Mercurial > repos > rnateam > reago

annotate reago.xml @ 1:31a354009216 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
author rnateam
date Thu, 02 Feb 2017 19:35:52 -0500
parents 715b263db9f3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
31a354009216 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
rnateam
parents: 0
diff changeset
1 <tool id="reago" name="Reago" version="1.1">
0
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
2 <description> to assemble rRNA</description>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
3
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
4 <requirements>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
5 <requirement type="package" version="1.1">reago</requirement>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
6 </requirements>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
7
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
8 <stdio>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
9 <exit_code range="1:" />
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
10 </stdio>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
11
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
12 <command>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
13 <![CDATA[
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
14 #set $r1_output=$os.path.splitext($os.path.basename(str($r1_file)))[0]
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
15 #set $r2_output=$os.path.splitext($os.path.basename(str($r2_file)))[0]
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
16
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
17 python $__tool_directory__/format_reago_input_files.py
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
18 --r1_input "$r1_file"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
19 --r2_input "$r2_file"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
20 --r1_output $r1_output
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
21 --r2_output $r2_output
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
22
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
23 &&
1
31a354009216 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
rnateam
parents: 0
diff changeset
24 filter_input.py
0
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
25 $r1_output
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
26 $r2_output
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
27 .
1
31a354009216 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
rnateam
parents: 0
diff changeset
28 \$(dirname \$(which reago.py))/cm/
0
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
29 $cm_to_use
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
30 "\${GALAXY_SLOTS:-4}"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
31
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
32 &&
1
31a354009216 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
rnateam
parents: 0
diff changeset
33 reago.py
0
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
34 "filtered.fasta"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
35 .
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
36 -l $read_length
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
37 -o $overlap
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
38 -t $tip_size
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
39 -b $path_finding_parameter
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
40 ]]>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
41 </command>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
42
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
43 <inputs>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
44 <param name="r1_file" type="data" format="fasta" label="R1 input sequence
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
45 file" help=""/>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
46
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
47 <param name="r2_file" type="data" format="fasta" label="R2 input sequence
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
48 file" help=""/>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
49
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
50 <param name="read_length" type="integer" min="1" max="1000" value="101"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
51 label="Read length" help="(-l)"/>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
52
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
53 <param name="overlap" type="float" min="0" max="1" value="0.8"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
54 label="Overlap" help="(-o)"/>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
55
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
56 <param name="tip_size" type="integer" min="0" max="1000" value="30"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
57 label="Tip size" help="(-t)"/>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
58
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
59 <param name="path_finding_parameter" type="integer" min="2" max="11"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
60 value="10" label="Path finding parameter" help="(-b)"/>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
61
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
62 <param name="cm_to_use" type="select" label="Database to use to to identify 16S reads" help="">
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
63 <option value="b">Bacteria only</option>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
64 <option value="a">Archea only</option>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
65 <option value="ab">Bacteria and archea</option>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
66 </param>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
67
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
68 </inputs>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
69
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
70 <outputs>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
71 <data format="fasta" name="full_genes"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
72 from_work_dir="full_genes.fasta"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
73 label="Full genes of ${on_string} (Framebot)" />
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
74 <data format="fasta" name="fragments"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
75 from_work_dir="fragments.fasta"
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
76 label="Fragment genes of ${on_string} (Framebot)" />
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
77 </outputs>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
78
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
79 <tests>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
80 <test>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
81 <param name="r1_file" value="reago_sample_1.fasta"/>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
82 <param name="r2_file" value="reago_sample_2.fasta"/>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
83 <param name="read_length" value="101" />
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
84 <param name="overlap" value="0.8" />
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
85 <param name="error_correction" value="0.05" />
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
86 <param name="tip_size" value="30" />
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
87 <param name="path_finding_parameter" value="10"/>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
88 <param name="cm_to_use" value="ab" />
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
89 <param name="cpu_nb" value="4" />
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
90
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
91 <output name="full_genes" file="reago_full_genes.fasta"/>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
92 <output name="fragments" file="reago_fragments.fasta"/>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
93 </test>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
94 </tests>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
95
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
96 <help>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
97 <![CDATA[
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
98
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
99 **What it does**
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
100
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
101 Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
102 More information on `Github repository <https://github.com/chengyuan/reago-1.1>`_.
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
103
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
104 -----
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
105
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
106 **Input**
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
107
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
108 Sequence files with r1 and r2 are required.
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
109
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
110 -----
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
111
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
112 **Parameters**
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
113
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
114 The parameters are
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
115
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
116 - The overlap percentage
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
117 - The threshold for error correction
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
118 - The tip size
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
119 - The parameter for path finding
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
120
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
121 -----
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
122
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
123 **Output**
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
124
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
125 Reago produces two output files:
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
126
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
127 - A sequence file with full genes
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
128 - A sequence file with fragment genes
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
129
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
130 ]]>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
131 </help>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
132
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
133 <citations>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
134 <citation type="doi">10.1093/bioinformatics/btv231</citation>
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
135 </citations>
1
31a354009216 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
rnateam
parents: 0
diff changeset
136 </tool>