Mercurial > repos > bebatut > metaphlan2

annotate metaphlan2.xml @ 1:8991e05c44e4 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/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
author bebatut
date Thu, 16 Jun 2016 06:08:11 -0400
parents d2448d2bf1f8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
1 <tool id="metaphlan2" name="MetaPhlAn2" version="2.5.0">
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
2
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
3 <description>to profile the composition of microbial communities</description>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
4
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
5 <macros>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
6 <import>metaphlan2_macros.xml</import>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
7 </macros>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
8
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
9 <expand macro="requirements"/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
10 <expand macro="stdio"/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
11
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
12 <version_command>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
13 <![CDATA[
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
14 metaphlan2.py -v
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
15 ]]>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
16 </version_command>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
17
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
18 <command>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
19 <![CDATA[
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
20 (which bowtie2 || exit 200)
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
21
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
22 &&
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
23
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
24 #if $db.db_selector == "history"
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
25 mkdir ref_db
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
26 &&
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
27 bowtie2-build $db.db_sequences ref_db/ref_db
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
28 &&
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
29 python $__tool_directory__/transform_json_to_pkl.py
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
30 --json_input $db_metadata
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
31 --pkl_output ref_db/metadata.pkl
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
32 &&
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
33 #end if
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
34
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
35 metaphlan2.py
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
36 $input_file
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
37 -o $output_file
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
38 --input_type ${input_file.datatype.file_ext}
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
39
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
40 --bowtie2_exe `which bowtie2`
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
41
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
42 #if $db.db_selector == "cached"
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
43 #set $table = dict([(_[0], _[2]) for _ in $db.cached_db.input.options.tool_data_table.data])
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
44 #set $db_choice = $db.cached_db.value
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
45 --bowtie2db $table[$db_choice]
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
46 --mpa_pkl $table[$db_choice]".pkl"
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
47 #else
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
48 --bowtie2db ref_db/ref_db
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
49 --mpa_pkl ref_db/metadata.pkl
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
50 #end if
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
51
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
52 --no_map
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
53
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
54 -t $analysis_type.analysis_type_select
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
55 #if $analysis_type.analysis_type_select == "rel_ab"
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
56 --tax_lev $analysis_type.taxonomic_level
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
57 #else if $analysis_type.analysis_type_select == "marker_ab_table"
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
58 --nreads $analysis_type.nreads
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
59 #else if $analysis_type.analysis_type_select == "marker_pres_table"
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
60 --pres_th $analysis_type.pres_th
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
61 #end if
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
62
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
63 --min_cu_len $min_cu_len
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
64 --min_alignment_len $min_alignment_len
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
65
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
66 $ignore_viruses
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
67 $ignore_eukaryotes
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
68 $ignore_bacteria
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
69 $ignore_archaea
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
70
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
71 --stat_q $stat_q
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
72 -s $sam_output_file
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
73 ]]>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
74 </command>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
75
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
76 <inputs>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
77 <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file" help=""/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
78
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
79 <conditional name="db">
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
80 <param name="db_selector" type="select" label="Database with clade-specific marker genes" help="">
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
81 <option value="cached" selected="true">Locally cached</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
82 <option value="history">From history</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
83 </param>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
84
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
85 <when value="cached">
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
86 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" >
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
87 <options from_data_table="metaphlan2_db" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
88 </param>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
89 </when>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
90 <when value="history">
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
91 <param name="db_sequences" type="data" format="fasta" label="Database with clade-specific marker genes from history" help="(--bowtie2db)"/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
92 <param name="db_metadata" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history" help="(--mpa_pkl)"/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
93 </when>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
94 </conditional>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
95
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
96 <conditional name="analysis_type">
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
97 <param name="analysis_type_select" type="select" label="Type of analysis to perform" help="(-t)">
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
98 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
99 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
100 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
101 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
102 <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
103 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
104 </param>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
105
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
106 <when value="rel_ab">
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
107 <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output" help="(--tax_lev)">
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
108 <option value="a" selected="true">All taxonomic levels</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
109 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
110 <option value="p">Phyla only</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
111 <option value="c">Classes only</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
112 <option value="o">Orders only</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
113 <option value="f">Families only</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
114 <option value="g">Genera only</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
115 <option value="s">Species only</option>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
116 </param>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
117 </when>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
118
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
119 <when value="reads_map"/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
120 <when value="clade_profiles"/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
121
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
122 <when value="marker_ab_table">
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
123 <param name="nreads" type="integer" value="0" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
124 </when>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
125
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
126 <when value="marker_counts"/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
127
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
128 <when value="marker_pres_table">
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
129 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
130 </when>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
131 </conditional>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
132
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
133 <param name="min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances" help=""/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
134
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
135 <param name="min_alignment_len" type="integer" value="0" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded." help=""/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
136
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
137 <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
138 <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
139
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
140 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
141
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
142 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
143
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
144 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
145 </inputs>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
146
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
147 <outputs>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
148 <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />
1
8991e05c44e4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
bebatut
parents: 0
diff changeset
149 <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" />
0
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
150 </outputs>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
151
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
152 <tests>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
153 <test>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
154 <param name="input_file" value="input_sequences.fasta"/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
155 <param name="db_selector" value="history" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
156 <param name="db_metadata" value="marker_metadata.json" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
157 <param name="db_sequences" value="marker_sequences.fasta" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
158 <param name="analysis_type_select" value="rel_ab" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
159 <param name="taxonomic_level" value="a" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
160 <param name="min_cu_len" value="2000" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
161 <param name="min_alignment_len" value="0" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
162 <param name="ignore_viruses" value="" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
163 <param name="ignore_eukaryotes" value="" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
164 <param name="ignore_bacteria" value="" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
165 <param name="ignore_archaea" value="" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
166 <param name="stat_q" value="0.1" />
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
167 <output name="output_file" file="community_profile.tabular"/>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
168 </test>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
169 </tests>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
170
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
171 <help><![CDATA[
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
172 **What it does**
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
173
1
8991e05c44e4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
bebatut
parents: 0
diff changeset
174 MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
0
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
175
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
176 **Inputs**
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
177
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
178 Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced SAM file.
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
179
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
180 It is also possible to use a custom database with clade-specific marker genes. In this case, a fasta file with marker gene sequences is required and also a file containing metadata. This file is a json file with:
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
181
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
182 ::
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
183
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
184 {
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
185 "taxonomy": {
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
186 "taxonomy of genome1": genome1_length,
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
187 "taxonomy of genome2": genome2_length,
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
188 ...
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
189 }
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
190 "markers": {
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
191 "marker1_name": {
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
192 "clade": the clade that the marker belongs to,
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
193 "ext": [list of external genomes where the marker appears],
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
194 "len": length of the marker,
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
195 "score": score of the marker,
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
196 "taxon": the taxon of the marker
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
197 }
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
198 ...
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
199 }
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
200 }
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
201
1
8991e05c44e4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
bebatut
parents: 0
diff changeset
202 The marker name correspond to the corresponding sequence name in the FastA file containing marker gene sequences.
0
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
203
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
204 **Outputs**
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
205
1
8991e05c44e4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit c641bf32192cd4281a14f504fc97f1dc6edd6f7a-dirty
bebatut
parents: 0
diff changeset
206 The main output file is a tab-separated file with the predicted taxon relative abundances.
0
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
207
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
208 ]]></help>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
209
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
210 <citations>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
211 <citation type="doi">10.1038/nmeth.3589</citation>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
212 </citations>
d2448d2bf1f8 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
diff changeset
213 </tool>