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	127
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	128 #if 'gg' in $output_graphs_list:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	129 mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" ;
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	130 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	131
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	132 #if 'gu' in $output_graphs_list:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	133 mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv";
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	134 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	135
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	136 #if 'gp' in $output_graphs_list:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	137 mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv";
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	138 #end if
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	139
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	140 exit_code_for_galaxy=\$?;
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	141 cat $temp_stderr 2>&1;
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	142 (exit \$exit_code_for_galaxy)
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	143 ]]>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	144 </command>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	145 <inputs>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	146
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	147 <repeat name="input_types" title="Input" min="1">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	148 <conditional name="input_type">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	149 <param name="input_type_selector" type="select" label="Input type"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	150 help="">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	151 <option value="rsid">Genetic variants - SNP rsId list</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	152 <option value="chrbp">Genetic variants - Chromosomes and base pairs</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	153 <option value="vcf">Genetic variants - Variant Call Format Specification</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	154 <option value="gene">Genes</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	155 <option value="peptide">Peptides - Simple list</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	156 <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	157 <option value="uniprot">Proteins - UniProt Accession list</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	158 <option value="ensembl">Proteins - Ensembl identifier list</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	159 <option value="proteoforms">Proteoforms</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	160 </param>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	161
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	162 <!-- Genetic variants -->
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	163 <when value="rsid">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	164 <param format="txt" name="input_rsid" type="data" label="SNP rsId list"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	165 help="The file contains one rsid identifier as defined in dbSNP[1] on each row.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	166 The list must be ordered by chromosome and base pair (bp). The list must not have duplicates.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	167 All rsids must appear in the human assembly GRCh37.p13. "/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	168 </when>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	169
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	170 <when value="chrbp">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	171 <param format="txt" name="input_chrbp" type="data" label="Chromosomes and base pairs"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	172 help="Genetic variants can also be represented using the chromosome and the base pair numbers.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	173 The input should be sorted by chromosome number and then by base pair. "/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	174 </when>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	175
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	176 <when value="vcf">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	177 <param format="vcf" name="input_vcf" type="data" label="Variant Call Format Specification"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	178 help="The input follows the Variant Call Format Specification[2] v4.3.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	179 It also allows the possibility to specify only the first 4 columns in the data section of the file:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	180 CHROM, POS, ID, REF. "/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	181 </when>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	182
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	183 <!-- Genes -->
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	184 <when value="gene">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	185 <param format="txt" name="input_gene" type="data" label="Genes"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	186 help="File with a one gene name in each line. Genes follow the HUGO gene nomenclature[3]."/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	187 </when>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	188
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	189 <!-- Peptides -->
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	190 <when value="peptide">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	191 <param format="txt" name="input_peptide" type="data" label="Simple list"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	192 help="File with a one peptide sequence in each line."/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	193
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	194 <expand macro="input_fasta" />
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	195
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	196 <param name="ptm_range" type="integer" value="0" label="PTM position range" optional="true"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	197 help="Plus minus positions for the same PTM site."/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	198 </when>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	199
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	200 <when value="modifiedpeptide">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	201 <param format="txt" name="input_modifiedpeptide" type="data" label="Peptide List with PTM types and sites"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	202 help="Each line of the file corresponds to a single peptide with post-translational modifications."/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	203
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	204 <expand macro="input_fasta" />
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	205
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	206 <param name="ptm_range" type="integer" value="0" label="PTM position range" optional="true"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	207 help="Plus minus positions for the same PTM site."/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	208 </when>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	209
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	210 <!-- Proteins -->
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	211 <when value="uniprot">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	212 <param format="txt" name="input_uniprot" type="data" label="UniProt Accession list"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	213 help="File with a one Uniprot Accession [4] in each line."/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	214 </when>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	215
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	216 <when value="ensembl">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	217 <param format="txt" name="input_ensembl" type="data" label="Ensembl identifier list"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	218 help="File with a one Ensembl identifier [5] in each line."/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	219 </when>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	220
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	221 <!-- Proteoforms -->
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	222 <when value="proteoforms">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	223 <param format="txt" name="input_proteoforms" type="data" label="Proteoforms"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	224 help="A proteoform defines a specific state of a protein.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	225 It is composed by the protein UniProt accession, isoform and set of post translational modifications.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	226 The input file contains one line for each proteoform. Each PTM is specified using a modification
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	227 identifier and a site, separated by ':'(semicolon). For example: '00046:133'.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	228 The identifier is a 5 digit id from the PSI-MOD Protein Modification Onthology [6]."/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	229
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	230 <param name="proteoform_match_criteria" type="select" label="Proteoform match criteria">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	231 <option value="STRICT">STRICT</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	232 <option value="ONE">ONE</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	233 <option value="SUPERSET" selected="True">SUPERSET</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	234 <option value="SUBSET">SUBSET</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	235 </param>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	236 </when>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	237
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	238 </conditional>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	239
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	240 </repeat>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	241
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	242 <section name="output_options" expanded="true" title="Output options">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	243
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	244 <param name="search_top_level_info" type="select" label="Add search top level info">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	245 <option value="0" selected="True">False</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	246 <option value="1">True</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	247 </param>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	248
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	249 <param name="output_graphs" type="select" display="checkboxes" multiple="True" label="Connection graphs"
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	250 help="Generates a zipped file with connection graphs as an additional output when executing the pathway search and analysis.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	251 The graph can use genes, proteins or proteoforms as vertices.">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	252 <option value="gg">Genes</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	253 <option value="gu">Proteins</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	254 <option value="gp">Proteoforms</option>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	255 </param>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	256
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	257 </section>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	258
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	259 </inputs>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	260 <outputs>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	261 <data name="search" format="tsv" from_work_dir="search.tsv" label="${tool.name} - search on ${on_string}" />
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	262 <data name="analysis" format="tsv" from_work_dir="analysis.tsv" label="${tool.name} - analysis on ${on_string}" />
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	263 <collection name="graphs_files" type="list" label="${tool.name} - graphs on ${on_string}" >
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	264 <filter>output_options['output_graphs'] != None</filter>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	265 <discover_datasets pattern="__name_and_ext__" directory="graphs" ext="tsv"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	266 </collection>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	267 </outputs>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	268
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	269
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	270 <tests>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	271
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	272 <!-- Test that genes search works -->
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	273 <test>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	274 <repeat name="input_types">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	275 <conditional name="input_type">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	276 <param name="input_type_selector" value="gene"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	277 <param name="input_gene" value="genes.txt" ftype="txt" />
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	278 </conditional>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	279 </repeat>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	280 <output name="search" file="genes_search.tsv" ftype="tsv" compare="sim_size" delta="3000" />
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	281 </test>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	282
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	283 <!-- Test graphs from proteoforms -->
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	284 <test>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	285 <repeat name="input_types">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	286 <conditional name="input_type">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	287 <param name="input_type_selector" value="proteoforms"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	288 <param name="input_proteoforms" value="proteoforms.txt" ftype="txt" />
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	289 </conditional>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	290 </repeat>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	291 <param name="output_graphs" value="gg,gu,gp" />
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	292 <output_collection name="graphs_files" type="list">
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	293 <element name="geneExternalEdges" ftype="tsv" file="proteoforms_graphs/geneExternalEdges.tsv" compare="sim_size" delta="1000" />
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	294 <element name="geneInternalEdges" ftype="tsv" file="proteoforms_graphs/geneInternalEdges.tsv" compare="sim_size" delta="1000"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	295 <element name="geneVertices" ftype="tsv" file="proteoforms_graphs/geneVertices.tsv" compare="sim_size" delta="1000"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	296 <element name="proteinExternalEdges" ftype="tsv" file="proteoforms_graphs/proteinExternalEdges.tsv" compare="sim_size" delta="10000"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	297 <element name="proteinInternalEdges" ftype="tsv" file="proteoforms_graphs/proteinInternalEdges.tsv" compare="sim_size" delta="1000"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	298 <element name="proteinVertices" ftype="tsv" file="proteoforms_graphs/proteinVertices.tsv" compare="sim_size" delta="1000"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	299 <element name="proteoformExternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformExternalEdges.tsv" compare="sim_size" delta="1000"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	300 <element name="proteoformInternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformInternalEdges.tsv" compare="sim_size" delta="1000"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	301 <element name="proteoformVertices" ftype="tsv" file="proteoforms_graphs/proteoformVertices.tsv" compare="sim_size" delta="1000"/>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	302 </output_collection>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	303 </test>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	304
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	305 </tests>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	306 <help>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	307
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	308 .. class:: infomark
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	309
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	310 Introduction
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	311
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	312 Biological pathways are an excellent resource to analyze the causes and consequences of certain phenotypes.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	313 Most of the components of the pathways are proteins. When searching for relevant pathways to perform analysis
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	314 of a patient sample proteins, it is very common to lose information due to lack of precision in the search.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	315
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	316 This leads to result sets with many extra selected pathways that are not really related to the input sample.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	317
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	318 .. class:: infomark
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	319
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	320 What it does
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	321
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	322 We present more fine grained approach to search, not only with the gene names, but also with post translational
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	323 modifications of the proteins, such as phosphorylation.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	324
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	325 Ultimately, any omics dataset with its mutations and
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	326 modifications will be mapped directly to the functional knowledgebases allowing the functional interpretation by
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	327 researchers and clinicians.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	328
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	329 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.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	330
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	331
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	332 .. class:: infomark
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	333
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	334 Inputs and outputs
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	335
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	336 PathwayMatcher can search for reactions and pathways with various input types, and generates mapping files to the database.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	337
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	338 The input can be:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	339
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	340 - Genetic variants
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	341 - Genes
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	342 - Peptides
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	343 - Protein
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	344 - Proteoforms
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	345
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	346 The output of PathwayMatcher is composed of two files, the Reaction and Pathway mapping and the statistical analysis of the relevant pathways.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	347
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	348 .. class:: infomark
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	349
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	350 Information included with this tool is a brief summary of the main one included in PathwayMatcher_.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	351
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	352 Specific information about PathwayMatcher's Input_ and Output_ may also be found there.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	353
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	354
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	355 .. class:: infomark
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	356
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	357 References
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	358
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	359 [1] dbSNP_
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	360
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	361 [2] VCF v4.3:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	362 http://samtools.github.io/hts-specs/VCFv4.3.pdf
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	363
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	364 [3] genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2015 Jan;43(Database issue):D1079-85. doi: 10.1093/nar/gku1071. :
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	365 https://www.ncbi.nlm.nih.gov/pubmed/25361968
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	366
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	367 [4] UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45: D158-D169 (2017):
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	368 http://dx.doi.org/doi:10.1093/nar/gkw1099
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	369
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	370 [5] Ensembl:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	371 https://www.ensembl.org/info/genome/stable_ids/index.html
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	372
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	373 [6] The PSI-MOD community standard for representation of protein modification data. Nature Biotechnology 26, 864 - 866 (2008):
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	374 http://www.nature.com/nbt/journal/v26/n8/full/nbt0808-864.html
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	375
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	376 .. _dbSNP: https://www.ncbi.nlm.nih.gov/projects/SNP/
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	377 .. _PathwayMatcher: https://github.com/LuisFranciscoHS/PathwayMatcher
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	378 .. _Input: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Input
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	379 .. _Output: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Output
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	380
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	381 </help>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	382
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a galaxyp parents: diff changeset	383 </tool>

Mercurial > repos > galaxyp > reactome_pathwaymatcher

annotate pathwaymatcher.xml @ 0:f66af2b04a98 draft