Mercurial > repos > iuc > metaphlan2

annotate metaphlan2.xml @ 2:5b7ee956d89b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
author iuc
date Fri, 19 Mar 2021 09:36:09 +0000
parents f279fc0892fc
children f23f49426a3c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
5b7ee956d89b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
iuc
parents: 1
diff changeset
1 <tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.1">
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
2
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
3 <description>to profile the composition of microbial communities</description>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
4
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
5 <macros>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
6 <import>metaphlan2_macros.xml</import>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
7 </macros>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
8
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
9 <expand macro="requirements">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
10 <requirement type="package" version="2.3.0">bowtie2</requirement>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
11 <requirement type="package" version="2.7.10">python</requirement>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
12 </expand>
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
13
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
14 <expand macro="stdio"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
15
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
16 <version_command>metaphlan2.py -v</version_command>
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
17
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
18 <command><![CDATA[
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
19 #if $db.db_selector == "history"
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
20 mkdir ref_db
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
21 &&
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
22 bowtie2-build '$db.bowtie2db' 'ref_db/ref_db'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
23 &&
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
24 python '$__tool_directory__/transform_json_to_pkl.py'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
25 --json_input '$db.mpa_pkl'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
26 --pkl_output 'ref_db/metadata.pkl'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
27 &&
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
28 #end if
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
29
2
5b7ee956d89b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
iuc
parents: 1
diff changeset
30 #if $input_file.datatype.file_ext.startswith("fastq")
5b7ee956d89b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
iuc
parents: 1
diff changeset
31 #set ext='fastq'
5b7ee956d89b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
iuc
parents: 1
diff changeset
32 #else
5b7ee956d89b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
iuc
parents: 1
diff changeset
33 #set ext=$input_file.datatype.file_ext
5b7ee956d89b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
iuc
parents: 1
diff changeset
34 #end if
5b7ee956d89b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
iuc
parents: 1
diff changeset
35
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
36 metaphlan2.py
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
37 '$input_file'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
38 -o '$output_file'
2
5b7ee956d89b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"
iuc
parents: 1
diff changeset
39 --input_type $ext
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
40 --bowtie2_exe `which bowtie2`
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
41
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
42 #if $db.db_selector == "cached"
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
43 #set $path = $db.cached_db.fields.path
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
44 #set $value = $db.cached_db.fields.value
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
45 --bowtie2db $path/$value
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
46 --mpa_pkl $path/$value'.pkl'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
47 #else
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
48 --bowtie2db 'ref_db/ref_db'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
49 --mpa_pkl 'ref_db/metadata.pkl'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
50 #end if
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
51
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
52 --no_map
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
53
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
54 -t '$analysis_type.analysis_type_select'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
55 #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats"
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
56 --tax_lev '$analysis_type.tax_lev'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
57 #else if $analysis_type.analysis_type_select == "marker_ab_table"
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
58 --nreads '$analysis_type.nreads'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
59 #else if $analysis_type.analysis_type_select == "marker_pres_table"
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
60 --pres_th '$analysis_type.pres_th'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
61 #end if
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
62
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
63 --min_cu_len '$min_cu_len'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
64 --min_alignment_len '$min_alignment_len'
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
65
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
66 $ignore_viruses
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
67 $ignore_eukaryotes
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
68 $ignore_bacteria
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
69 $ignore_archaea
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
70
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
71 --stat_q '$stat_q'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
72 -s '$sam_output_file'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
73 --biom '$biom_output_file'
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
74 ]]></command>
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
75
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
76 <inputs>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
77 <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
78 <conditional name="db">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
79 <param name="db_selector" type="select" label="Database with clade-specific marker genes">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
80 <option value="cached" selected="true">Locally cached</option>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
81 <option value="history">From history</option>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
82 </param>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
83 <when value="cached">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
84 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
85 <options from_data_table="metaphlan2_database"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
86 </param>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
87 </when>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
88 <when value="history">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
89 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
90 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
91 </when>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
92 </conditional>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
93 <conditional name="analysis_type">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
94 <param name="analysis_type_select" type="select" label="Type of analysis to perform" argument="-t">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
95 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
96 <option value="rel_ab_w_read_stats">Profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade</option>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
97 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
98 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
99 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
100 <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
101 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
102 </param>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
103 <when value="rel_ab">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
104 <expand macro="tax_lev"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
105 </when>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
106 <when value="rel_ab_w_read_stats">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
107 <expand macro="tax_lev"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
108 </when>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
109 <when value="reads_map"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
110 <when value="clade_profiles"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
111 <when value="marker_ab_table">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
112 <param argument="--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"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
113 </when>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
114 <when value="marker_counts"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
115 <when value="marker_pres_table">
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
116 <param argument="--pres_th" type="integer" value="0" label=" Threshold for calling a marker present"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
117 </when>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
118 </conditional>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
119 <param argument="--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"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
120 <param argument="--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."/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
121 <param argument="--ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
122 <param argument="--ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
123 <param argument="--ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
124 <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
125 <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
126 </inputs>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
127
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
128 <outputs>
1
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
129 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Community profile" />
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
130 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file" />
f279fc0892fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit feaab4dd23dedf18b6369db43c25e0c695b8cc0d
iuc
parents: 0
diff changeset
131 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
0
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
132 </outputs>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
133
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
134 <tests>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
135 <test>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
136 <param name="input_file" value="input_sequences.fasta"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
137 <param name="db_selector" value="history" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
138 <param name="mpa_pkl" value="marker_metadata.json" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
139 <param name="bowtie2db" value="marker_sequences.fasta" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
140 <param name="analysis_type_select" value="rel_ab" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
141 <param name="taxonomic_level" value="a" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
142 <param name="min_cu_len" value="2000" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
143 <param name="min_alignment_len" value="0" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
144 <param name="ignore_viruses" value="" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
145 <param name="ignore_eukaryotes" value="" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
146 <param name="ignore_bacteria" value="" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
147 <param name="ignore_archaea" value="" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
148 <param name="stat_q" value="0.1" />
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
149 <output name="output_file" file="community_profile.tabular"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
150 </test>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
151 </tests>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
152
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
153 <help><![CDATA[
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
154 **What it does**
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
155
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
156 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/>`_.
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
157
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
158 **Inputs**
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
159
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
160 Metaphlan2 takes as input a sequence file in Fasta, FastQ, a SAM file.
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
161
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
162 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:
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
163
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
164 ::
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
165
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
166 {
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
167 "taxonomy": {
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
168 "taxonomy of genome1": genome1_length,
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
169 "taxonomy of genome2": genome2_length,
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
170 ...
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
171 }
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
172 "markers": {
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
173 "marker1_name": {
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
174 "clade": the clade that the marker belongs to,
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
175 "ext": [list of external genomes where the marker appears],
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
176 "len": length of the marker,
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
177 "score": score of the marker,
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
178 "taxon": the taxon of the marker
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
179 }
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
180 ...
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
181 }
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
182 }
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
183
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
184 The marker name correspond to the corresponding sequence name in the FastA file containing marker gene sequences.
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
185
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
186 **Outputs**
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
187
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
188 The main output file is a tab-separated file with the predicted taxon relative abundances.
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
189
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
190 ]]></help>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
191
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
192 <expand macro="citations"/>
a12c7f019bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8
iuc
parents:
diff changeset
193 </tool>