Mercurial > repos > iuc > roary

annotate roary.xml @ 0:e02e9af2743f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
author iuc
date Fri, 23 Jun 2017 07:53:29 -0400
parents
children a9098353ae22
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
1 <tool id="roary" name="Roary" version="0.1.0">
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
2 <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
3
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
4 <requirements>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
5 <requirement type="package" version="3.8.2">roary</requirement>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
6 </requirements>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
7
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
9
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
10 #for $counter, $gff in enumerate($gff_input.gffs)
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
11 cp $gff temp${counter}.gff &&
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
12 #end for
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
13
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
14 roary
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
15 -f out
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
16 -p \${GALAXY_SLOTS:-1}
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
17 -e
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
18 -n
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
19 -i '$percent_ident'
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
20 -cd '$core_diff'
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
21 -g '$advanced.maxclust'
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
22 $advanced.split_para
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
23 -t '$advanced.trans_tab'
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
24 -iv '$advanced.mcl'
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
25
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
26 temp*.gff
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
27
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
28 ]]></command>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
29
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
30 <inputs>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
31 <conditional name="gff_input">
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
32 <param name="gff_input_selector" type="select" label="Individual gff files or a dataset collection" help="Select between individual gff files or a collection of gff files">
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
33 <option value="individual">Individual</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
34 <option value="collection">Collection</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
35 </param>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
36 <when value="individual">
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
37 <param name="gffs" type="data" multiple="true" format="gff3" label="select gff inputs to Roary" help="Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file." />
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
38 </when>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
39 <when value='collection'>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
40 <param name="gffs" type="data_collection" collection_type="list" format="gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." />
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
41 </when>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
42 </conditional>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
43 <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
44 <param name="core_diff" type="float" label="percentage of isolates a gene must be in to be core" help="The total percentage of the isolates that must have the gene for it to be considered a core gene." value="99.0"/>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
45
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
46 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs" help="Summary statistics, core gene alignments and Gene Presence/Absence tables are always produced.">
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
47 <option value="abg_fa">Accessory binary genes in fasta format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
48 <option value="accgraph">Accessory graph in dot format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
49 <option value="acchead_embl">Accessory header file in embl format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
50 <option value="acctab">Accessory gene table in tabular format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
51 <option value="blastfreq">Blast Identity Frequency Rtab file</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
52 <option value="clust">Clustered proteins file</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
53 <option value="coreaccgraph">Core Accessory Graph in dot format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
54 <option value="coreaccembl">Core Accessory table in embl format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
55 <option value="coreacctab">Core Accessory table in tabular format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
56 <option value="genepa_rtab">Gene Presence Absence file in Rtab format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
57 <option value="numcons_rtab">Number of Conserved Genes in Rtab format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
58 <option value="numpangene_rtab">Number of Genes in Pan Genome in Rtab format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
59 <option value="numnew_rtab">Number of New Genes in Rtab format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
60 <option value="numuniq_rtab">Number of Unique Genes in Rtab format</option>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
61 </param>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
62
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
63 <section name="advanced" title="Advanced options" expanded="false">
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
64 <param name="maxclust" type="integer" value="50000" label="Maximum number of clusters" help="The maximum number of clusters to assign proteins" />
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
65 <param name="split_para" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Don't split paralogs" help="Click yes so that paralogs aren't split."/>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
66 <param name="trans_tab" type="integer" value="11" label="Translation table to use [1 or 4 or 11]" help="DNA -> RNA translation table to use. Roary is designed for prokaryotes and so tables 1, 4 or 11 will work, others could be problematic." />
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
67 <param name="mcl" type="float" value="1.5" label="MCL inflation value" help="This is an advanced setting, change only if you know what you are doing and then at your own risk!" />
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
68 </section>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
69
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
70 </inputs>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
71
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
72 <outputs>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
73 <data format="tabular" name="sumstats" label="${tool.name} on ${on_string} Summary statistics" from_work_dir="out/summary_statistics.txt" />
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
74 <data format="fasta" name="core_gene_aln" label="${tool.name} on ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln" />
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
75 <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv" />
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
76 <data format="fasta" name="acc_bin" label="${tool.name} on ${on_string} Accessory Binary Genes" from_work_dir="out/accessory_binary_genes.fa" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
77 <filter>outputs and 'abg_fa' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
78 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
79 <data format="dot" name="acc_graph" label="${tool.name} on ${on_string} Acsessory Graph" from_work_dir="out/accessory_graph.dot">
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
80 <filter>outputs and 'accgraph' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
81 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
82 <data format="embl" name="acc_head_embl" label="${tool.name} on ${on_string} Accessory Header" from_work_dir="out/accessory.header.embl" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
83 <filter>outputs and 'acchead_embl' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
84 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
85 <data format="tabular" name="acc_tab" label="${tool.name} on ${on_string} Accessory Gene Table" from_work_dir="out/accessory.tab" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
86 <filter>outputs and 'acctab' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
87 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
88 <data format="txt" name="blast_freq" label="${tool.name} on ${on_string} Blast Identity Frequencies" from_work_dir="out/blast_identity_frequency.Rtab" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
89 <filter>outputs and 'blastfreq' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
90 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
91 <data format="txt" name="clust_file" label="${tool.name} on ${on_string} Clustered Proteins" from_work_dir="out/clustered_proteins" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
92 <filter>outputs and 'clust' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
93 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
94 <data format="dot" name="core_acc_graph" label="${tool.name} on ${on_string} Core Accessory Graph" from_work_dir="out/core_accessory_graph.dot" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
95 <filter>outputs and 'coreaccgraph' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
96 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
97 <data format="embl" name="core_acc_embl" label="${tool.name} on ${on_string} Core Accessory EMBL" from_work_dir="out/core_accessory.header.embl" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
98 <filter>outputs and 'coreaccembl' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
99 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
100 <data format="tabular" name="core_acc_tab" label="${tool.name} on ${on_string} Core Accessory Table" from_work_dir="out/core_accessory.tab" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
101 <filter>outputs and 'coreacctab' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
102 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
103 <data format="txt" name="gene_p_a_rtab" label="${tool.name} on ${on_string} Gene Presence Absence Rtab" from_work_dir="out/gene_presence_absence.Rtab" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
104 <filter>outputs and 'genepa_rtab' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
105 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
106 <data format="txt" name="num_cons_rtab" label="${tool.name} on ${on_string} Number of Conserved Genes" from_work_dir="out/number_of_conserved_genes.Rtab" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
107 <filter>outputs and 'numcons_rtab' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
108 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
109 <data format="txt" name="num_pangene_rtab" label="${tool.name} on ${on_string} Number of Genes in Pan Geneome" from_work_dir="out/number_of_genes_in_pan_genome.Rtab" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
110 <filter>outputs and 'numpangene_rtab' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
111 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
112 <data format="txt" name="num_new_rtab" label="${tool.name} on ${on_string} Number of New Genes" from_work_dir="out/number_of_new_genes.Rtab" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
113 <filter>outputs and 'numnew_rtab' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
114 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
115 <data format="txt" name="num_uniq_rtab" label="${tool.name} on ${on_string} Number of Unique Genes" from_work_dir="out/number_of_unique_genes.Rtab" >
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
116 <filter>outputs and 'numuniq_rtab' in outputs</filter>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
117 </data>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
118 </outputs>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
119
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
120 <tests>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
121 <test>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
122 <param name="gff_input_selector" value="individual"/>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
123 <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3"/>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
124 <output name="sumstats" file="out/summary_statistics.txt" ftype="tabular"/>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
125 </test>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
126 <test>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
127 <param name="gff_input_selector" value="individual"/>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
128 <param name="gffs" value="ex1.gff,ex2.gff" ftype="gff3"/>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
129 <param name="percent_ident" value="50"/>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
130 <param name="core_diff" value="50.0"/>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
131 <output name="sumstats" file="test2/summary_statistics.txt" ftype="tabular"/>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
132 </test>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
133 </tests>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
134
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
135 <help><![CDATA[
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
136 **Roary**
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
137
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
138 Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM.
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
139
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
140 To use Roary, select two or more gff3 files OR a collection of gff3 files
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
141
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
142 **Options**:
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
143
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
144
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
145 - Minimum percentage identity for blastp - an integer, default is [95]
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
146
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
147
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
148 - Percentage of isolates a gene must be in to be core - a float, default is [99.0]
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
149
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
150
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
151 **Advanced Options**:
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
152
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
153 - Maximum number of clusters - integer, default is [50000]
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
154
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
155
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
156 - Don't split paralogs - check box
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
157
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
158
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
159 - Translation table - which translation table to use, an integer, default is [11]
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
160
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
161
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
162 - Change the MCL inflation value - a float, default is [1.5]
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
163
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
164
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
165 For further info see: http://sanger-pathogens.github.io/Roary/
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
166
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
167 ]]></help>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
168
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
169 <citations>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
170 <citation type="doi">http://doi.org/10.1093/bioinformatics/btv421</citation>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
171 </citations>
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
172
e02e9af2743f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 1fbe605d5ac8fd5d91fec6fb24fcfc51788c62b6
iuc
parents:
diff changeset
173 </tool>