annotate pathview.xml @ 3:f1691de443a7 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
author iuc
date Mon, 09 May 2022 20:12:57 +0000
parents fe154a7af404
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
fe154a7af404 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
parents: 1
diff changeset
1 <tool id="pathview" name="Pathview" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
0
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
2 <description>for pathway based data integration and visualization</description>
2
fe154a7af404 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
parents: 1
diff changeset
3 <xrefs>
fe154a7af404 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
parents: 1
diff changeset
4 <xref type="bio.tools">pathview</xref>
fe154a7af404 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
parents: 1
diff changeset
5 </xrefs>
0
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
6 <macros>
3
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
7 <token name="@TOOL_VERSION@">1.34.0</token>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
8 <token name="@VERSION_SUFFIX@">0</token>
0
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
9 </macros>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
10 <requirements>
2
fe154a7af404 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
parents: 1
diff changeset
11 <requirement type="package" version="@TOOL_VERSION@">bioconductor-pathview</requirement>
3
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
12 <requirement type="package" version="3.14.0">bioconductor-org.ag.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
13 <requirement type="package" version="3.14.0">bioconductor-org.at.tair.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
14 <requirement type="package" version="3.14.0">bioconductor-org.bt.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
15 <requirement type="package" version="3.14.0">bioconductor-org.ce.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
16 <requirement type="package" version="3.14.0">bioconductor-org.cf.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
17 <requirement type="package" version="3.14.0">bioconductor-org.dm.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
18 <requirement type="package" version="3.14.0">bioconductor-org.dr.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
19 <requirement type="package" version="3.14.0">bioconductor-org.eck12.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
20 <requirement type="package" version="3.14.0">bioconductor-org.ecsakai.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
21 <requirement type="package" version="3.14.0">bioconductor-org.gg.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
22 <requirement type="package" version="3.14.0">bioconductor-org.hs.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
23 <requirement type="package" version="3.14.0">bioconductor-org.mm.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
24 <requirement type="package" version="3.14.0">bioconductor-org.mmu.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
25 <requirement type="package" version="3.14.0">bioconductor-org.pf.plasmo.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
26 <requirement type="package" version="3.14.0">bioconductor-org.pt.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
27 <requirement type="package" version="3.14.0">bioconductor-org.rn.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
28 <requirement type="package" version="3.14.0">bioconductor-org.sc.sgd.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
29 <requirement type="package" version="3.14.0">bioconductor-org.ss.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
30 <requirement type="package" version="3.14.0">bioconductor-org.xl.eg.db</requirement>
f1691de443a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"
iuc
parents: 2
diff changeset
31 <requirement type="package" version="1.7.1">r-optparse</requirement>
0
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
32 </requirements>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
33 <version_command><![CDATA[
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
34 echo $(R --version | grep version | grep -v GNU)", pathview version" $(R --vanilla --slave -e "library(pathview); cat(sessionInfo()\$otherPkgs\$pathview\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", dplyr version" $(R --vanilla --slave -e "library(dplyr); cat(sessionInfo()\$otherPkgs\$dplyr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
35 ]]></version_command>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
36 <command detect_errors="exit_code"><![CDATA[
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
37 Rscript '$__tool_directory__/pathview.r'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
38
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
39 #if str($pathway.nb) == 'one'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
40 --pathway_id '$pathway.one_id'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
41 #else
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
42 --pathway_id_fp '$pathway.tabular'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
43 --pathway_id_header $pathway.header
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
44 #end if
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
45
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
46 --species '$species'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
47
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
48 #if str($gene_data.gd) == 'true'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
49 --gene_data '$gene_data.tabular'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
50 --gd_header $gene_data.header
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
51 --gene_idtype '$gene_data.idtype'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
52 #end if
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
53
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
54 #if str($cpd_data.cpd) == 'true'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
55 --cpd_data '$cpd_data.tabular'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
56 --cpd_header $cpd_data.header
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
57 --cpd_idtype '$cpd_data.idtype'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
58 #end if
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
59
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
60 --multi_state $multi_state
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
61 --match_data $match_data
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
62
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
63 --kegg_native $out.kegg_native.out
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
64 --same_layer $out.kegg_native.same_layer
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
65 #if str($out.kegg_native.out) == 'TRUE'
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
66 --map_null $out.kegg_native.map_null
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
67 #else
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
68 --split_group $out.kegg_native.split_group
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
69 --expand_node $out.kegg_native.expand_node
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
70 --sign_pos $out.kegg_native.sign_pos
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
71 #end if
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
72
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
73 &&
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
74 ls .
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
75 ]]></command>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
76 <inputs>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
77 <conditional name="pathway">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
78 <param name="nb" type="select" label="Number of pathways to plot">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
79 <option value="one" selected="true">One</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
80 <option value="multiple">Multiple</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
81 </param>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
82 <when value="one">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
83 <param name="one_id" type="text" label="KEGG pathway" help="KEGG pathway ID with 5 digits and without the 3 letter KEGG species code.">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
84 <validator type="regex" message="It should be the 5 digits of the KEGG pathway ID.">^(?:\d\d\d\d\d)?$</validator>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
85 </param>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
86 </when>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
87 <when value="multiple">
2
fe154a7af404 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
iuc
parents: 1
diff changeset
88 <param name="tabular" type="data" format="txt,tabular" optional="true" label="KEGG pathways" help="A table with one-column with KEGG pathways to plot"/>
0
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
89 <param name="header" type="boolean" checked="true" label="Does the file have header (a first line with column names)?"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
90 </when>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
91 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
92 <param name="species" type="select" label="Species to use">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
93 <option value="aga">Anopheles</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
94 <option value="ath">Arabidopsis</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
95 <option value="bta">Bovine</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
96 <option value="cel">Worm</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
97 <option value="cfa">Canine</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
98 <option value="dme">Fly</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
99 <option value="dre">Zebrafish</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
100 <option value="eco">E coli strain K12</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
101 <option value="ecs">E coli strain Sakai</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
102 <option value="gga">Chicken</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
103 <option value="hsa" selected="true">Human</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
104 <option value="mmu">Mouse</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
105 <option value="mcc">Rhesus</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
106 <option value="pfa">Malaria</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
107 <option value="ptr">Chimp</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
108 <option value="rno">Rat</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
109 <option value="sce">Yeast</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
110 <option value="ssc">Pig</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
111 <option value="xla">Xenopus</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
112 </param>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
113 <conditional name="gene_data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
114 <param name="gd" type="select" label="Provide a gene data file?" help="Gene data is a broad concept including genes, transcripts, protein, enzymes and their expression, modifications and any measurable attributes.">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
115 <option value="true">Yes</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
116 <option value="false">No</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
117 </param>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
118 <when value="true">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
119 <param name="tabular" type="data" format="tabular" label="Gene data" help="It should be a table with first column being the gene ids and other being information (p-value, fold change, levels, etc) from one or several samples."/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
120 <param name="header" type="boolean" checked="true" label="Does the file have header (a first line with sample names)?"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
121 <param name="idtype" type="select" label="Format for gene data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
122 <option value="entrez" selected="true">Entrez Gene ID</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
123 <option value="symbol">Gene Symbol</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
124 <option value="genename">Gene Name</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
125 <option value="ensembl">Ensembl Gene ID</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
126 <option value="ensemblprot">Ensembl Protein ID</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
127 <option value="ensembltrans">Ensembl Trans ID</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
128 <option value="unigene">UniGene</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
129 <option value="uniprot">UniProt</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
130 <option value="refseq">RefSeq</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
131 <option value="enzyme">Enzyme</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
132 <option value="tair">TAIR</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
133 <option value="prosite">Prosite</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
134 <option value="orf">ORF</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
135 </param>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
136 </when>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
137 <when value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
138 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
139 <conditional name="cpd_data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
140 <param name="cpd" type="select" label="Provide a compound data file?" help="compound data is a broad concept including metabolites, drugs, their measurements and attributes.">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
141 <option value="true">Yes</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
142 <option value="false" selected="true">No</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
143 </param>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
144 <when value="true">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
145 <param name="tabular" type="data" format="tabular" label="Compound data" help="It should be a table with first column being the gene ids and other being information (p-value, fold change, levels, etc) from one or several samples."/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
146 <param name="header" type="boolean" checked="true" label="Does the file have header (a first line with sample names)?"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
147 <param name="idtype" type="select" label="Format for compound data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
148 <option value="kegg" selected="true">KEGG (include compound, glycan and drug accessions)</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
149 </param>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
150 </when>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
151 <when value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
152 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
153 <param name="multi_state" type="boolean" checked="true" label="Should multiple states of gene or compond data be intergrated and plotted in the same graph?" help="Gene or compound nodes will be sliced into multiple pieces corresponding to the number of states in the data" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
154 <param name="match_data" type="boolean" checked="true" label="Are the gene and compound data paired?" help="When let sample sizes of gene and compound be m and n, when m>n, extra columns of NA's (mapped to no color) will be added to make the sample size the same" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
155 <section name="out" title="Output Options" expanded="true">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
156 <conditional name="kegg_native">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
157 <param name="out" type="select" label="Output for pathway">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
158 <option value="TRUE" selected="true">KEGG native</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
159 <option value="FALSE">Graphviz</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
160 </param>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
161 <when value="TRUE">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
162 <param name="same_layer" type="boolean" checked="true" label="Plot on same layer?" help="If yes, node colors will be plotted in the same layer as the pathway graph." />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
163 <param name="map_null" type="boolean" checked="true" label="Map the NULL gene or compound data to pathway?" help="When NULL data are mapped, the gene or compound nodes in the pathway will berendered as actually mapped nodes, except with NA-valued color. When NULL data are not mapped, the nodes are rendered as unmapped nodes." />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
164 </when>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
165 <when value="FALSE">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
166 <param name="same_layer" type="boolean" checked="true" label="Plot on same layer?" help="If yes, edge/node type legend will be plotted in the same page." />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
167 <param name="split_group" type="boolean" checked="false" label="Split node groups into individual nodes?" help="Each split member nodes inherits all edges from the node group. This option also effects most metabolic pathways even without group nodes defined orginally. For these pathways, genes involved in the same reaction are grouped automatically when converting reactions to edges unless split.group is true." />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
168 <param name="expand_node" type="boolean" checked="false" label="Expand multiple-gene nodes into single-gene nodes?" help="Each expanded single-gene nodes inherits all edges from the original multiple-gene node. This option is not effective for most metabolic pathways where it conflits with converting reactions to edges." />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
169 <param name="sign_pos" type="select" label="Position of pathview signature">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
170 <option value="bottomright" selected="true">Bottom right</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
171 <option value="bottomleft">Bottom left</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
172 <option value="topleft">Top left</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
173 <option value="topright">Top right</option>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
174 </param>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
175 </when>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
176 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
177 </section>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
178 </inputs>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
179 <outputs>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
180 <data name="one_kegg_native" format="png" from_work_dir="*.pathview.png" label="${tool.name} on ${on_string}: KEGG Pathway (${species}${pathway.one_id})">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
181 <filter>pathway['nb'] == 'one'</filter>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
182 <filter>out['kegg_native']['out'] == 'TRUE'</filter>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
183 </data>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
184 <data name="one_graphviz" format="pdf" from_work_dir="*.pathview.pdf" label="${tool.name} on ${on_string}: KEGG Pathway (${species}${pathway.one_id}), Graphviz format">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
185 <filter>pathway['nb'] == 'one'</filter>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
186 <filter>out['kegg_native']['out'] == 'FALSE'</filter>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
187 </data>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
188 <collection name="multiple_kegg_native" type="list" label="${tool.name} on ${on_string}: KEGG Pathways">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
189 <filter>pathway['nb'] == 'multiple'</filter>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
190 <filter>out['kegg_native']['out'] == 'TRUE'</filter>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
191 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview\.png" directory="." ext="png"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
192 </collection>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
193 <collection name="multiple_graphviz" type="list" label="${tool.name} on ${on_string}: KEGG Pathways, Graphviz format">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
194 <filter>pathway['nb'] == 'multiple'</filter>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
195 <filter>out['kegg_native']['out'] == 'FALSE'</filter>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
196 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview\.pdf" directory="." ext="pdf"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
197 </collection>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
198 </outputs>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
199 <tests>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
200 <test>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
201 <conditional name="pathway">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
202 <param name="nb" value="one" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
203 <param name="one_id" value="00010"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
204 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
205 <param name="species" value="dme"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
206 <conditional name="gene_data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
207 <param name="gd" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
208 <param name="tabular" value="gene_data.tabular"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
209 <param name="header" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
210 <param name="idtype" value="ensembl"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
211 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
212 <conditional name="cpd_data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
213 <param name="cpd" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
214 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
215 <param name="multi_state" value="true" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
216 <param name="match_data" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
217 <section name="out">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
218 <conditional name="kegg_native">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
219 <param name="out" value="TRUE" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
220 <param name="same_layer" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
221 <param name="map_null" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
222 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
223 </section>
1
03c13085aecc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 3204d188b632f08ba74b3c27c5bb910b9c4ba7ab"
iuc
parents: 0
diff changeset
224 <output name="one_kegg_native" ftype="png" file="dme00010.png" compare="sim_size" delta="40000"/>
0
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
225 </test>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
226 <test>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
227 <conditional name="pathway">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
228 <param name="nb" value="one" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
229 <param name="one_id" value="00010"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
230 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
231 <param name="species" value="dme"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
232 <conditional name="gene_data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
233 <param name="gd" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
234 <param name="tabular" value="gene_data.tabular"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
235 <param name="header" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
236 <param name="idtype" value="ensembl"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
237 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
238 <conditional name="cpd_data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
239 <param name="cpd" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
240 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
241 <param name="multi_state" value="true" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
242 <param name="match_data" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
243 <section name="out">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
244 <conditional name="kegg_native">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
245 <param name="out" value="FALSE" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
246 <param name="same_layer" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
247 <param name="split_group" value="false" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
248 <param name="expand_node" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
249 <param name="sign_pos" value="bottomright"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
250 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
251 </section>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
252 <output name="one_graphviz" ftype="pdf" file="dme00010.pdf" compare="sim_size"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
253 </test>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
254 <test>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
255 <conditional name="pathway">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
256 <param name="nb" value="multiple" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
257 <param name="tabular" value="pathways.tabular"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
258 <param name="header" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
259 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
260 <param name="species" value="dme"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
261 <conditional name="gene_data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
262 <param name="gd" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
263 <param name="tabular" value="gene_data.tabular"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
264 <param name="header" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
265 <param name="idtype" value="ensembl"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
266 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
267 <conditional name="cpd_data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
268 <param name="cpd" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
269 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
270 <param name="multi_state" value="true" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
271 <param name="match_data" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
272 <section name="out">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
273 <conditional name="kegg_native">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
274 <param name="out" value="TRUE" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
275 <param name="same_layer" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
276 <param name="map_null" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
277 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
278 </section>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
279 <output_collection name="multiple_kegg_native" count="2">
1
03c13085aecc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 3204d188b632f08ba74b3c27c5bb910b9c4ba7ab"
iuc
parents: 0
diff changeset
280 <element name="dme00010" ftype="png" file="dme00010.png" compare="sim_size" delta="40000"/>
03c13085aecc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 3204d188b632f08ba74b3c27c5bb910b9c4ba7ab"
iuc
parents: 0
diff changeset
281 <element name="dme00480" ftype="png" file="dme00480.png" compare="sim_size" delta="50000"/>
0
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
282 </output_collection>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
283 </test>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
284 <test>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
285 <conditional name="pathway">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
286 <param name="nb" value="multiple" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
287 <param name="tabular" value="pathways.tabular"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
288 <param name="header" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
289 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
290 <param name="species" value="dme"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
291 <conditional name="gene_data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
292 <param name="gd" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
293 <param name="tabular" value="gene_data.tabular"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
294 <param name="header" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
295 <param name="idtype" value="ensembl"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
296 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
297 <conditional name="cpd_data">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
298 <param name="cpd" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
299 <param name="tabular" value="cpd_data.tabular"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
300 <param name="header" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
301 <param name="idtype" value="kegg"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
302 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
303 <param name="multi_state" value="true" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
304 <param name="match_data" value="true"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
305 <section name="out">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
306 <conditional name="kegg_native">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
307 <param name="out" value="FALSE" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
308 <param name="same_layer" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
309 <param name="split_group" value="false" />
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
310 <param name="expand_node" value="false"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
311 <param name="sign_pos" value="bottomright"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
312 </conditional>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
313 </section>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
314 <output_collection name="multiple_graphviz" count="2">
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
315 <element name="dme00010" ftype="pdf" file="dme00010_cpd.pdf" compare="sim_size"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
316 <element name="dme00480" ftype="pdf" file="dme00480_cpd.pdf" compare="sim_size"/>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
317 </output_collection>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
318 </test>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
319 </tests>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
320 <help><![CDATA[
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
321
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
322 .. class:: infomark
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
323
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
324 **What it does**
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
325
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
326 Pathview is a stand-alone software package for pathway based data integration and visualization.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
327
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
328 This package can be divided into four functional modules: the Downloader, Parser, Mapper andViewer.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
329 Mostly importantly, pathview maps and renders user data on relevant pathway graphs.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
330
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
331 Notice that KEGG requires subscription for FTP access since May 2011.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
332 However,Pathview downloads individual pathway graphs and data files through API or HTTP access, which is freely available (for academic and non-commerical uses).
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
333 Pathview uses KEGGgraph (Zhang and Wiemann, 2009) when parsing KEGG xml data files.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
334
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
335
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
336 Options map closely to the excellent pathview manual_.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
337
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
338 -----
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
339
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
340 **Inputs**
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
341
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
342 Pathview provides strong support for data integration. It works with:
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
343
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
344 - essentially all types of biological data mappable to pathways (gene expression, protein expression, genetic association, metabolite, genomic data, literature, etc)
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
345 - over 10 types of gene or protein IDs, and 20 types of compound or metabolite IDs
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
346 - pathways for about 4800 species as well as KEGG orthology
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
347 - various data attributes and formats, i.e. continuous/discrete data, matrices/vectors, single/multiple samples etc.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
348
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
349 Pathview can be directly used for metagenomic, microbiome or unknown species data when the data are mapped to KEGG ortholog pathways.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
350
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
351 *Pathway ids*
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
352
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
353 Either just the name or a table with one column with the different pathway ids to represent.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
354
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
355
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
356 *Gene data*
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
357
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
358 The first input of Pathview is a gene data table. Here gene data is a broad concept including genes, transcripts, protein, enzymes and their expression, modifications and any measurable attributes.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
359
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
360 It should be a table with first column being the gene ids and other being information (p-value, fold change, levels, etc) from one or several samples.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
361 The first line can include the sample names.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
362
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
363 Here gene id is a generic concepts, including multiple types of gene, transcript and protein uniquely mappable to KEGG gene IDs. KEGG ortholog IDs are also treated as gene IDs as to handle metagenomic data.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
364
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
365 Example:
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
366
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
367 =========== =================
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
368 FBgn0039155 -4.14844993705661
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
369 FBgn0003360 -2.99977727873544
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
370 FBgn0026562 -2.38016404989418
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
371 FBgn0025111 2.69993883050214
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
372 FBgn0029167 -2.10506155636758
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
373 =========== =================
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
374
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
375 *Compound data*
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
376
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
377 We also frequently want to look at metabolic pathways too. Besides gene nodes, these pathways also have compound nodes.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
378 Therefore, we may integrate or visualize both gene data and compound data with metabolic pathways.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
379
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
380 Here compound data is a broad concept including metabolites, drugs, their measurements and attributes.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
381
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
382 The format is similar to the gene data table, except named with IDs mappable to KEGG compound IDs.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
383 Over 20 types of IDs included in CHEMBL database can be used here.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
384
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
385 -----
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
386
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
387 **Outputs**
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
388
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
389 Pathview generates both native KEGG view and Graphviz view for pathways.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
390
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
391 KEGG view keeps all the meta-data on pathways, spacial and temporal information, tissue/cell types, inputs, outputs and connections. This is important for human reading and interpretation of pathway biology.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
392
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
393 .. image:: $PATH_TO_IMAGES/dme00010_native.png
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
394 :width: 60 %
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
395
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
396 Graphviz view provides better control of node and edge attributes, better view of pathway topology, better understanding of the pathway analysis statistics.
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
397
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
398 .. image:: $PATH_TO_IMAGES/dme00010_graphviz.png
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
399 :width: 60 %
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
400
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
401 .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/pathview/inst/doc/pathview.pdf
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
402 .. _KEGG: http://www.genome.jp/kegg
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
403
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
404 ]]></help>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
405 <citations>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
406 <citation type="doi">10.1093/bioinformatics/btt285</citation>
bd99e8fbde97 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
iuc
parents:
diff changeset
407 </citations>
1
03c13085aecc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 3204d188b632f08ba74b3c27c5bb910b9c4ba7ab"
iuc
parents: 0
diff changeset
408 </tool>