Mercurial > repos > bebatut > metaphlan2

annotate metaphlan2.xml @ 1:11bb77fab91f draft

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/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
author bebatut
date Wed, 28 Oct 2015 11:37:45 -0400
parents 35d3ad2fb7a4
children 9f341c9cfa6a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
1 <tool id="metaphlan2" name="MetaPhlAn2" version="0.1.0">
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
2
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
3 <description>to profile the composition of microbial communities</description>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
4
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
5 <requirements>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
6 <requirement type="package" version="2.2.5">bowtie2</requirement>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
7 <requirement type="package" version="2.0">metaphlan2</requirement>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
8 </requirements>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
9
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
10 <stdio>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
11 <exit_code range="1:" />
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
12 </stdio>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
13
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
14 <version_command>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
15 <![CDATA[
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
16 python \${METAPHLAN2_DIR}/metaphlan.py -v
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
17 ]]>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
18 </version_command>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
19
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
20 <command><![CDATA[
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
21 python \${METAPHLAN2_DIR}/metaphlan.py
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
22 $input_file
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
23 -o $output_file
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
24
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
25 --input_type ${input_reads.datatype.file_ext}
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
26 --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
27 --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
28
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
29 $bowtie2_output
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
30 #if $bowtie2_output == '':
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
31 --bowtie2out $bowtie2_output
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
32 #end if
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
33
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
34 -t $analysis_type
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
35
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
36 #if $analysis_type.analysis_type_select == "rel_ab"
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
37 --tax_lev $analysis_type.taxonomic_level
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
38 #elif $analysis_type.analysis_type_select == "marker_ab_table"
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
39 #if $analysis_type.nreads != ''
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
40 --nreads $analysis_type.nreads
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
41 #end if
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
42 #elif $analysis_type.analysis_type_select == "marker_pres_table"
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
43 #if $analysis_type.pres_th != ''
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
44 --pres_th $analysis_type.pres_th
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
45 #end if
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
46 #end if
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
47
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
48 --min_cu_len $min_cu_len
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
49
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
50 #if $min_alignment_len != ''
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
51 --min_alignment_len $min_alignment_len
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
52 #end if
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
53
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
54 $ignore_viruses
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
55 $ignore_eukaryotes
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
56 $ignore_bacteria
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
57 $ignore_archaea
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
58
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
59 --stat_q $stat_q
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
60
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
61 #if $sam_output:
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
62 -s $sam_output_file
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
63 #endif
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
64 #if $biom_output:
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
65 -biom $biom_output_file
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
66 #endif
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
67
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
68 ]]></command>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
69
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
70 <inputs>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
71 <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
72
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
73 <conditional name="analysis_type">
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
74 <param name="analysis_type_select" type="select" label="Type of analysis to perform">
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
75 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
76 <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>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
77 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
78 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
79 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
80 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
81 </param>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
82 <when value="rel_ab">
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
83 <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
84 <option value="a" selected="true">All taxonomic levels</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
85 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
86 <option value="p">Phyla only</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
87 <option value="c">Classes only</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
88 <option value="o">Orders only</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
89 <option value="f">Families only</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
90 <option value="g">Genera only</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
91 <option value="s">Species only</option>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
92 </param>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
93 </when>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
94 <when value="marker_ab_table">
1
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
95 <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"/>
0
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
96 </when>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
97 <when value="marker_pres_table">
1
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
98 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
0
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
99 </when>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
100 </conditional>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
101
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
102 <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=""/>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
103
1
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
104 <param name="min_alignment_len" type="integer" value="0" label="The sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded." help=""/>
0
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
105
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
106 <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" />
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
107 <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" />
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
108 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
109 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
110
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
111 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
112
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
113 <param name="bowtie2_output" type='boolean' checked="true" truevalue='' falsevalue='--no_map' label="Store the output of BowTie2?" help="" />
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
114 <param name="sam_output" type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Output a sam file?" help="" />
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
115 <param name="biom_output" type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Output a biom file?" help="" />
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
116 </inputs>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
117
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
118 <outputs>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
119 <data format_source="txt" name="output_file"
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
120 metadata="input_sequence_file"
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
121 label="Profile of communities on ${on_string} (MetaPhlAn)" />
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
122
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
123 <data format_source="bowtie2" name="bowtie2_output_file"
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
124 metadata="input_sequence_file"
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
125 label="Bowtie2 output on ${on_string} (MetaPhlAn)">
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
126 <filter>!bowtie2_output</filter>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
127 </data>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
128
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
129 <data format_source="sam" name="sam_output_file"
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
130 metadata="input_sequence_file"
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
131 label="Sam output on ${on_string} (MetaPhlAn)">
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
132 <filter>sam_output</filter>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
133 </data>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
134 <data format_source="biom" name="biom_output_file"
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
135 metadata="input_sequence_file"
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
136 label="Biom output on ${on_string} (MetaPhlAn)">
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
137 <filter>biom_output</filter>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
138 </data>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
139 </outputs>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
140
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
141 <tests>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
142 <test>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
143 <param name="input_file" value="input_sequences.fastq"/>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
144 <output name="output_file" file="profiled_metagenome.txt"/>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
145 </test>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
146 </tests>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
147
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
148 <help><![CDATA[
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
149
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
150 **What it does**
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
151
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
152 MetaPhlAn is a computational tool for profiling the composition of microbial
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
153 communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
154 sequencing data with species level resolution
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
155
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
156 .. _MetaPhlAn2 user manual: https://bitbucket.org/biobakery/metaphlan2
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
157
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
158 -----
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
159
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
160 **Input**
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
161
1
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
162 Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
163 SAM file or an intermediary mapping file of the metagenome generated by a
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
164 previous MetaPhlAn
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
165
0
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
166 -----
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
167
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
168 **Parameters**
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
169
1
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
170 Several parameters can modulate the MetaPhlAn execution
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
171
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
172 - Mapping arguments
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
173 - Test to avoid saving the output of BowTie2
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
174 - Post-mapping arguments
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
175 - Taxonomic level for the relative abundance output
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
176 - Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
177 - Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
178 - Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
179 - Quantile value
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
180 - Additional analysis types and arguments
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
181 - Type of analyse to perform and some parameters for specific analysis type
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
182
0
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
183 -----
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
184
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
185 **Outputs**
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
186
1
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
187 The main output file is a tab-separated output file of the predicted taxon
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
188 relative abundances.
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
189
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
190 Given the choosen parameters, other output files can be:
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
191
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
192 - a sam output file
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
193 - a biom output fime
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
194 - a BowTie2 output file
11bb77fab91f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 3f43a4146305ef11621ab786ab20b3ab46aca139-dirty
bebatut
parents: 0
diff changeset
195
0
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
196 ]]></help>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
197
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
198 <citations>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
199 <citation type="doi">10.1038/nmeth.3589</citation>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
200 </citations>
35d3ad2fb7a4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 32fa724f84e56b46f52254e98d276849a26a9faa-dirty
bebatut
parents:
diff changeset
201 </tool>