Mercurial > repos > jvolkening > centrifuge

annotate centrifuge.xml @ 0:be7bba8229c6 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/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
author jvolkening
date Fri, 01 Nov 2019 13:53:15 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
1 <tool id="centrifuge" name="Centrifuge" version="1.0.4_beta">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
2
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
3 <description>Read-based metagenome characterization</description>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
4
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
5 <!-- ***************************************************************** -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
6
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
7 <requirements>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
8 <requirement type="package" version="1.0.4_beta">centrifuge</requirement>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
9 </requirements>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
10
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
11 <!-- ***************************************************************** -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
12
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
13 <version_command>centrifuge --version | perl -wnE'print "$1\n" for /centrifuge\S+ version (\S+)/g'</version_command>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
14
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
15 <!-- ***************************************************************** -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
16
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
17 <command detect_errors="aggressive">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
18 <![CDATA[
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
19
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
20 centrifuge
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
21
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
22 ##--Output Options------------------------------
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
23
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
24 --out-fmt $outputs.out_fmt
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
25 --tab-fmt-cols $outputs.tab_fmt_cols
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
26
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
27 ##--General Options-----------------------------
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
28
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
29 --threads \${GALAXY_SLOTS:-1}
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
30
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
31 #if $general.skip != "":
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
32 --skip $general.skip
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
33 #end if
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
34 #if $general.upto != "":
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
35 --upto $general.upto
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
36 #end if
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
37 #if $general.trim5 != "":
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
38 --trim5 $general.trim5
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
39 #end if
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
40 #if $general.trim3 != "":
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
41 --trim3 $general.trim3
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
42 #end if
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
43
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
44 $general.ignore_quals
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
45 $general.nofw
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
46 $general.norc
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
47 $general.non_deterministic
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
48
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
49 #if $general.seed != "":
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
50 --seed $general.seed
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
51 #end if
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
52
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
53 ##--Classification------------------------------
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
54
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
55 --min-hitlen $classification.min_hitlen
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
56
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
57 #if $classification.min_totallen != "":
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
58 --min-totallen $classification.min_totallen
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
59 #end if
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
60
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
61 #if $classification.host_taxids != "":
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
62 --host-taxids $classification.host_taxids
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
63 #end if
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
64
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
65 #if $classification.exclude_taxids != "":
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
66 --exclude-taxids $classification.exclude_taxids
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
67 #end if
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
68
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
69 ##--Inputs--------------------------------------
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
70
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
71 -x '${inputs.db.fields.path}'
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
72
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
73 #for $s in $inputs.unpaired
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
74 -U '${s.u_reads}'
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
75 #end for
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
76
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
77 #for $s in $inputs.paired
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
78 -1 '${s.p_reads.forward}'
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
79 -2 '${s.p_reads.reverse}'
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
80 #end for
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
81
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
82 #if $inputs.sra:
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
83 --sra-acc $inputs.sra
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
84 #end if
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
85
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
86 #if $outputs.out_fmt == "tab":
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
87 -S $out_tab
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
88 #elif $outputs.out_fmt == "sam":
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
89 -S $out_sam
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
90 #end if
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
91
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
92 --report-file $report
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
93
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
94 ]]>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
95 </command>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
96
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
97 <!-- ***************************************************************** -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
98
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
99 <inputs>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
100
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
101 <section name="inputs" title="Inputs" expanded="True">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
102
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
103 <repeat name="unpaired" title="Unpaired reads" min="0" default="0">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
104 <param name="u_reads" type="data" format="fastq" label="Unpaired reads"/>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
105 </repeat>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
106
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
107 <repeat name="paired" title="Paired reads" min="0" default="0">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
108 <param name="p_reads" type="data_collection" collection_type="paired" format="fastq" label="Paired read collection"/>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
109 </repeat>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
110
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
111 <param name="sra" type="text" label="SRA accession">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
112 <sanitizer invalid_char="">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
113 <valid initial="string.letters,string.digits">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
114 <add value="," />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
115 </valid>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
116 </sanitizer>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
117 </param>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
118
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
119 <param name="db" type="select" label="Select a reference database">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
120 <options from_data_table="centrifuge_indices">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
121 <filter type="sort_by" column="2"/>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
122 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
123 </options>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
124 </param>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
125
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
126 </section>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
127
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
128 <section name="outputs" title="Outputs" expanded="False">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
129
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
130 <param argument="--out-fmt" name="out_fmt" type="select" label="Output format">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
131 <option value="tab" selected="true">tabular</option>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
132 <option value="sam">SAM</option>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
133 </param>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
134
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
135 <param argument="--tab-fmt-cols" name="tab_fmt_cols" type="text" label="Output columns" value="readID,seqID,taxID,score,2ndBestScore,hitLength,queryLength,numMatches">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
136 <sanitizer invalid_char="">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
137 <valid initial="string.letters,string.digits">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
138 <add value="," />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
139 </valid>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
140 </sanitizer>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
141 </param>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
142
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
143 </section>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
144
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
145 <section name="general" title="General options" expanded="False">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
146
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
147 <param argument="--skip" type="integer" value="" optional="true" label="Initial reads to skip" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
148 <param argument="--upto" type="integer" value="" optional="true" label="Stop after reads" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
149 <param argument="--trim5" type="integer" value="" optional="true" label="Trim 5' bases" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
150 <param argument="--trim3" type="integer" value="" optional="true" label="Trim 3' bases" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
151
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
152 <param argument="--ignore-quals" name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" checked="no" label="Ignore qualities" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
153
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
154 <param argument="--nofw" type="boolean" truevalue="--nofw" falsevalue="" checked="no" label="Don't map forward strand" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
155 <param argument="--norc" type="boolean" truevalue="--norc" falsevalue="" checked="no" label="Don't map rev-com strand" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
156
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
157 <param argument="--seed" type="integer" value="" min="0" optional="true" label="Starting seed" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
158 <param argument="--non-deterministic" name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" checked="no" label="Use non-deterministic seeding" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
159
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
160 </section>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
161
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
162 <section name="classification" title="Classification" expanded="True">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
163
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
164 <param argument="--min-hitlen" name="min_hitlen" type="integer" value="22" min="16" label="Minimum hit length" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
165 <param argument="--min-totallen" name="min_totallen" type="integer" optional="true" min="0" label="Minimum summed length" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
166
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
167 <param argument="--host-taxids" name="host_taxids" type="text" label="Host taxonomic IDs">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
168 <sanitizer invalid_char="">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
169 <valid initial="string.digits">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
170 <add value="," />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
171 </valid>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
172 </sanitizer>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
173 </param>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
174 <param argument="--exclude-taxids" name="exclude_taxids" type="text" label="Excluded taxonomic IDs">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
175 <sanitizer invalid_char="">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
176 <valid initial="string.digits">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
177 <add value="," />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
178 </valid>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
179 </sanitizer>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
180 </param>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
181
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
182 </section>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
183
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
184 </inputs>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
185
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
186 <!-- ***************************************************************** -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
187
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
188 <outputs>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
189
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
190 <data name="out_tab" format="tabular" label="Centrifuge on ${on_string}: Output">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
191 <filter>(outputs['out_fmt'] == "tab")</filter>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
192 </data>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
193 <data name="out_sam" format="sam" label="Centrifuge on ${on_string}: Output">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
194 <filter>(outputs['out_fmt'] == "sam")</filter>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
195 </data>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
196 <data name="report" format="tabular" label="Centrifuge on ${on_string}: Report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
197
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
198 </outputs>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
199
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
200 <!-- ***************************************************************** -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
201
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
202 <tests>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
203 <!-- default unpaired -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
204 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
205 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
206 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
207 <output name="out_tab" file="defaults.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
208 <output name="report" file="defaults.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
209 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
210 <!-- default paired -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
211 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
212 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
213 <param name="p_reads">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
214 <collection type="paired">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
215 <element name="forward" value="input_f.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
216 <element name="reverse" value="input_r.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
217 </collection>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
218 </param>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
219 <output name="out_tab" file="paired.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
220 <output name="report" file="paired.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
221 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
222 <!-- default combined -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
223 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
224 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
225 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
226 <param name="p_reads">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
227 <collection type="paired">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
228 <element name="forward" value="input_f.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
229 <element name="reverse" value="input_r.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
230 </collection>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
231 </param>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
232 <output name="out_tab" file="both.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
233 <output name="report" file="both.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
234 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
235 <!-- exclude IDs -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
236 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
237 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
238 <param name="exclude_taxids" value="9913" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
239 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
240 <output name="out_tab" file="exclude.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
241 <output name="report" file="exclude.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
242 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
243 <!-- specify host -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
244 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
245 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
246 <param name="host_taxids" value="9913" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
247 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
248 <output name="out_tab" file="host.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
249 <output name="report" file="host.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
250 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
251 <!-- minimum length -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
252 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
253 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
254 <param name="min_hitlen" value="83" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
255 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
256 <output name="out_tab" file="minlen83.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
257 <output name="report" file="minlen83.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
258 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
259 <!-- norc -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
260 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
261 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
262 <param name="norc" value="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
263 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
264 <output name="out_tab" file="norc.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
265 <output name="report" file="norc.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
266 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
267 <!-- nofw -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
268 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
269 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
270 <param name="nofw" value="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
271 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
272 <output name="out_tab" file="nofw.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
273 <output name="report" file="nofw.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
274 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
275 <!-- set seed -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
276 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
277 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
278 <param name="seed" value="123" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
279 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
280 <output name="out_tab" file="seed123.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
281 <output name="report" file="seed123.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
282 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
283 <!-- 5' trim -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
284 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
285 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
286 <param name="trim5" value="10" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
287 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
288 <output name="out_tab" file="trim5_10.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
289 <output name="report" file="trim5_10.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
290 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
291 <!-- 3' trim -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
292 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
293 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
294 <param name="trim3" value="5" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
295 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
296 <output name="out_tab" file="trim3_5.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
297 <output name="report" file="trim3_5.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
298 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
299 <!-- skip start -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
300 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
301 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
302 <param name="skip" value="3" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
303 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
304 <output name="out_tab" file="skip3.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
305 <output name="report" file="skip3.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
306 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
307 <!-- skip end -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
308 <test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
309 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
310 <param name="upto" value="6" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
311 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
312 <output name="out_tab" file="upto6.tsv" sort="true" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
313 <output name="report" file="upto6.report" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
314 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
315 <!-- invalid parameter value -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
316 <test expect_failure="true">
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
317 <param name="db" value="test_db" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
318 <param name="tab_fmt_cols" value="FooBar" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
319 <param name="u_reads" ftype="fastq" value="input_u.fq" />
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
320 </test>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
321
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
322 </tests>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
323
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
324 <!-- ***************************************************************** -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
325
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
326 <help>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
327 <![CDATA[
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
328
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
329 Overview
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
330 --------
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
331
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
332 **Centrifuge** is a very rapid and memory-efficient system for the
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
333 classification of DNA sequences from microbial samples, with better
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
334 sensitivity than and comparable accuracy to other leading systems. The system
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
335 uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
336 the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
337 classification problem. Centrifuge requires a relatively small index (e.g.,
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
338 4.3 GB for ~4,100 bacterial genomes) yet provides very fast classification
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
339 speed, allowing it to process a typical DNA sequencing run within an hour.
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
340 Together these advances enable timely and accurate analysis of large
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
341 metagenomics data sets on conventional desktop computers.
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
342
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
343 Usage
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
344 -----
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
345
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
346 Following is the manpage for `centrifuge`, which can be linked with the
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
347 options above using the help text. Note that not all options are available in
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
348 the Galaxy wrapper.
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
349
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
350 ::
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
351
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
352 centrifuge [options]* -x <cf-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <filename>] [--report-file <report>]
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
353
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
354 <cf-idx> Index filename prefix (minus trailing .X.cf).
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
355 <m1> Files with #1 mates, paired with files in <m2>.
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
356 Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
357 <m2> Files with #2 mates, paired with files in <m1>.
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
358 Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
359 <r> Files with unpaired reads.
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
360 Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
361 <SRA accession number> Comma-separated list of SRA accession numbers, e.g. --sra-acc SRR353653,SRR353654.
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
362 <filename> File for classification output (default: stdout)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
363 <report> File for tabular report output (default: centrifuge_report.tsv)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
364
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
365 <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
366 specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
367
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
368 Options (defaults in parentheses):
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
369
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
370 Input:
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
371 -q query input files are FASTQ .fq/.fastq (default)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
372 --qseq query input files are in Illumina's qseq format
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
373 -f query input files are (multi-)FASTA .fa/.mfa
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
374 -r query input files are raw one-sequence-per-line
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
375 -c <m1>, <m2>, <r> are sequences themselves, not files
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
376 -s/--skip <int> skip the first <int> reads/pairs in the input (none)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
377 -u/--upto <int> stop after first <int> reads/pairs (no limit)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
378 -5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
379 -3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
380 --phred33 qualities are Phred+33 (default)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
381 --phred64 qualities are Phred+64
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
382 --int-quals qualities encoded as space-delimited integers
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
383 --ignore-quals treat all quality values as 30 on Phred scale (off)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
384 --nofw do not align forward (original) version of read (off)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
385 --norc do not align reverse-complement version of read (off)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
386 --sra-acc SRA accession ID
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
387
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
388 Classification:
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
389 --min-hitlen <int> minimum length of partial hits (default 22, must be greater than 15)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
390 --min-totallen <int> minimum summed length of partial hits per read (default 0)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
391 --host-taxids <taxids> comma-separated list of taxonomic IDs that will be preferred in classification
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
392 --exclude-taxids <taxids> comma-separated list of taxonomic IDs that will be excluded in classification
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
393
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
394 Output:
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
395 --out-fmt <str> define output format, either 'tab' or 'sam' (tab)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
396 --tab-fmt-cols <str> columns in tabular format, comma separated
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
397 default: readID,seqID,taxID,score,2ndBestScore,hitLength,queryLength,numMatches
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
398 -t/--time print wall-clock time taken by search phases
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
399 --un <path> write unpaired reads that didn't align to <path>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
400 --al <path> write unpaired reads that aligned at least once to <path>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
401 --un-conc <path> write pairs that didn't align concordantly to <path>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
402 --al-conc <path> write pairs that aligned concordantly at least once to <path>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
403 (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
404 --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
405 --quiet print nothing to stderr except serious errors
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
406 --met-file <path> send metrics to file at <path> (off)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
407 --met-stderr send metrics to stderr (off)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
408 --met <int> report internal counters & metrics every <int> secs (1)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
409
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
410 Performance:
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
411 -o/--offrate <int> override offrate of index; must be >= index's offrate
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
412 -p/--threads <int> number of alignment threads to launch (1)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
413 --mm use memory-mapped I/O for index; many 'bowtie's can share
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
414
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
415 Other:
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
416 --qc-filter filter out reads that are bad according to QSEQ filter
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
417 --seed <int> seed for random number generator (0)
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
418 --non-deterministic seed rand. gen. arbitrarily instead of using read attributes
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
419 --version print version information and quit
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
420 -h/--help print this usage message
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
421
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
422 ]]>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
423 </help>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
424
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
425 <!-- ***************************************************************** -->
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
426
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
427 <citations>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
428 <citation type="doi">10.1101/gr.210641.116</citation>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
429 </citations>
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
430
be7bba8229c6 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/centrifuge commit 5d9e0a6e2ad278547892c86f0acded93814a1356-dirty
jvolkening
parents:
diff changeset
431 </tool>