Mercurial > repos > pimarin > recentrifuge

annotate recentrifuge.xml @ 7:9940b2fbc06f 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/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit b537a57a1de919afa1c6a23048862676b87d7c18"
author pimarin
date Tue, 24 May 2022 06:35:06 +0000
parents 512dc05a0e5a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents:
diff changeset
2
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents:
diff changeset
3 <tool id="recentrifuge" name="Recentrifuge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
4
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
4 <description>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
5 Robust comparative analysis and contamination removal for metagenomics
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
6 </description>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
7 <macros>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
8 <import>macro.xml</import>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
9 </macros>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
10 <expand macro='xrefs'/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
11 <expand macro="requirements" />
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
12 <expand macro="version_command" />
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
13 <command detect_errors="aggressive"><![CDATA[
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
14 #*======================================
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
15 database input
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
16 ======================================*#
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
17 #if $database.db_type.db_select == "cached"
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
18 #set $rcf_db = $database.db_type.cached_db.fields.path
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
19 #else if $database.db_type.db_select == "history"
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
20 mkdir rcf_db &&
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
21 #for i in $database.db_type.history_db
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
22 ln -s '$i' 'rcf_db/$i.element_identifier' &&
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
23 #end for
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
24 #set $rcf_db = "rcf_db"
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
25 #end if
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
26 rcf
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
27 -n $rcf_db
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
28 #*======================================
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
29 Recentrifuge input file
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
30 ======================================*#
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
31 #if $input_option.file_type.filetype == "centrifuge"
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
32 -f '$input_option.input_file'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
33 #set $default_scoring = 'SHEL'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
34 #else if $input_option.file_type.filetype == "lmat"
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
35 -l '$input_option.input_file'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
36 #set $default_scoring = 'LMAT'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
37 #else if $input_option.file_type.filetype == "clark"
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
38 -r '$input_option.input_file'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
39 #set $default_scoring = 'SHEL'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
40 #else if $input_option.file_type.filetype == "kraken"
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
41 -k '$input_option.input_file'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
42 #set $default_scoring = 'KRAKEN'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
43 #else if $input_option.file_type.filetype == "generic"
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
44 -g '$input_option.input_file'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
45 --format '$input_option.file_type.format'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
46 #set $default_scoring = 'GENERIC'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
47 #end if
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
48 #*======================================
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
49 Output options
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
50 ======================================*#
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
51 -e $output_option.extra
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
52 -o output
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
53 $output_option.nohtml
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
54 #*======================================
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
55 Advanced options
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
56 ======================================*#
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
57 #if $advanced_option.controls
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
58 --controls '$advanced_option.controls'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
59 #end if
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
60 #if $advanced_option.scoring
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
61 --scoring '$advanced_option.scoring'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
62 #else
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
63 --scoring '$default_scoring'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
64 #end if
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
65 #if $advanced_option.minscore_value
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
66 --minscore '$advanced_option.minscore_value'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
67 #end if
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
68 #if $advanced_option.mintaxa
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
69 --mintaxa '$advanced_option.mintaxa'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
70 #end if
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
71 #if $advanced_option.exclude_taxa_name
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
72 --exclude '$advanced_option.exclude_taxa_name'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
73 #end if
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
74 #if $advanced_option.include_taxa_name
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
75 --include '$advanced_option.include_taxa_name'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
76 #end if
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
77 $advanced_option.avoidcross
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
78 #*======================================
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
79 More advanced options
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
80 ======================================*#
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
81 #if $more_advanced_option.ctrlminscore
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
82 --ctrlminscore '$more_advanced_option.ctrlminscore'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
83 #end if
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
84 #if $more_advanced_option.ctrlmintaxa
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
85 --ctrlmintaxa '$more_advanced_option.ctrlmintaxa'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
86 #end if
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
87 --summary $more_advanced_option.summary
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
88 $more_advanced_option.takeoutroot
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
89 $more_advanced_option.nokollapse
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
90 $more_advanced_option.strain
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
91 $more_advanced_option.sequential
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
92 #*======================================
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
93 Log file output
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
94 ======================================*#
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
95 &> '$logfile'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
96 ]]>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
97 </command>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
98 <inputs>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
99 <!-- INPUT FILES -->
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
100 <section name="input_option" title="Input options" expanded="true">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
101 <param name="input_file" type="data" format="tabular" label="Select taxonomy file tabular formated"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
102 <conditional name="file_type">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
103 <param name="filetype" type="select" display="radio" label="Type of input file (Centrifuge, CLARK, Generic, Kraken, LMAT)" help="(-f, -r, -g, -k, -l)">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
104 <option value="centrifuge">Centrifuge</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
105 <option value="clark">CLARK</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
106 <option value="generic">Generic</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
107 <option value="lmat" >LMAT</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
108 <option value="kraken" >Kraken</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
109 </param>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
110 <when value="centrifuge"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
111 <when value="lmat"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
112 <when value="clark"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
113 <when value="kraken"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
114 <when value="generic">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
115 <param argument="--format" type="text" label="Format of the output files from a generic classifier"
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
116 help="string like 'TYP:csv,TID:1,LEN:3,SCO:6,UNC:0'
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
117 where valid file Types are csv/tsv/ssv, and the rest of fields indicate the number of column used (starting in 1)
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
118 for the TaxIDs assigned,the LENgth of the read, the SCOre given to the assignment">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
119 </param>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
120 </when>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
121 </conditional>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
122 </section>
0
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents:
diff changeset
123 <!-- taxa databases -->
4
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
124 <section name="database" title="Database type" expanded="true">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
125 <conditional name="db_type">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
126 <param name="db_select" type="select" label="Cached database with clade-specific marker genes">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
127 <option value="cached" selected="true">Locally installed</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
128 <option value="history">From history</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
129 </param>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
130 <when value="cached">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
131 <param name="cached_db" type="select" label="Cached database whith taxa ID">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
132 <options from_data_table="ncbi_taxonomy">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
133 <validator message="No NCBI database is available" type="no_options"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
134 </options>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
135 </param>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
136 </when>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
137 <when value="history">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
138 <param name="history_db" type="data" multiple="true" format="txt" label="Database from history"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
139 </when>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
140 </conditional>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
141 </section>
0
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents:
diff changeset
142 <!-- output name -->
4
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
143 <section name="output_option" title="Output options">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
144 <param argument="--extra" type="select" label="Type of extra output to be generated (default on CSV)" help="Default : CSV">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
145 <option value="CSV" selected="true" >CSV</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
146 <option value="DYNOMICS">DYNOMICS</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
147 <option value="FULL">FULL</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
148 <option value="MULTICSV">MULTICSV</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
149 <option value="TSV" >TSV</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
150 </param>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
151 <param argument="--nohtml" type="boolean" truevalue="--nohtml" falsevalue="" label="Suppress saving the HTML output file" help="remove html output"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
152 </section>
0
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents:
diff changeset
153 <!-- ADVANCED OPTIONS -->
4
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
154 <section name="advanced_option" title="Coarse tuning of algorithm parameters">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
155 <param name="controls" type="integer" optional="true" value="0" label="Number of first samples will be treated as negative controls" help="Add control samples (default is 0)"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
156 <param name="scoring" type="select" optional="true" label="Type of scoring to be applied" help="Scoring algorithm, depending of the input files, see the help section of the tools">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
157 <option value="SHEL">SHEL</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
158 <option value="LENGTH">LENGTH</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
159 <option value="LOGLENGTH">LOGLENGTH</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
160 <option value="NORMA">NORMA</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
161 <option value="LMAT">LMAT (only for LMAT input)</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
162 <option value="CLARK_C">CLARK_C (only for Clark input)</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
163 <option value="CLARK_G">CLARK_G (only for Clark input)</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
164 <option value="KRAKEN">KRAKEN (only for kraken input)</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
165 <option value="GENERIC">GENERIC (only for generic input)</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
166 </param>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
167 <param name="minscore_value" type="integer" optional="true" min="0" value="0" label="Minimum score/confidence of the classification of a
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
168 read to pass the quality filter" help="All pass by default (--minscore)"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
169 <param name="mintaxa" type="integer" optional="true" min="0" value="0" label="Minimum taxa to avoid collapsing one level into the
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
170 parent" help="If not specified a value will be automatically
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
171 assigned (--mintaxa)"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
172 <param name="exclude_taxa_name" argument="--exclude" type="text" optional="true" label="NCBI taxid code to exclude a taxon and all underneath" help="Default: no exclude">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
173 <sanitizer invalid_char="">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
174 <valid initial="string.letters,string.digits">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
175 <add value="," />
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
176 </valid>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
177 </sanitizer>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
178 <validator type="regex">[A-Za-z0-9,]+</validator>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
179 </param>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
180
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
181 <param name="include_taxa_name" argument="--include" type="text" optional="true" label="NCBI taxid code to include a taxon and all underneath" help="Default: all included">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
182 <sanitizer invalid_char="">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
183 <valid initial="string.letters,string.digits">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
184 <add value="," />
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
185 </valid>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
186 </sanitizer>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
187 <validator type="regex">[A-Za-z0-9,]+</validator>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
188 </param>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
189 <param argument="--avoidcross" type="boolean" truevalue="--avoidcross" falsevalue="" label="Avoid cross analysis" help="Default: no"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
190 </section>
0
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents:
diff changeset
191 <!-- Detailed more fine parameters -->
4
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
192 <section name="more_advanced_option" title=" Fine tuning of algorithm parameters">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
193 <param name="ctrlminscore" argument="--ctrlminscore" type="integer" optional="true" value="0" label="Minimum score in control samples to pass the filter" help="Minimum score/confidence of the classification of a read in control samples to pass the quality filter; it defaults to minscore"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
194 <param name="ctrlmintaxa" argument="--ctrlmintaxa" type="integer" optional="true" value="0" label="Minimum taxa to avoid collapsing one level into the parent" help="If not specified a value will be automatically assigned"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
195 <param name="summary" argument="--summary" type="select" label="Add a summary of the analysis (default is Add)" help="Select to 'add' summary samples to other samples, or to 'only' show summary samples or to 'avoid' summaries at all">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
196 <option value="ADD" selected="true">Add</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
197 <option value="ONLY">Only</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
198 <option value="AVOID">Avoid</option>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
199 </param>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
200 <param argument="--takeoutroot" type="boolean" truevalue="--takeoutroot" falsevalue="" label="Remove counts directly assigned to the root level"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
201 <param argument="--nokollapse" type="boolean" truevalue="--nokollapse" falsevalue="" label="Show the cellular organisms taxon" />
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
202 <param argument="--strain" type="boolean" truevalue="--strain" falsevalue="" label="Strain level instead of species as the resolution limit for the robust contamination removal algorithm; use with caution, this is an experimental feature"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
203 <param argument="--sequential" type="boolean" truevalue="--sequential" falsevalue="" label="Deactivate parallel processing"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
204 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
205 </inputs>
0
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents:
diff changeset
206 <!-- OUTPUT FILE, TYPE DEPENDING ON extra PARAMETER -->
4
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
207 <outputs>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
208 <data name="html_report" format="html" from_work_dir="output.rcf.html" label="${tool.name} on ${on_string}: html report">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
209 <filter> output_option['nohtml'] == False</filter>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
210 </data>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
211 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
212 <data name="data_csv" format="tabular" from_work_dir="output.rcf.data.csv" label="${tool.name} on ${on_string}: data.csv">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
213 <filter> output_option['extra'] == 'CSV' </filter>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
214 </data>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
215 <data name="stat_csv" format="tabular" from_work_dir="output.rcf.stat.csv" label="${tool.name} on ${on_string}: stat csv">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
216 <filter> output_option['extra'] == 'CSV' or output_option['extra'] == 'MULTICSV' </filter>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
217 </data>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
218 <data name="data_tsv" format="tabular" from_work_dir="output.rcf.data.tsv" label="${tool.name} on ${on_string}: data tsv">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
219 <filter> output_option['extra'] == 'TSV' </filter>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
220 </data>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
221 <data name="stat_tsv" format="tabular" from_work_dir="output.rcf.stat.tsv" label="${tool.name} on ${on_string}: stat tsv">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
222 <filter> output_option['extra'] == 'TSV' </filter>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
223 </data>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
224 <data name="xls_report" format="xlsx" from_work_dir="output.rcf.xlsx" label="${tool.name} on ${on_string}: xlsx report">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
225 <filter> output_option['extra'] == 'FULL' or output_option['extra'] == 'DYNOMICS'</filter>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
226 </data>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
227 </outputs>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
228 <tests>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
229 <test expect_num_outputs="4"> <!-- kraken input and CSV output TEST_1-->
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
230 <section name="database">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
231 <conditional name="db_type">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
232 <param name="db_select" value="cached"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
233 <param name="cached_db" value="test-db-2022"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
234 </conditional>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
235 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
236 <section name="input_option">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
237 <param name="input_file" value="kraken_test/kraken.out"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
238 <conditional name="file_type">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
239 <param name="filetype" value="kraken"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
240 </conditional>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
241 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
242 <section name="output_option">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
243 <param name="output_type" value="default_type"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
244 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
245 <section name="more_advanced_option">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
246 <param name="summary" value="AVOID"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
247 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
248 <output name="data_csv" file="kraken_test/test1_csv.rcf.data.csv" lines_diff="2"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
249 <output name="stat_csv" file="kraken_test/test1_csv.rcf.stat.csv" lines_diff="2"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
250 <output name="html_report" file="kraken_test/test1_csv.rcf.html" lines_diff="2"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
251 <output name="logfile" file="kraken_test/test1_csv.log" lines_diff="8"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
252 </test>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
253 <test expect_num_outputs="2"> <!-- centrifuge input and full options with imported database TEST_2 -->
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
254 <section name="database">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
255 <conditional name="db_type">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
256 <param name="db_select" value="history"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
257 <param name="history_db" value="test-db/delnodes.dmp,test-db/division.dmp,test-db/gc.prt,test-db/gencode.dmp,test-db/merged.dmp,test-db/names.dmp,test-db/nodes.dmp,test-db/readme.txt"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
258 </conditional>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
259 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
260 <section name="input_option">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
261 <param name="input_file" value="centrifuge_test/centrifuge.out"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
262 <conditional name="file_type">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
263 <param name="filetype" value="centrifuge"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
264 </conditional>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
265 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
266 <section name="output_option">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
267 <param name="extra" value="MULTICSV"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
268 <param name="nohtml" value="true"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
269 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
270 <section name="advanced_option">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
271 <param name="controls" value="0"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
272 <param name="scoring" value="NORMA"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
273 <param name="minscore" value="specify_minscore"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
274 <param name="minscore_value" value="0"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
275 <param name="avoidcross" value="true"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
276 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
277 <section name="more_advanced_option">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
278 <param name="minscore_select" value="specify_minscore"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
279 <param name="ctrlminscore" value="0"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
280 <param name="summary" value="AVOID"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
281 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
282 <output name="stat_csv" file="centrifuge_test/test2_multicsv.rcf.stat.csv" lines_diff="2"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
283 <output name="logfile" file="centrifuge_test/test2_multicsv.log" lines_diff="20"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
284 </test>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
285 <test expect_num_outputs="3"> <!-- kraken input cached DB several option added TEST_3 -->
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
286 <section name="database">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
287 <conditional name="db_type">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
288 <param name="db_select" value="cached"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
289 <param name="cached_db" value="test-db-2022"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
290 </conditional>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
291 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
292 <section name="input_option">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
293 <param name="input_file" value="kraken_test/kraken.out"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
294 <conditional name="file_type">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
295 <param name="filetype" value="kraken"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
296 </conditional>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
297 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
298 <section name="output_option" >
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
299 <param name="extra" value="TSV"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
300 <param name="nohtml" value="true"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
301 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
302 <section name="advanced_option">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
303 <param name="scoring" value="LOGLENGTH"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
304 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
305 <section name="more_advanced_option">
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
306 <param name="summary" value="ONLY"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
307 <param name="strain" value="true"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
308 </section>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
309 <output name="data_tsv" file="kraken_test/test3_rcf.data.tsv" lines_diff="2"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
310 <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
311 <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="20"/>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
312 </test>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
313 </tests>
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
314 <help><![CDATA[
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
315 **What it does**
0
e5474449c35d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents:
diff changeset
316
4
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
317 With Recentrifuge, researchers can interactively explore what organisms are in their samples and at which level of confidence, enabling robust comparative analysis of multiple samples in any metagenomic study.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
318
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
319 * Removes diverse contaminants, including crossovers, using a novel robust contamination removal algorithm.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
320 * Provides a confidence level for every result, since the calculated score propagates to all the downstream analysis and comparisons.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
321 * Unveils the generalities and specificities in the metagenomic samples, thanks to a new comparative analysis engine.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
322
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
323
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
324 Recentrifuge is especially useful when a more reliable detection of minority organisms is needed (e.g. in the case of low microbial biomass metagenomic studies)
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
325 in clinical, environmental, or forensic analysis. Beyond the standard confidence levels, Recentrifuge implements others devoted to variable length reads,
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
326 very convenient for complex datasets generated by nanopore sequencers.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
327
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
328 **Input option**
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
329 Recentrifuge can deal with some different taxonomic output files.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
330 Input files can come from centrifuge, kraken, clark of lmat software.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
331 A generic fonction to accept other files is available but need to add information of the file content.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
332 If generic is choose, the option format need a string like : 'TYP:csv,TID:1,LEN:3,SCO:6,UNC:0'.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
333 Where TYP are csv/tsv/ssv, and the rest of fields indicate the number of column used (starting in 1)
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
334 for the TaxIDs assigned,the LENgth of the read, the SCOre given to the assignment"
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
335
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
336
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
337 **Database for recentrifuge**
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
338 Recentrifuge first need the taxonomic database from NCBI (nodes.dmp and names.dmp).
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
339 We also provide the option to directly load necessary files from history as a dataset list.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
340 1. cached for already installed taxonomic databases
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
341 2. history to load from your history
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
342
3
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
343
4
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
344 **Output options**
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
345 1. Depending of the option provided, the file output format can be csv, tsv or xlsx and be combine in one or more files (extra).
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
346 3. By default a html file is generated to visualize data, could be remove using the nohtml option
3
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
347
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
348
4
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
349 **Advanced options**
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
350 1. Recentrifuge can integrate sample in the data which are negative control to normalize the data
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
351 2. Scoring is an option to choose the score method for the read classified by taxonomic tools :
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
352 SHEL (Single Hit Equivalent Length): This is a score value in pair bases roughly equivalent to a single hit to the database.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
353 KRAKEN: This scoring scheme is only available for this classifier. It divides the k-mer hit count of the top assignment by the total k-mers in the read and multiplies the result by 100 to give a percentage of coverage (the fraction of the read k-mers covered by k-mers belonging to the read final assignment). This is the default scoring scheme for Kraken samples, and it supports the mixing of samples with different read length.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
354 LENGTH: The score of a read will be its length (or the combined length of mate pairs).
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
355 LOGLENGTH: Logarithm (base 10) of the length score.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
356 NORMA: This score is the normalized score SHEL / LENGTH in percentage, so it takes into account both the assignment quality and the length of the read. Very useful when both the score assignments and lengths are variable among the reads.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
357 LMAT: This scoring scheme is only available for this classifier.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
358 CLARK_C: This scoring scheme is not available for other classifiers. It takes the confidence score as the score for a read, conf=h1/(h1+h2), or 1-conf=h2/(h1+h2) in case the majority of a read is not classified (1st assignment unclassified). See CLARK's README file for details on how h1 and h2 are calculated. If you use this scoring, you will probably want to filter to a minimum of 0.5 (-y 0.5) or beyond, as under 0.5 the assignments have very low confidence.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
359 CLARK_G: This scheme scores every read with its CLARK gamma score, so it is only available for this classifier.
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
360 3. You can choose a filter for read quality using the minscore option (--minscore)
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
361 4. You can include or exclude specific taxa using the NCBI taxid code
3
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
362
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
363
4
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
364 **More advanced options**
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
365 1. You can choose a filter for read quality specifically on the control samples
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
366 2. You cans specify the minimum taxa value to avoid collapsing one level into parent
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
367 3. A summary option is available produce a summary file
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
368 Some other options are available and explicite in the more advanced panel of the tool
3
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
369
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
370
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
371 rcf - Release 1.8.1 - Mar 2022
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
372
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
373 Copyright (C) 2017–2022, Jose Manuel Martí Martínez
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
374
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
375 This program is free software: you can redistribute it and/or modify
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
376 it under the terms of the GNU Affero General Public License as
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
377 published by the Free Software Foundation, either version 3 of the
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
378 License, or (at your option) any later version.
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
379
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
380 This program is distributed in the hope that it will be useful,
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
381 but WITHOUT ANY WARRANTY; without even the implied warranty of
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
382 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
383 GNU Affero General Public License for more details.
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
384
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
385 You should have received a copy of the GNU Affero General Public License
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
386 along with this program. If not, see <https://www.gnu.org/licenses/>.
2890083b1a84 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 2
diff changeset
387 ]]></help>
4
512dc05a0e5a "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
pimarin
parents: 3
diff changeset
388 <expand macro="citations"/>
2
b135c5908e8c "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 000b196a8781301582ee706ab287f65f27478a12-dirty"
pimarin
parents: 0
diff changeset
389 </tool>