Mercurial > repos > bebatut > sortmerna

annotate sortmerna.xml @ 19:4f476a49f079 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
author bebatut
date Mon, 12 Jun 2017 08:06:02 -0400
parents 63e6d7aefbe6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.4">
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
2 <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
3 <macros>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
4 <import>macros.xml</import>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
5 </macros>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
6 <requirements>
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
7 <requirement type="package" version="@VERSION@">sortmerna</requirement>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
8 </requirements>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
9 <stdio>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
10 <regex match="This program builds a Burst trie on an input rRNA database"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
11 source="both"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
12 level="fatal"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
13 description="Buildtrie program failed to execute." />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
14 <regex match="The database name"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
15 source="both"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
16 level="fatal"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
17 description="The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA." />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
18 <regex match="ERROR"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
19 source="both"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
20 level="fatal"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
21 description="ERROR" />
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
22 </stdio>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
23 <version_command>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
24 <![CDATA[
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
25 sortmerna --version 2>&1|grep 'SortMeRNA version'
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
26 ]]>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
27 </version_command>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
28 <command>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
29 <![CDATA[
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
30 #set $ref = ''
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
31 #set $sep=''
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
32 #if str( $databases_type.databases_selector ) == 'history'
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
33 #for $db in $databases_type.database_name
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
34 #set $ref += $sep + str($db) + ',' + $os.path.splitext($os.path.basename(str($db)))[0]
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
35 #set $sep = ':'
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
36 #end for
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
37 #else if str( $databases_type.databases_selector ) == 'cached_to_index'
18
63e6d7aefbe6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 17
diff changeset
38 #for $db in $databases_type.input_databases.fields.path.split(",")
19
4f476a49f079 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 18
diff changeset
39 #set $ref += $sep + $db + ',' + $os.path.splitext($db)[0] + '-reindexed'
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
40 #set $sep = ':'
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
41 #end for
19
4f476a49f079 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 18
diff changeset
42 #else
18
63e6d7aefbe6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 17
diff changeset
43 #for $db in $databases_type.input_databases.fields.path.split(",")
19
4f476a49f079 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 18
diff changeset
44 #set $ref += $sep + $db + ',' + $os.path.splitext($db)[0]
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
45 #set $sep = ':'
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
46 #end for
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
47 #end if
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
48
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
49 #if str( $databases_type.databases_selector ) != 'cached':
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
50 indexdb_rna
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
51 --ref $ref
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
52 -L $databases_type.seed_length
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
53 --max_pos $databases_type.max_pos
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
54 &&
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
55 #end if
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
56
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
57 sortmerna
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
58 --ref $ref
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
59 --reads $input_reads
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
60 --aligned aligned
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
61
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
62 #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
63 $sequencing_type.paired_type
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
64 #end if
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
65
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
66 $strand_search
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
67 $aligned_fastx.aligned_fastx_selector
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
68 #if $aligned_fastx.aligned_fastx_selector == '--fastx'
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
69 #if $aligned_fastx.other
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
70 --other other_file
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
71 #end if
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
72 #end if
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
73 $aligned_sam.aligned_sam_selector
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
74 #if $aligned_sam.aligned_sam_selector == '--sam'
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
75 $aligned_sam.sq
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
76 #end if
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
77 #if $aligned_blast.aligned_blast_selector == '--blast'
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
78 --blast "$aligned_blast.aligned_blast_format"
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
79 #end if
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
80
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
81 $log
3
9c19086ae626 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty
bebatut
parents: 2
diff changeset
82
6
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
83 #if $report.report_type == 'best'
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
84 #if $report.report_best.report_best_type == '1'
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
85 --best 1
6
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
86 --min_lis $report.report_best.report_best_min_lis
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
87 #else
6
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
88 --best $report.report_best.report_best_value
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
89 --min_lis $report.report_best.report_best_min_lis
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
90 #end if
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
91 #else
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
92 #if $report.report_num_alignments.report_num_alignments_type == 'other_value'
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
93 --num_alignments $report.report_num_alignments.report_num_alignments_value
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
94 #else
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
95 --num_alignments $report.report_num_alignments.report_num_alignments_type
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
96 #end if
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
97 #end if
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
98
2
48ab7cdab700 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty
bebatut
parents: 1
diff changeset
99 -e $e_value
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
100 --match $match
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
101 --mismatch $mismatch
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
102 --gap_open $gap_open
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
103 --gap_ext $gap_ext
2
48ab7cdab700 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty
bebatut
parents: 1
diff changeset
104 -N $ambiguous_letter
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
105 -a \${GALAXY_SLOTS:-1}
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
106 ]]>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
107 </command>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
108 <inputs>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
109 <param format="fasta,fastq" name="input_reads" type="data" label="Querying sequences" help="In FASTA or FASTQ format (--reads)"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
110 <conditional name="sequencing_type">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
111 <param name="sequencing_type_selector" type="select" label="Sequencing type">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
112 <option value="not_paired">Reads are not paired</option>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
113 <option value="paired">Reads are paired</option>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
114 </param>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
115 <when value="not_paired" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
116 <when value="paired">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
117 <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
118 <option value="">leave the reads split between aligned and rejected files</option>
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
119 <option value="--paired_in">output both reads to aligned file (--paired_in)</option>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
120 <option value="--paired_out">output both reads to rejected file (--paired_out)</option>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
121 </param>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
122 </when>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
123 </conditional>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
124
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
125 <param name="strand_search" type="select" label="Which strands to search">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
126 <option value="">Search both strands</option>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
127 <option value="-F">Search only the forward strand (-F)</option>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
128 <option value="-R">Search only the reverse-complementary strand (-R)</option>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
129 </param>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
130
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
131 <conditional name="databases_type">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
132 <param name="databases_selector" type="select" label="Databases to query"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
133 help="Public rRNA databases provided with SortMeRNA have been indexed.
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
134 On the contrary, personal databases must be indexed each time SortMeRNA is launched.
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
135 Please be patient, this may take some time depending on the size of the given database.">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
136 <option value="cached" selected="true">Public pre-indexed ribosomal databases</option>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
137 <option value="cached_to_index">Public ribosomal databases to index with non default parameters</option>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
138 <option value="history">Databases from your history</option>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
139 </param>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
140 <when value="cached">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
141 <param name="input_databases" label="rRNA databases" type="select" display="checkboxes" multiple="true">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
142 <options from_data_table="rRNA_databases" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
143 <validator type="no_options" message="Select at least one database"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
144 </param>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
145 </when>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
146 <when value="cached_to_index">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
147 <param name="input_databases" label="rRNA databases" type="select" display="checkboxes" multiple="true">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
148 <options from_data_table="rRNA_databases" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
149 <validator type="no_options" message="Select at least one database"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
150 </param>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
151 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
152 <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
153 </when>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
154 <when value="history">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
155 <param name="database_name" type="data" format="fasta" multiple="true" label="rRNA databases"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
156 help="Your databases will be indexed first, which may take up to several minutes."/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
157 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
158 <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
159 </when>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
160 </conditional>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
161
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
162 <!-- Outputs -->
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
163 <conditional name="aligned_fastx">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
164 <param name="aligned_fastx_selector" type="select" label="Include aligned reads in FASTA/FASTQ format?">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
165 <option value="--fastx">Yes (--fastx)</option>
6
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
166 <option value="">No</option>
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
167 </param>
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
168 <when value="--fastx">
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
169 <param name="other" type="boolean" label="Include rejected reads file?" help="(--other)" />
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
170 </when>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
171 <when value="" />
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
172 </conditional>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
173 <conditional name="aligned_sam">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
174 <param name="aligned_sam_selector" type="select" label="Include alignments in SAM format?">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
175 <option value="--sam">Yes (--sam)</option>
6
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
176 <option value="">No</option>
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
177 </param>
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
178 <when value="--sam">
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
179 <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" />
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
180 </when>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
181 <when value="" />
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
182 </conditional>
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
183 <conditional name="aligned_blast">
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
184 <param name="aligned_blast_selector" type="select" label="Include alignments in BLAST-like format?">
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
185 <option value="--blast">Yes</option>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
186 <option value="" selected="true">No</option>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
187 </param>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
188 <when value="--blast">
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
189 <param name="aligned_blast_format" type="select" label="BLAST-like format?">
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
190 <option value="0">pairwise (--blast '0')</option>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
191 <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
192 <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
193 <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
194 <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
195 </param>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
196 </when>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
197 <when value="" />
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
198 </conditional>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
199 <param name="log" type="boolean" checked="false" truevalue="--log" falsevalue="" label="Generate statistics file"
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
200 help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
201 </param>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
202 <conditional name="report">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
203 <param name="report_type" type="select" label="Parameters for filtering and read mapping" help="">
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
204 <option value="best" selected="true">Report best alignments per read reaching E-value</option>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
205 <option value="num_alignments">Report first alignements per read reaching E-value</option>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
206 </param>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
207 <when value="best">
6
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
208 <conditional name="report_best">
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
209 <param name="report_best_type" type="select" label="Number of searched alignments" help="Only the best alignment is reported (--best)">
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
210 <option value="1" selected="true">Only one high-candidate reference sequence is searched for alignments (fast). The high-candidate sequences are determined heuristically using a LIS of seed matches)</option>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
211 <option value="other_value">A custom number of reference sequences are searched for alignments (speed decrease for high value)</option>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
212 </param>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
213 <when value="1">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
214 <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
215 </when>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
216 <when value="other_value">
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
217 <param name="report_best_value" type="integer" min="2" max="100" value="2" label="Number of alignments to be made" help="Only the best one is reported. The computation speed decrease with high value"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
218 <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
219 </when>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
220 </conditional>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
221 </when>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
222 <when value="num_alignments">
6
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
223 <conditional name="report_num_alignments">
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
224 <param name="report_num_alignments_type" type="select" label="Number of output alignments" help="(--num_alignments)">
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
225 <option value="0">All alignments reaching the E-value threshold are reported (very slow, this option is not suggested for high similarity rRNA databases)</option>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
226 <option value="1" selected="true">The first alignment passing E-value threshold are reported (very fast, best choice if only filtering is needed)</option>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
227 <option value="other_value">A custom number of alignments are made and reported (speed decrease for high value)</option>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
228 </param>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
229 <when value="0" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
230 <when value="1" />
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
231 <when value="other_value">
6
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
232 <param name="report_num_alignments_value" type="integer" min="0" max="100" value="1" label="Number of alignments to be made and reported" help=""/>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
233 </when>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
234 </conditional>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
235 </when>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
236 </conditional>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
237
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
238 <param name="e_value" type="float" min="0" max="10" value="1" label="E-value threshold" help="(-e)"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
239 <param name="match" type="integer" min="0" max="10" value="2" label="SW score for a match" help="(--match)"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
240 <param name="mismatch" type="integer" min="-10" max="0" value="-3" label="SW penalty for a mismatch" help="(--mismatch)"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
241 <param name="gap_open" type="integer" min="0" max="10" value="5" label="SW penalty for introducing a gap" help="(--gap_open)"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
242 <param name="gap_ext" type="integer" min="0" max="10" value="2" label="SW penalty for extending a gap" help="(--gap_ext)"/>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
243 <param name="ambiguous_letter" type="integer" min="-10" max="0" value="-3" label="SW penalty for ambiguous letters (N's)" help="(-N)"/>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
244 </inputs>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
245 <outputs>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
246 <data format_source="input_reads" name="output_fastx" from_work_dir="aligned.dat"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
247 label="Aligned reads on ${on_string} (${input_reads.datatype.file_ext})">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
248 <filter>aligned_fastx['aligned_fastx_selector']</filter>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
249 </data>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
250 <data format_source="input_reads" name="output_other" from_work_dir="other_file.dat"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
251 label="Rejected reads on ${on_string} (${input_reads.datatype.file_ext})">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
252 <filter>aligned_fastx['aligned_fastx_selector'] and aligned_fastx['other']</filter>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
253 </data>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
254 <data format="sam" name="output_sam" from_work_dir="aligned.sam"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
255 label="Alignments on ${on_string} (SAM)">
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
256 <filter>aligned_sam['aligned_sam_selector']</filter>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
257 </data>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
258 <data format="tabular" name="output_blast" from_work_dir="aligned.blast"
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
259 label="Alignments on ${on_string} (BLAST)">
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
260 <filter>aligned_blast['aligned_blast_selector']</filter>
3
9c19086ae626 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty
bebatut
parents: 2
diff changeset
261 <change_format>
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
262 <when input="aligned_blast.aligned_blast_format" value="0" format="txt" />
3
9c19086ae626 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty
bebatut
parents: 2
diff changeset
263 </change_format>
9c19086ae626 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty
bebatut
parents: 2
diff changeset
264 </data>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
265 <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log">
4
5d7ec21f6d4c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 4d9df680f128bc18183ebba6f85fc24f11207571-dirty
bebatut
parents: 3
diff changeset
266 <filter>log</filter>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
267 </data>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
268 </outputs>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
269 <tests>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
270 <test>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
271 <param name="input_reads" value="read_small.fastq" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
272 <param name="sequencing_type_selector" value="not_paired" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
273 <param name="strand_search" value="" />
6
817fb14fc739 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
bebatut
parents: 5
diff changeset
274 <param name="databases_selector" value="history" />
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
275 <param name="database_name" value="ref_small.fasta" />
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
276 <param name="aligned_fastx_selector" value="--fastx" />
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
277 <param name="other" value="True" />
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
278 <param name="aligned_sam_selector" value="--sam" />
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
279 <param name="aligned_blast_selector" value="--blast"/>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
280 <param name="aligned_blast_format" value="1 cigar qcov" />
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
281 <param name="log" value="" />
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
282 <param name="report_type" value="best" />
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
283 <param name="report_best_type" value="1" />
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
284 <param name="e_value" value="1"/>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
285 <param name="match" value="2"/>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
286 <param name="mismatch" value="-3" />
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
287 <param name="gap_open" value="5"/>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
288 <param name="gap_ext" value="2"/>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
289 <param name="ambiguous_letter" value="-3"/>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
290 <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
291 <output name="output_other" file="sortmerna_wrapper_other1.fastq" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
292 <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
293 </test>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
294 <test>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
295 <param name="input_reads" value="read_small.fasta" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
296 <param name="sequencing_type_selector" value="not_paired" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
297 <param name="strand_search" value="" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
298 <param name="databases_selector" value="history" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
299 <param name="database_name" value="ref_small.fasta" />
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
300 <param name="aligned_fastx_selector" value="--fastx" />
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
301 <param name="other" value="True" />
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
302 <param name="aligned_sam_selector" value="--sam" />
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
303 <param name="aligned_blast" value="" />
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
304 <param name="log" value="" />
16
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
305 <param name="report_type" value="best" />
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
306 <param name="report_best_type" value="1" />
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
307 <param name="report_type" value="best" />
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
308 <param name="report_best_type" value="1" />
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
309 <param name="e_value" value="1"/>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
310 <param name="match" value="2"/>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
311 <param name="mismatch" value="-3" />
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
312 <param name="gap_open" value="5"/>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
313 <param name="gap_ext" value="2"/>
1a4662c2d6db planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
bebatut
parents: 15
diff changeset
314 <param name="ambiguous_letter" value="-3"/>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
315 <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
316 <output name="output_other" file="sortmerna_wrapper_other2.fasta" />
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
317 <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
318 </test>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
319 </tests>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
320 <help>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
321 <![CDATA[
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
322 **What it does**
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
323
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
324 SortMeRNA_ is a software designed to rapidly filter ribosomal RNA fragments
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
325 from metatransriptomic data produced by next-generation sequencers.
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
326 It is capable of handling large RNA databases and sorting out all fragments
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
327 matching to the database with high accuracy and specificity.
11
b8ba70feb088 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit f612dbbae7f8347555e561d8a09664296ce96b76-dirty
bebatut
parents: 10
diff changeset
328
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
329 .. _SortMeRNA: http://bioinfo.lifl.fr/RNA/sortmerna/
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
330
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
331
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
332 **Input**
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
333
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
334 The input is one file of reads in FASTA or FASTQ format and any number of rRNA databases to search against.
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
335 If the user has two foward-reverse paired-sequencing reads files, they may use
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
336 the script "merge_paired_reads.sh" to interleave the reads into one file, preserving their order.
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
337
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
338 If the sequencing type for the reads is paired-ended, the user has two options under
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
339 "Sequencing type" to filter the reads and preserve their order in the file.
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
340 For a further example of each option, please refer to Section 4.2.3 in the `SortMeRNA User Manual`_.
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
341
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
342 .. _sortmerna user manual: http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
343
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
344
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
345 **Output**
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
346
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
347 The output will follow the same format (FASTA or FASTQ) as the reads. Optionally, a statistic file for the rRNA content of reads, as well as rRNA subunit distribution can be generated.
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
348
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
349
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
350 **rRNA databases**
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
351
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
352 SortMeRNA is distributed with 8 representative rRNA databases, which were
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
353 all constructed from the SILVA SSU,LSU (version 111) and the RFAM 5/5.8S
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
354 (version 11.0) databases using the tool UCLUST.
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
355
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
356 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
357 | Representative database | id % | average id% | # seq (clustered) | Origin | # seq (original) |
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
358 +==========================+======+=============+===================+========================+===================+
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
359 | SILVA 16S bacteria | 85 | 91.6 | 8174 | SILVA SSU Ref NR v.111 | 244077 |
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
360 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
361 | SILVA 16S archaea | 95 | 96.7 | 3845 | SILVA SSU Ref NR v.111 | 10919 |
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
362 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
363 | SILVA 18S eukarya | 95 | 96.7 | 4512 | SILVA SSU Ref NR v.111 | 31862 |
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
364 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
365 | SILVA 23S bacteria | 98 | 99.4 | 3055 | SILVA LSU Ref v.111 | 19580 |
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
366 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
367 | SILVA 23s archaea | 98 | 99.5 | 164 | SILVA LSU Ref v.111 | 405 |
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
368 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
369 | SILVA 28S eukarya | 98 | 99.1 | 4578 | SILVA LSU Ref v.111 | 9321 |
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
370 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
371 | Rfam 5S archaea/bacteria | 98 | 99.2 | 59513 | RFAM | 116760 |
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
372 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
373 | Rfam 5.8S eukarya | 98 | 98.9 | 13034 | RFAM | 225185 |
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
374 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
375
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
376 id %: members of the cluster must have identity at least 'id %' identity with the representative sequence
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
377
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
378 average id %: average identity of a cluster member to the representative sequence
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
379
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
380 The user may also choose to use their own rRNA databases.
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
381
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
382 .. class:: warningmark
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
383
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
384 Note that your personal databases are indexed each time. The public ribosomal
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
385 databases are indexed when added, but they can be re-indexed with non-default indexing
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
386 parameters. The indexing may take some time depending on the size of the given database.
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
387
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
388 ]]>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
389 </help>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
390
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
391 <citations>
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
392 <citation type="doi">10.1093/bioinformatics/bts611</citation>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
393 <citation type="doi">10.1093/nar/gks1219</citation>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
394 <citation type="doi">10.1093/nar/gks1005</citation>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
395 <citation type="doi">10.1093/bioinformatics/btq461</citation>
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
396 <citation type="doi">10.1038/nbt.2198</citation>
0
87327d15b045 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 556070f12fb6442e52820d852f7e7a85a28117f2-dirty
bebatut
parents:
diff changeset
397 </citations>
15
baab049d3aff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit e20e66ff81239452b3d75dec16e9e0cc8eb46266-dirty
bebatut
parents: 13
diff changeset
398 </tool>