annotate ragoo.xml @ 6:29700a47518f draft

Uploaded
author dereeper
date Mon, 26 Jul 2021 17:25:39 +0000
parents fb38284b11f8
children f98ddf3006f0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
90611c479c08 Uploaded
dereeper
parents:
diff changeset
1 <tool id="ragoo" name="RaGOO" version="1.0">
90611c479c08 Uploaded
dereeper
parents:
diff changeset
2 <description>Order and assign scaffolds</description>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
3 <requirements>
5
fb38284b11f8 Uploaded
dereeper
parents: 0
diff changeset
4 <requirement type="package" version="3.0.2">intervaltree</requirement>
0
90611c479c08 Uploaded
dereeper
parents:
diff changeset
5 </requirements>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
6
90611c479c08 Uploaded
dereeper
parents:
diff changeset
7 <command>perl ${__tool_directory__}/ragoo.pl $input $reference $output $output2
90611c479c08 Uploaded
dereeper
parents:
diff changeset
8 </command>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
9
90611c479c08 Uploaded
dereeper
parents:
diff changeset
10
90611c479c08 Uploaded
dereeper
parents:
diff changeset
11 <inputs>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
12 <param format="fasta" name="input" type="data" label="Fasta file with contigs to be ordered and oriented: "/>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
13 <param format="fasta" name="reference" type="data" label="Reference fasta file"/>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
14
90611c479c08 Uploaded
dereeper
parents:
diff changeset
15 </inputs>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
16
90611c479c08 Uploaded
dereeper
parents:
diff changeset
17 <outputs>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
18 <data format="fasta" name="output" label="Fasta output of assigned scaffolds"/>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
19 <data format="fasta" name="output2" label="Fasta output of assigned scaffolds (without Chr0)"/>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
20 </outputs>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
21
90611c479c08 Uploaded
dereeper
parents:
diff changeset
22 <help>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
23 For full documentation, please go to the RaGOO website : https://github.com/malonge/RaGOO
90611c479c08 Uploaded
dereeper
parents:
diff changeset
24
90611c479c08 Uploaded
dereeper
parents:
diff changeset
25 </help>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
26
90611c479c08 Uploaded
dereeper
parents:
diff changeset
27 <citations>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
28 <citation type="doi"> 10.1186/s13059-019-1829-6 </citation>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
29
90611c479c08 Uploaded
dereeper
parents:
diff changeset
30 </citations>
90611c479c08 Uploaded
dereeper
parents:
diff changeset
31 </tool>