Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate amplicon_analysis_pipeline.xml @ 32:d94f2d7e8574 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 283f59740e90fa714c305007af40041ce39a74aa-dirty
author pjbriggs
date Tue, 02 Oct 2018 10:18:02 -0400
parents b195d76c70e1
children c4cde1f435f4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 24
diff changeset
1 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.3.0">
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
2 <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
3 <requirements>
23
545f23776953 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 993dae6791b28d776b116153e834192435084ef5
pjbriggs
parents: 19
diff changeset
4 <!-- non-bioconda dependencies -->
27
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 24
diff changeset
5 <requirement type="package" version="1.2.3">amplicon_analysis_pipeline</requirement>
23
545f23776953 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 993dae6791b28d776b116153e834192435084ef5
pjbriggs
parents: 19
diff changeset
6 <requirement type="package" version="2010-04-29">microbiomeutil-chimeraslayer</requirement>
545f23776953 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 993dae6791b28d776b116153e834192435084ef5
pjbriggs
parents: 19
diff changeset
7 <requirement type="package" version="1.2.22">uclust-qiime</requirement>
545f23776953 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 993dae6791b28d776b116153e834192435084ef5
pjbriggs
parents: 19
diff changeset
8 <!-- bioconda dependencies -->
5
bbfc9638ba84 First version with (partial) bioconda deps.
pjbriggs
parents: 4
diff changeset
9 <requirement type="package" version="2.7">python</requirement>
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
10 <requirement type="package" version="1.11">cutadapt</requirement>
5
bbfc9638ba84 First version with (partial) bioconda deps.
pjbriggs
parents: 4
diff changeset
11 <requirement type="package" version="1.33">sickle-trim</requirement>
bbfc9638ba84 First version with (partial) bioconda deps.
pjbriggs
parents: 4
diff changeset
12 <requirement type="package" version="1.0">bioawk</requirement>
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
13 <requirement type="package" version="2.8.1">pandaseq</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
14 <requirement type="package" version="3.5.0">spades</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
15 <requirement type="package" version="0.11.3">fastqc</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
16 <requirement type="package" version="1.8.0">qiime</requirement>
5
bbfc9638ba84 First version with (partial) bioconda deps.
pjbriggs
parents: 4
diff changeset
17 <requirement type="package" version="2.2.26">blast-legacy</requirement>
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
18 <requirement type="package" version="0.2.4">fasta-splitter</requirement>
5
bbfc9638ba84 First version with (partial) bioconda deps.
pjbriggs
parents: 4
diff changeset
19 <requirement type="package" version="2.2">rdp_classifier</requirement>
23
545f23776953 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 993dae6791b28d776b116153e834192435084ef5
pjbriggs
parents: 19
diff changeset
20 <requirement type="package" version="1.1.3">vsearch</requirement>
31
b195d76c70e1 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 283f59740e90fa714c305007af40041ce39a74aa-dirty
pjbriggs
parents: 27
diff changeset
21 <!-- explicitly specify libgfortran=1.0 otherwise qiime is broken -->
32
d94f2d7e8574 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 283f59740e90fa714c305007af40041ce39a74aa-dirty
pjbriggs
parents: 31
diff changeset
22 <requirement type="package" version="1.0">libgfortran</requirement>
27
b5e43dfe07ac planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979
pjbriggs
parents: 24
diff changeset
23 <!-- toolshed dependencies -->
6
45db1f97795c planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e75f078692e313af3295d2d991fcd8d61270242f
pjbriggs
parents: 5
diff changeset
24 <requirement type="package" version="3.2.1">R</requirement>
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
25 </requirements>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
26 <stdio>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
27 <exit_code range="1:" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
28 </stdio>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
29 <command><![CDATA[
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
30 ## Set the reference database name
2
a898ee628343 Updated to version 1.2.1.0
pjbriggs
parents: 0
diff changeset
31 #if $reference_database == "-S"
a898ee628343 Updated to version 1.2.1.0
pjbriggs
parents: 0
diff changeset
32 #set reference_database_name = "silva"
a898ee628343 Updated to version 1.2.1.0
pjbriggs
parents: 0
diff changeset
33 #else if $reference_database == "-H"
a898ee628343 Updated to version 1.2.1.0
pjbriggs
parents: 0
diff changeset
34 #set reference_database_name = "homd"
a898ee628343 Updated to version 1.2.1.0
pjbriggs
parents: 0
diff changeset
35 #else
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
36 #set reference_database_name = "gg"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
37 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
38
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
39 ## Run the amplicon analysis pipeline wrapper
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
40 python $__tool_directory__/amplicon_analysis_pipeline.py
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
41 ## Set options
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
42 #if str( $forward_pcr_primer ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
43 -g "$forward_pcr_primer"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
44 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
45 #if str( $reverse_pcr_primer ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
46 -G "$reverse_pcr_primer"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
47 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
48 #if str( $trimming_threshold ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
49 -q $trimming_threshold
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
50 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
51 #if str( $sliding_window_length ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
52 -l $sliding_window_length
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
53 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
54 #if str( $minimum_overlap ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
55 -O $minimum_overlap
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
56 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
57 #if str( $minimum_length ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
58 -L $minimum_length
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
59 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
60 -P $pipeline
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
61 -r \$AMPLICON_ANALYSIS_REF_DATA_PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
62 #if str( $reference_database ) != ""
2
a898ee628343 Updated to version 1.2.1.0
pjbriggs
parents: 0
diff changeset
63 ${reference_database}
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
64 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
65 #if str($categories_file_in) != 'None'
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
66 -c "${categories_file_in}"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
67 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
68 ## Input files
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
69 "${metatable_file_in}"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
70 ## FASTQ pairs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
71 #if str($input_type.pairs_or_collection) == "collection"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
72 #set fastq_pairs = $input_type.fastq_collection
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
73 #else
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
74 #set fastq_pairs = $input_type.fastq_pairs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
75 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
76 #for $fq_pair in $fastq_pairs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
77 "${fq_pair.name}" "${fq_pair.forward}" "${fq_pair.reverse}"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
78 #end for
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
79 &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
80
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
81 ## Collect outputs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
82 cp Metatable_log/Metatable_mod.txt "${metatable_mod}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
83 cp ${pipeline}_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
84 cp ${pipeline}_OTU_tables/otus.tre "${otus_tre_file}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
85 cp RESULTS/${pipeline}_${reference_database_name}/OTUs_count.txt "${otus_count_file}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
86 cp RESULTS/${pipeline}_${reference_database_name}/table_summary.txt "${table_summary_file}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
87 cp Multiplexed_files/${pipeline}_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta "${dereplicated_nonchimera_otus_fasta}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
88 cp QUALITY_CONTROL/Reads_count.txt "$read_counts_out" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
89 cp fastqc_quality_boxplots.html "${fastqc_quality_boxplots_html}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
90
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
91 ## HTML outputs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
92
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
93 ## OTU table
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
94 mkdir $heatmap_otu_table_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
95 cp -r RESULTS/${pipeline}_${reference_database_name}/Heatmap/js $heatmap_otu_table_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
96 cp RESULTS/${pipeline}_${reference_database_name}/Heatmap/otu_table.html "${heatmap_otu_table_html}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
97
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
98 ## Phylum genus barcharts
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
99 mkdir $phylum_genus_dist_barcharts_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
100 cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/charts $phylum_genus_dist_barcharts_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
101 cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/raw_data $phylum_genus_dist_barcharts_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
102 cp RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/bar_charts.html "${phylum_genus_dist_barcharts_html}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
103
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
104 ## Beta diversity weighted 2d plots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
105 mkdir $beta_div_even_weighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
106 cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/* $beta_div_even_weighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
107 cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_weighted_2d_plots}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
108
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
109 ## Beta diversity unweighted 2d plots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
110 mkdir $beta_div_even_unweighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
111 cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/* $beta_div_even_unweighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
112 cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_unweighted_2d_plots}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
113
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
114 ## Alpha diversity rarefaction plots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
115 mkdir $alpha_div_rarefaction_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
116 cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/rarefaction_plots.html $alpha_div_rarefaction_plots &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
117 cp -r RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/average_plots $alpha_div_rarefaction_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
118
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
119 ## Categories data
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
120 #if str($categories_file_in) != 'None'
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
121 ## Alpha diversity boxplots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
122 mkdir $alpha_div_boxplots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
123 cp alpha_diversity_boxplots.html "$alpha_div_boxplots" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
124 cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/Alpha_diversity_boxplot/Categories_shannon/*.pdf $alpha_div_boxplots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
125 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
126
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
127 ## Pipeline outputs (log files etc)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
128 mkdir $log_files.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
129 cp Amplicon_analysis_pipeline.log $log_files.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
130 cp pipeline.log $log_files.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
131 cp Pipeline_outputs.txt $log_files.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
132 cp Metatable_log/Metatable.html $log_files.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
133 cp pipeline_outputs.html "$log_files"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
134 ]]></command>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
135 <inputs>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
136 <param name="title" type="text" value="test" size="25"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
137 label="Title" help="Optional text that will be added to the output dataset names" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
138 <param type="data" name="metatable_file_in" format="tabular"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
139 label="Input Metatable.txt file" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
140 <param type="data" name="categories_file_in" format="txt"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
141 label="Input Categories.txt file" optional="true"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
142 help="(optional)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
143 <conditional name="input_type">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
144 <param name="pairs_or_collection" type="select"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
145 label="Input FASTQ type">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
146 <option value="pairs_of_files">Pairs of datasets</option>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
147 <option value="collection" selected="true">Dataset pairs in a collection</option>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
148 </param>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
149 <when value="collection">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
150 <param name="fastq_collection" type="data_collection"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
151 format="fastqsanger,fastq" collection_type="list:paired"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
152 label="Collection of FASTQ forward and reverse (R1/R2) pairs"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
153 help="Each FASTQ pair will be treated as one sample; the name of each sample will be taken from the first column of the Metatable file " />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
154 </when>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
155 <when value="pairs_of_files">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
156 <repeat name="fastq_pairs" title="Input fastq pairs" min="1">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
157 <param type="text" name="name" value=""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
158 label="Final name for FASTQ pair" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
159 <param type="data" name="fastq_r1" format="fastqsanger,fastq"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
160 label="FASTQ with forward reads (R1)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
161 <param type="data" name="fastq_r2" format="fastqsanger,fastq"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
162 label="FASTQ with reverse reads (R2)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
163 </repeat>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
164 </when>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
165 </conditional>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
166 <param type="text" name="forward_pcr_primer" value=""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
167 label="Forward PCR primer sequence"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
168 help="Optional; must not include barcode or adapter sequence (-g)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
169 <param type="text" name="reverse_pcr_primer" value=""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
170 label="Reverse PCR primer sequence"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
171 help="Optional; must not include barcode or adapter sequence (-G)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
172 <param type="integer" name="trimming_threshold" value="20"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
173 label="Threshold quality below which read will be trimmed"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
174 help="Phred score; default is 20 (-q)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
175 <param type="integer" name="minimum_overlap" value="10"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
176 label="Minimum overlap in bp between forward and reverse reads"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
177 help="Default is 10 (-O)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
178 <param type="integer" name="minimum_length" value="200"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
179 label="Minimum length in bp to keep sequence after overlapping"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
180 help="Default is 200 (-L)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
181 <param type="integer" name="sliding_window_length" value="10"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
182 label="Minimum length in bp to retain a read after trimming"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
183 help="Supplied to Sickle; default is 10 (-l)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
184 <param type="select" name="pipeline"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
185 label="Pipeline to use for analysis">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
186 <option value="Vsearch" selected="true" >Vsearch</option>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
187 <!--
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
188 Remove the QIIME and Uparse options for now
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
189 <option value="QIIME">QIIME</option>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
190 <option value="Uparse">Uparse</option>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
191 -->
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
192 </param>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
193 <param type="select" name="reference_database"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
194 label="Reference database">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
195 <option value="" selected="true">GreenGenes</option>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
196 <option value="-S">Silva</option>
2
a898ee628343 Updated to version 1.2.1.0
pjbriggs
parents: 0
diff changeset
197 <option value="-H">Human Oral Microbiome Database (HOMD)</option>
0
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
198 </param>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
199 </inputs>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
200 <outputs>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
201 <data format="tabular" name="metatable_mod"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
202 label="${tool.name}:${title} Metatable_mod.txt" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
203 <data format="tabular" name="read_counts_out"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
204 label="${tool.name} (${pipeline}):${title} read counts" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
205 <data format="biom" name="tax_otu_table_biom_file"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
206 label="${tool.name} (${pipeline}):${title} tax OTU table (biom format)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
207 <data format="tabular" name="otus_tre_file"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
208 label="${tool.name} (${pipeline}):${title} otus.tre" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
209 <data format="html" name="phylum_genus_dist_barcharts_html"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
210 label="${tool.name} (${pipeline}):${title} phylum genus dist barcharts HTML" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
211 <data format="tabular" name="otus_count_file"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
212 label="${tool.name} (${pipeline}):${title} OTUs count file" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
213 <data format="tabular" name="table_summary_file"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
214 label="${tool.name} (${pipeline}):${title} table summary file" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
215 <data format="fasta" name="dereplicated_nonchimera_otus_fasta"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
216 label="${tool.name} (${pipeline}):${title} multiplexed linearized dereplicated mc2 repset nonchimeras OTUs FASTA" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
217 <data format="html" name="fastqc_quality_boxplots_html"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
218 label="${tool.name} (${pipeline}):${title} FastQC per-base quality boxplots HTML" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
219 <data format="html" name="heatmap_otu_table_html"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
220 label="${tool.name} (${pipeline}):${title} heatmap OTU table HTML" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
221 <data format="html" name="beta_div_even_weighted_2d_plots"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
222 label="${tool.name} (${pipeline}):${title} beta diversity weighted 2D plots HTML" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
223 <data format="html" name="beta_div_even_unweighted_2d_plots"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
224 label="${tool.name} (${pipeline}):${title} beta diversity unweighted 2D plots HTML" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
225 <data format="html" name="alpha_div_rarefaction_plots"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
226 label="${tool.name} (${pipeline}):${title} alpha diversity rarefaction plots HTML" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
227 <data format="html" name="alpha_div_boxplots"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
228 label="${tool.name} (${pipeline}):${title} alpha diversity boxplots">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
229 <filter>categories_file_in is not None</filter>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
230 </data>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
231 <data format="html" name="log_files"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
232 label="${tool.name} (${pipeline}):${title} log files" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
233 </outputs>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
234 <tests>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
235 </tests>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
236 <help><![CDATA[
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
237
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
238 What it does
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
239 ------------
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
240
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
241 This pipeline has been designed for the analysis of 16S rRNA data from
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
242 Illumina Miseq (Casava >= 1.8) paired-end reads.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
243
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
244 Usage
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
245 -----
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
246
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
247 1. Preparation of the mapping file and format of unique sample id
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
248 *****************************************************************
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
249
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
250 Before using the amplicon analysis pipeline it would be necessary to
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
251 follow the steps as below to avoid analysis failures and ensure samples
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
252 are labelled appropriately. Sample names for the labelling are derived
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
253 from the fastq files names that are generated from the sequencing. The
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
254 labels will include everything between the beginning of the name and
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
255 the sample number (from C11 to S19 in Fig. 1)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
256
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
257 .. image:: Pipeline_description_Fig1.png
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
258 :height: 46
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
259 :width: 382
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
260
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
261 **Figure 1**
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
262
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
263 If analysing 16S data from multiple runs:
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
264
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
265 The samples from different runs may have identical IDs. For example,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
266 when sequencing the same samples twice, by chance, these could be at
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
267 the same position in both the runs. This would cause the fastq files
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
268 to have exactly the same IDs (Fig. 2).
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
269
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
270 .. image:: Pipeline_description_Fig2.png
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
271 :height: 100
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
272 :width: 463
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
273
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
274 **Figure 2**
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
275
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
276 In case of identical sample IDs the pipeline will fail to run and
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
277 generate an error at the beginning of the analysis.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
278
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
279 To avoid having to change the file names, before uploading the files,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
280 ensure that the samples IDs are not repeated.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
281
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
282 2. To upload the file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
283 *********************
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
284
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
285 Click on **Get Data/Upload File** from the Galaxy tool panel on the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
286 left hand side.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
287
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
288 From the pop-up window, choose how to upload the file. The
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
289 **Choose local file** option can be used for files up to 4Gb. Fastq files
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
290 from Illumina MiSeq will rarely be bigger than 4Gb and this option is
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
291 recommended.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
292
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
293 After choosing the files click **Start** to begin the upload. The window can
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
294 now be closed and the files will be uploaded onto the Galaxy server. You
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
295 will see the progress on the ``HISTORY`` panel on the right
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
296 side of the screen. The colour will change from grey (queuing), to yellow
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
297 (uploading) and finally green (uploaded).
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
298
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
299 Once all the files are uploaded, click on the operations on multiple
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
300 datasets icon and select the fastq files that need to be analysed.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
301 Click on the tab **For all selected...** and on the option
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
302 **Build List of Dataset pairs** (Fig. 3).
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
303
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
304 .. image:: Pipeline_description_Fig3.png
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
305 :height: 247
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
306 :width: 586
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
307
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
308 **Figure 3**
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
309
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
310 Change the filter parameter ``_1`` and ``_2`` to be ``_R1`` and ``_R2``.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
311 The fastq files forward R1 and reverse R2 should now appear in the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
312 corresponding columns.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
313
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
314 Select **Autopair**. This creates a collection of paired fastq files for
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
315 the forward and reverse reads for each sample. The name of the pairs will
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
316 be the ones used by the pipeline. You are free to change the names at this
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
317 point as long as they are the same used in the Metatable file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
318 (see section 3).
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
319
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
320 Name the collection and click on **create list**. This reduces the time
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
321 required to input the forward and reverse reads for each individual sample.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
322
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
323 3. Create the Metatable files
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
324 *****************************
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
325
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
326 Metatable.txt
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
327 ~~~~~~~~~~~~~
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
328
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
329 Click on the list of pairs you just created to see the name of the single
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
330 pairs. The name of the pairs will be the ones used by the pipeline,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
331 therefore, these are the names that need to be used in the Metatable file.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
332
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
333 The Metatable file has to be in QIIME format. You can find a description
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
334 of it on QIIME website http://qiime.org/documentation/file_formats.html
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
335
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
336 EXAMPLE::
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
337
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
338 #SampleID BarcodeSequence LinkerPrimerSequence Disease Gender Description
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
339 Mock-RUN1 TAAGGCGAGCGTAAGA PsA Male Control
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
340 Mock-RUN2 CGTACTAGGCGTAAGA PsA Male Control
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
341 Mock-RUN3 AGGCAGAAGCGTAAGA PsC Female Control
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
342
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
343 Briefly: the column ``LinkerPrimerSequence`` is empty but it cannot be
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
344 deleted. The header is very important. ``#SampleID``, ``Barcode``,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
345 ``LinkerPrimerSequence`` and ``Description`` are mandatory. Between
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
346 ``LinkerPrimerSequence`` and ``Description`` you can add as many columns
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
347 as you want. For every column a PCoA plot will be created (see
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
348 **Results** section). You can create this file in Excel and it will have
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
349 to be saved as ``Text(Tab delimited)``.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
350
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
351 During the analysis the Metatable.txt will be checked to ensure that the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
352 file has the correct format. If necessary, this will be modified and will
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
353 be available as Metatable_corrected.txt in the history panel. If you are
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
354 going to use the metatable file for any other statistical analyses,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
355 remember to use the ``Metatable_mod.txt`` one, otherwise the sample
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
356 names might not match!
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
357
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
358 Categories.txt (optional)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
359 ~~~~~~~~~~~~~~~~~~~~~~~~~
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
360
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
361 This file is required if you want to get box plots for comparison of
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
362 alpha diversity indices (see **Results** section). The file is a list
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
363 (without header and IN ONE COLUMN) of categories present in the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
364 Metatable.txt file. THE NAMES YOU ARE USING HAVE TO BE THE SAME AS THE
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
365 ONES USED IN THE METATABLE.TXT. You can create this file in Excel and
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
366 will have to be saved as ``Text(Tab delimited)``.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
367
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
368 EXAMPLE::
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
369
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
370 Disease
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
371 Gender
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
372
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
373 Metatable and categories files can be uploaded using Get Data as done
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
374 with the fatsq files.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
375
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
376 4. Analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
377 ***********
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
378
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
379 Under **Amplicon_Analysis_Pipeline**
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
380
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
381 * **Title** Name to distinguish between the runs. It will be shown at
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
382 the beginning of each output file name.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
383
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
384 * **Input Metatable.txt file** Select the Metatable.txt file related to
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
385 this analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
386
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
387 * **Input Categories.txt file (Optional)** Select the Categories.txt file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
388 related to this analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
389
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
390 * **Input FASTQ type** select *Dataset pairs in a collection* and, then,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
391 the collection of pairs you created earlier.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
392
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
393 * **Forward/Reverse PCR primer sequence** if the PCR primer sequences
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
394 have not been removed from the MiSeq during the fastq creation, they
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
395 have to be removed before the analysis. Insert the PCR primer sequence
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
396 in the corresponding field. DO NOT include any barcode or adapter
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
397 sequence. If the PCR primers have been already trimmed by the MiSeq,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
398 and you include the sequence in this field, this would lead to an error.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
399 Only include the sequences if still present in the fastq files.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
400
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
401 * **Threshold quality below which reads will be trimmed** Choose the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
402 Phred score used by Sickle to trim the reads at the 3’ end.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
403
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
404 * **Minimum length to retain a read after trimming** If the read length
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
405 after trimming is shorter than a user defined length, the read, along
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
406 with the corresponding read pair, will be discarded.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
407
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
408 * **Minimum overlap in bp between forward and reverse reads** Choose the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
409 minimum basepair overlap used by Pandaseq to assemble the reads.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
410 Default is 10.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
411
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
412 * **Minimum length in bp to keep a sequence after overlapping** Choose the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
413 minimum sequence length used by Pandaseq to keep a sequence after the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
414 overlapping. This depends on the expected amplicon length. Default is
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
415 380 (used for V3-V4 16S sequencing; expected length ~440bp)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
416
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
417 * **Pipeline to use for analysis** Choose the pipeline to use for OTU
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
418 clustering and chimera removal. The Galaxy tool currently supports
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
419 ``Vsearch`` only. ``Uparse`` and ``QIIME`` are planned to be added
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
420 shortly (the tools are already available for the stand-alone pipeline).
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
421
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
422 * **Reference database** Choose between ``GreenGenes`` and ``Silva``
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
423 databases for taxa assignment.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
424
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
425 Click on **Execute** to start the analysis.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
426
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
427 5. Results
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
428 **********
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
429
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
430 Results are entirely generated using QIIME scripts. The results will
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
431 appear in the History panel when the analysis is completed
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
432
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
433 * **Vsearch_tax_OTU_table (biom format)** The OTU table in BIOM format
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
434 (http://biom-format.org/)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
435
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
436 * **Vsearch_OTUs.tree** Phylogenetic tree constructed using
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
437 ``make_phylogeny.py`` (fasttree) QIIME script
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
438 (http://qiime.org/scripts/make_phylogeny.html)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
439
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
440 * **Vsearch_phylum_genus_dist_barcharts_HTML** HTML file with bar
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
441 charts at Phylum, Genus and Species level
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
442 (http://qiime.org/scripts/summarize_taxa.html and
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
443 http://qiime.org/scripts/plot_taxa_summary.html)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
444
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
445 * **Vsearch_OTUs_count_file** Summary of OTU counts per sample
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
446 (http://biom-format.org/documentation/summarizing_biom_tables.html)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
447
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
448 * **Vsearch_table_summary_file** Summary of sequences counts per sample
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
449 (http://biom-format.org/documentation/summarizing_biom_tables.html)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
450
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
451 * **Vsearch_multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta**
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
452 Fasta file with OTU sequences
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
453
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
454 * **Vsearch_heatmap_OTU_table_HTML** Interactive OTU heatmap
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
455 (http://qiime.org/1.8.0/scripts/make_otu_heatmap_html.html )
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
456
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
457 * **Vsearch_beta_diversity_weighted_2D_plots_HTML** PCoA plots in HTML
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
458 format using weighted Unifrac distance measure. Samples are grouped
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
459 by the column names present in the Metatable file. The samples are
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
460 firstly rarefied to the minimum sequencing depth
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
461 (http://qiime.org/scripts/beta_diversity_through_plots.html )
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
462
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
463 * **Vsearch_beta_diversity_unweighted_2D_plots_HTML** PCoA plots in HTML
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
464 format using Unweighted Unifrac distance measure. Samples are grouped
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
465 by the column names present in the Metatable file. The samples are
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
466 firstly rarefied to the minimum sequencing depth
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
467 (http://qiime.org/scripts/beta_diversity_through_plots.html )
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
468
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
469 Code availability
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
470 -----------------
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
471
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
472 **Code is available at** https://github.com/MTutino/Amplicon_analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
473
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
474 Credits
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
475 -------
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
476
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
477 Pipeline author: Mauro Tutino
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
478
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
479 Galaxy tool: Peter Briggs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
480
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
481 ]]></help>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
482 <citations>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
483 <citation type="bibtex">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
484 @misc{githubAmplicon_analysis,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
485 author = {Tutino, Mauro},
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
486 year = {2017},
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
487 title = {Amplicon Analysis Pipeline},
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
488 publisher = {GitHub},
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
489 journal = {GitHub repository},
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
490 url = {https://github.com/MTutino/Amplicon_analysis},
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
491 }</citation>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
492 </citations>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
493 </tool>