Mercurial > repos > iuc > megan_blast2rma

annotate blast2rma.xml @ 2:5be253dd3e08 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 374a2824a264468316f04281ed211079015503b5"
author iuc
date Tue, 07 Dec 2021 10:17:22 +0000
parents 2f8d3924bb3b
children d326b943f5e2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
1 <tool id="megan_blast2rma" name="MEGAN: Generate RMA files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
2 <description>from BLAST output</description>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
3 <macros>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
5 </macros>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
6 <expand macro="bio_tools"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
9 #import re
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
10
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
11 #if str($input_type_cond.input_type) in ['single', 'pair']:
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
12 #set read1 = $input_type_cond.read1
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
13 #set blast1 = $input_type_cond.blast1
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
14 #else:
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
15 ## Processing paired reads are tricky if we're
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
16 ## downstream from MALT. MALT doesn’t have a
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
17 ## paired-read mode, so it won’t attempt to analyze
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
18 ## reads in pairs. To do paired read processing,
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
19 ## set MALT to generate SAM files and then import the
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
20 ## SAM files into MEGAN, specifying paired read mode
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
21 ## there. If you have multiple SAM files for the same
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
22 ## sample, then import them all at the same time to
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
23 ## create one unified rma6 file.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
24
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
25 #set read1 = $input_type_cond.reads_collection['forward']
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
26 #set blast1 = $input_type_cond.blast1
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
27 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
28
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
29 #if $read1.is_of_type('fasta', 'fasta.gz'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
30 #set read_ext = '.fasta'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
31 #else:
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
32 #set read_ext = '.fastq'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
33 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
34 #if $read1.ext.endswith('.gz'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
35 #set read_ext = $read_ext + '.gz'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
36 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
37
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
38 #if $blast1.is_of_type('daa'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
39 #set blast_format = 'DAA'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
40 #else if $blast1.is_of_type('txt'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
41 #set blast_format = 'BlastText'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
42 #else if $blast1.is_of_type('blastxml'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
43 #set blast_format = 'BlastXML'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
44 #else if $blast1.is_of_type('tabular'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
45 #set blast_format = 'BlastTab'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
46 #else if $blast1.is_of_type('sam'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
47 #set blast_format = 'SAM'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
48 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
49 #set blast_ext = '.' + $blast_format
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
50 #if $blast1.ext.endswith('.gz'):
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
51 #set blast_ext = $blast_ext + '.gz'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
52 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
53
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
54 #set read1_identifier = 'read1' + $read_ext
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
55 ln -s '${read1}' '${read1_identifier}' &&
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
56
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
57 #set blast1_identifier = 'blast1' + $blast_ext
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
58 ln -s '${blast1}' '${blast1_identifier}' &&
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
59
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
60 #if str($input_type_cond.input_type) in ['pair', 'paired']:
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
61 #if str($input_type_cond.input_type) == 'pair':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
62 #set read2 = $input_type_cond.read2
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
63 #set blast2 = $input_type_cond.blast2
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
64 #else if str($input_type_cond.input_type) == 'paired':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
65 #set read2 = $input_type_cond.reads_collection['reverse']
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
66 #set blast2 = $input_type_cond.blast2
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
67 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
68 #set read2_identifier = 'read2' + $read_ext
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
69 ln -s '${read2}' '${read2_identifier}' &&
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
70 #set blast2_identifier = 'blast2' + $blast_ext
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
71 ln -s '${blast2}' '${blast2_identifier}' &&
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
72 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
73
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
74 blast2rma
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
75 #if str($input_type_cond.input_type) == 'single':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
76 --in '${blast1_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
77 --reads '${read1_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
78 --out '${rma6_output}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
79 #else if str($input_type_cond.input_type) == 'pair':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
80 --in '${blast1_identifier}' '${blast2_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
81 --reads '${read1_identifier}' '${read2_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
82 --paired
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
83 --pairedSuffixLength $input_type_cond.pairedSuffixLength
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
84 --out '${rma6_output}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
85 #else if str($input_type_cond.input_type) == 'paired':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
86 --in '${blast1_identifier}' '${blast2_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
87 --reads '${read1_identifier}' '${read2_identifier}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
88 --paired
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
89 --pairedSuffixLength $input_type_cond.pairedSuffixLength
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
90 ## Strangely, megan requires an output
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
91 ## directory when processing paired reads
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
92 ## even though it produces a single file.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
93 ## We'll accommodate thie by prepending ./
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
94 ## to a temporary output file and then move
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
95 ## it later.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
96 --out './tmp.rma6'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
97 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
98 --format '${blast_format}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
99 --blastMode '${blastMode}'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
100 --threads \${GALAXY_SLOTS:-8}
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
101 --useCompression false
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
102 $advanced_options.longReads
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
103 --maxMatchesPerRead '$advanced_options.maxMatchesPerRead'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
104 $advanced_options.classify
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
105 --minScore $advanced_options.minScore
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
106 --maxExpected $advanced_options.maxExpected
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
107 --minPercentIdentity $advanced_options.minPercentIdentity
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
108 --topPercent $advanced_options.topPercent
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
109 --minSupportPercent $advanced_options.minSupportPercent
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
110 --minSupport $advanced_options.minSupport
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
111 --minPercentReadCover $advanced_options.minPercentReadCover
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
112 --minPercentReferenceCover $advanced_options.minPercentReferenceCover
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
113 --minReadLength $advanced_options.minReadLength
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
114 --lcaAlgorithm '$advanced_options.lcaAlgorithm'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
115 --lcaCoveragePercent $advanced_options.lcaCoveragePercent
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
116 --readAssignmentMode '$advanced_options.readAssignmentMode'
1
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
117 #if $advanced_options.conFile:
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
118 --conFile '$advanced_options.conFile'
0
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
119 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
120 #if str($input_type_cond.input_type) == 'paired':
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
121 && mv './tmp.rma6' '$rma6_output'
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
122 #end if
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
123 ]]></command>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
124 <inputs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
125 <expand macro="input_type_cond"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
126 <param argument="--blastMode" type="select" label="Blast mode">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
127 <expand macro="blast_mode_options"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
128 </param>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
129 <section name="advanced_options" title="Advanced options" expanded="false">
1
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
130 <expand macro="long_reads_param"/>
2
5be253dd3e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 374a2824a264468316f04281ed211079015503b5"
iuc
parents: 1
diff changeset
131 <expand macro="max_matches_per_read_param"/>
1
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
132 <expand macro="classify_param"/>
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
133 <expand macro="blast_params"/>
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
134 <expand macro="min_max_params"/>
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
135 <expand macro="lca_params"/>
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
136 <expand macro="read_assignment_mode_param"/>
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
137 <expand macro="con_file_param"/>
0
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
138 </section>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
139 </inputs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
140 <outputs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
141 <data name="rma6_output" format="rma6"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
142 </outputs>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
143 <tests>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
144 <!-- Single dataset input -->
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
145 <test expect_num_outputs="1">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
146 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
147 <param name="blast1" value="blast_R1.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
148 <param name="blastMode" value="BlastN"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
149 <output name="rma6_output" ftype="rma6">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
150 <assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
151 <has_size value="19596"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
152 </assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
153 </output>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
154 </test>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
155 <!-- Single dataset input, contaminants file -->
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
156 <test expect_num_outputs="1">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
157 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
158 <param name="blast1" value="blast_R1.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
159 <param name="blastMode" value="BlastN"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
160 <param name="conFile" value="contaminants.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
161 <output name="rma6_output" ftype="rma6">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
162 <assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
163 <has_size value="19596"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
164 </assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
165 </output>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
166 </test>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
167 <!-- Dataset pair input -->
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
168 <test expect_num_outputs="1">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
169 <param name="input_type" value="pair"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
170 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
171 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
172 <param name="blast1" value="blast_R1.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
173 <param name="blast2" value="blast_R2.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
174 <param name="blastMode" value="BlastN"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
175 <output name="rma6_output" ftype="rma6">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
176 <assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
177 <has_size value="39887"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
178 </assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
179 </output>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
180 </test>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
181 <!-- List of dataset pairs input -->
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
182 <test expect_num_outputs="1">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
183 <param name="input_type" value="paired"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
184 <param name="reads_collection">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
185 <collection type="paired">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
186 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
187 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
188 </collection>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
189 </param>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
190 <param name="blast1" value="blast_R1.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
191 <param name="blast2" value="blast_R2.txt" ftype="txt"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
192 <param name="blastMode" value="BlastN"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
193 <output name="rma6_output" ftype="rma6">
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
194 <assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
195 <has_size value="39806"/>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
196 </assert_contents>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
197 </output>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
198 </test>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
199 </tests>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
200 <help>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
201 **What it does**
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
202
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
203 Computes MEGAN RMA files from BLAST (or similar) files. Inputs consist of reads in fasta or fasqsanger format (gzip compressin
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
204 is supported) and associated Blast files. Each read file should have been used previously as the Blast input to produce the
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
205 associated Blast file for this tool.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
206
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
207 This wrapper supports the following formats for the input Blast file. The SAM, Tabular and Text formats can be produced by
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
208 The Galaxy MALT Analyzer tool. When these formats are used, this tool will apply the SAM, BlastText and BlastTab format options
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
209 required by MEGAN.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
210
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
211 * **Direct Access Archive (DAA)** - a proprietary file format developed by PowerISO Computing for disk image files
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
212 * **BlastXML** - XML output from Blast
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
213 * **Sequence Alignment/Map (SAM)** - a tab-delimited text format consisting of a header section, which is optional, and an alignment section
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
214 * **Tabular** - information presented in the form of a table with rows and columns
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
215 * **Text** - plain text format
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
216
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
217 This tool outputs a RealMedia Audio (RMA) file. MEGAN uses an update of the original RMA file format known as RMA6. This update
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
218 requires less disk space for files.
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
219 </help>
1
2f8d3924bb3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents: 0
diff changeset
220 <expand macro="citations"/>
0
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
221 </tool>
fa3c3a64c993 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
iuc
parents:
diff changeset
222