amplicon_analysis_pipeline: amplicon_analysis

annotate amplicon_analysis_pipeline.xml @ 4:013bf1e2cc8f draft

Updated to Amplicon_Analysis_pipeline v1.2.2.

author	pjbriggs
date	Wed, 13 Jun 2018 07:43:57 -0400
parents	a898ee628343
children	bbfc9638ba84

rev	line source
4 013bf1e2cc8f Updated to Amplicon_Analysis_pipeline v1.2.2. pjbriggs parents: 2 diff changeset	1 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.2.0">
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>
4 013bf1e2cc8f Updated to Amplicon_Analysis_pipeline v1.2.2. pjbriggs parents: 2 diff changeset	4 <requirement type="package" version="1.2.2">amplicon_analysis_pipeline</requirement>
0 b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	5 <requirement type="package" version="1.11">cutadapt</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	6 <requirement type="package" version="1.33">sickle</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	7 <requirement type="package" version="27-08-2013">bioawk</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	8 <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	9 <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	10 <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	11 <requirement type="package" version="1.8.0">qiime</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	12 <requirement type="package" version="2.2.26">blast</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	13 <requirement type="package" version="0.2.4">fasta-splitter</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	14 <requirement type="package" version="2.2">rdp-classifier</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	15 <requirement type="package" version="3.2.0">R</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	16 <requirement type="package" version="1.1.3">vsearch</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	17 <requirement type="package" version="2010-04-29">microbiomeutil</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	18 <requirement type="package">fasta_number</requirement>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	19 </requirements>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	20 <stdio>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	21 <exit_code range="1:" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	22 </stdio>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	23 <command><![CDATA[
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	24 ## Set the reference database name
2 a898ee628343 Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	25 #if $reference_database == "-S"
a898ee628343 Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	26 #set reference_database_name = "silva"
a898ee628343 Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	27 #else if $reference_database == "-H"
a898ee628343 Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	28 #set reference_database_name = "homd"
a898ee628343 Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	29 #else
0 b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	30 #set reference_database_name = "gg"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	31 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	32
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	33 ## Run the amplicon analysis pipeline wrapper
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	34 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	35 ## Set options
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	36 #if str( $forward_pcr_primer ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	37 -g "$forward_pcr_primer"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	38 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	39 #if str( $reverse_pcr_primer ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	40 -G "$reverse_pcr_primer"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	41 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	42 #if str( $trimming_threshold ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	43 -q $trimming_threshold
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( $sliding_window_length ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	46 -l $sliding_window_length
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( $minimum_overlap ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	49 -O $minimum_overlap
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( $minimum_length ) != ""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	52 -L $minimum_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 -P $pipeline
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	55 -r \$AMPLICON_ANALYSIS_REF_DATA_PATH
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	56 #if str( $reference_database ) != ""
2 a898ee628343 Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	57 ${reference_database}
0 b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	58 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	59 #if str($categories_file_in) != 'None'
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	60 -c "${categories_file_in}"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	61 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	62 ## Input files
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	63 "${metatable_file_in}"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	64 ## FASTQ pairs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	65 #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	66 #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	67 #else
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	68 #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	69 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	70 #for $fq_pair in $fastq_pairs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	71 "${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	72 #end for
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	73 &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	74
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	75 ## Collect outputs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	76 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	77 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	78 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	79 cp RESULTS/${pipeline}_${reference_database_name}/OTUs_count.txt "${otus_count_file}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	80 cp RESULTS/${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	81 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	82 cp QUALITY_CONTROL/Reads_count.txt "$read_counts_out" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	83 cp fastqc_quality_boxplots.html "${fastqc_quality_boxplots_html}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	84
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	85 ## HTML outputs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	86
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	87 ## OTU table
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	88 mkdir $heatmap_otu_table_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	89 cp -r RESULTS/${pipeline}_${reference_database_name}/Heatmap/js $heatmap_otu_table_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	90 cp RESULTS/${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	91
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	92 ## Phylum genus barcharts
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	93 mkdir $phylum_genus_dist_barcharts_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	94 cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/charts $phylum_genus_dist_barcharts_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	95 cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/raw_data $phylum_genus_dist_barcharts_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	96 cp RESULTS/${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	97
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	98 ## Beta diversity weighted 2d plots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	99 mkdir $beta_div_even_weighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	100 cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/* $beta_div_even_weighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	101 cp RESULTS/${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	102
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	103 ## Beta diversity unweighted 2d plots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	104 mkdir $beta_div_even_unweighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	105 cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/* $beta_div_even_unweighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	106 cp RESULTS/${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	107
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	108 ## Alpha diversity rarefaction plots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	109 mkdir $alpha_div_rarefaction_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	110 cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/rarefaction_plots.html $alpha_div_rarefaction_plots &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	111 cp -r RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/average_plots $alpha_div_rarefaction_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	112
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	113 ## Categories data
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	114 #if str($categories_file_in) != 'None'
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	115 ## Alpha diversity boxplots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	116 mkdir $alpha_div_boxplots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	117 cp alpha_diversity_boxplots.html "$alpha_div_boxplots" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	118 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	119 #end if
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	120
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	121 ## Pipeline outputs (log files etc)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	122 mkdir $log_files.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	123 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	124 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	125 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	126 cp Metatable_log/Metatable.html $log_files.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	127 cp pipeline_outputs.html "$log_files"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	128 ]]></command>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	129 <inputs>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	130 <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	131 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	132 <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	133 label="Input Metatable.txt file" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	134 <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	135 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	136 help="(optional)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	137 <conditional name="input_type">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	138 <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	139 label="Input FASTQ type">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	140 <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	141 <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	142 </param>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	143 <when value="collection">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	144 <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	145 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	146 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	147 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	148 </when>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	149 <when value="pairs_of_files">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	150 <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	151 <param type="text" name="name" value=""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	152 label="Final name for FASTQ pair" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	153 <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	154 label="FASTQ with forward reads (R1)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	155 <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	156 label="FASTQ with reverse reads (R2)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	157 </repeat>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	158 </when>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	159 </conditional>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	160 <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	161 label="Forward PCR primer sequence"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	162 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	163 <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	164 label="Reverse PCR primer sequence"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	165 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	166 <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	167 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	168 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	169 <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	170 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	171 help="Default is 10 (-O)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	172 <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	173 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	174 help="Default is 200 (-L)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	175 <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	176 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	177 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	178 <param type="select" name="pipeline"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	179 label="Pipeline to use for analysis">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	180 <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	181 <!--
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	182 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	183 <option value="QIIME">QIIME</option>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	184 <option value="Uparse">Uparse</option>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	185 -->
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	186 </param>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	187 <param type="select" name="reference_database"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	188 label="Reference database">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	189 <option value="" selected="true">GreenGenes</option>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	190 <option value="-S">Silva</option>
2 a898ee628343 Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	191 <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	192 </param>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	193 </inputs>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	194 <outputs>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	195 <data format="tabular" name="metatable_mod"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	196 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	197 <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	198 label="${tool.name} (${pipeline}):${title} read counts" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	199 <data format="biom" name="tax_otu_table_biom_file"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	200 label="${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	201 <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	202 label="${tool.name} (${pipeline}):${title} otus.tre" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	203 <data format="html" name="phylum_genus_dist_barcharts_html"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	204 label="${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	205 <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	206 label="${tool.name} (${pipeline}):${title} OTUs count file" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	207 <data format="tabular" name="table_summary_file"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	208 label="${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	209 <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	210 label="${tool.name} (${pipeline}):${title} multiplexed linearized dereplicated mc2 repset nonchimeras OTUs FASTA" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	211 <data format="html" name="fastqc_quality_boxplots_html"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	212 label="${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	213 <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	214 label="${tool.name} (${pipeline}):${title} heatmap OTU table HTML" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	215 <data format="html" name="beta_div_even_weighted_2d_plots"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	216 label="${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	217 <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	218 label="${tool.name} (${pipeline}):${title} beta diversity unweighted 2D plots HTML" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	219 <data format="html" name="alpha_div_rarefaction_plots"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	220 label="${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	221 <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	222 label="${tool.name} (${pipeline}):${title} alpha diversity boxplots">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	223 <filter>categories_file_in is not None</filter>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	224 </data>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	225 <data format="html" name="log_files"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	226 label="${tool.name} (${pipeline}):${title} log files" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	227 </outputs>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	228 <tests>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	229 </tests>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	230 <help><![CDATA[
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	231
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	232 What it does
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	233 ------------
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	234
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	235 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	236 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	237
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	238 Usage
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 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	242 *****************************************************************
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 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	245 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	246 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	247 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	248 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	249 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	250
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	251 .. image:: Pipeline_description_Fig1.png
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	252 :height: 46
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	253 :width: 382
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	254
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	255 Figure 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 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	258
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	259 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	260 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	261 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	262 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	263
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	264 .. image:: Pipeline_description_Fig2.png
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	265 :height: 100
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	266 :width: 463
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	267
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	268 Figure 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 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	271 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	272
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	273 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	274 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	275
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	276 2. To upload the file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	277 *********************
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 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	280 left hand side.
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 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	283 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	284 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	285 recommended.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	286
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	287 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	288 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	289 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	290 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	291 (uploading) and finally green (uploaded).
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 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	294 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	295 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	296 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	297
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	298 .. image:: Pipeline_description_Fig3.png
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	299 :height: 247
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	300 :width: 586
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	301
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	302 Figure 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 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	305 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	306 corresponding columns.
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 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	309 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	310 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	311 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	312 (see section 3).
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 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	315 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	316
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	317 3. Create the Metatable files
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	318 *****************************
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 Metatable.txt
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	321 ~~~~~~~~~~~~~
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 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	324 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	325 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	326
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	327 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	328 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	329
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	330 EXAMPLE::
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	331
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	332 #SampleID BarcodeSequence LinkerPrimerSequence Disease Gender Description
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	333 Mock-RUN1 TAAGGCGAGCGTAAGA PsA Male Control
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	334 Mock-RUN2 CGTACTAGGCGTAAGA PsA Male Control
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	335 Mock-RUN3 AGGCAGAAGCGTAAGA PsC Female Control
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	336
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	337 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	338 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	339 ``LinkerPrimerSequence`` and ``Description`` are mandatory. Between
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	340 ``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	341 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	342 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	343 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	344
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	345 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	346 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	347 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	348 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	349 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	350 names might not match!
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	351
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	352 Categories.txt (optional)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	353 ~~~~~~~~~~~~~~~~~~~~~~~~~
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	354
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	355 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	356 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	357 (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	358 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	359 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	360 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	361
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	362 EXAMPLE::
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	363
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	364 Disease
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	365 Gender
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	366
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	367 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	368 with the fatsq files.
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 4. Analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	371 ***********
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 Under Amplicon_Analysis_Pipeline
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	374
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	375 * 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	376 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	377
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	378 * 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	379 this analysis
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 * 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	382 related to this analysis
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 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	385 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	386
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	387 * 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	388 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	389 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	390 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	391 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	392 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	393 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	394
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	395 * 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	396 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	397
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	398 * 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	399 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	400 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	401
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	402 * 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	403 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	404 Default is 10.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	405
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	406 * 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	407 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	408 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	409 380 (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	410
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	411 * 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	412 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	413 ``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	414 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	415
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	416 * 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	417 databases for taxa assignment.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	418
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	419 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	420
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	421 5. Results
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	422 **********
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	423
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	424 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	425 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	426
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	427 * 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	428 (http://biom-format.org/)
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 * 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	431 ``make_phylogeny.py`` (fasttree) QIIME script
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	432 (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	433
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	434 * 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	435 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	436 (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	437 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	438
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	439 * 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	440 (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	441
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	442 * 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	443 (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	444
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	445 * 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	446 Fasta file with OTU sequences
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_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	449 (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	450
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	451 * 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	452 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	453 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	454 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	455 (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	456
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	457 * 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	458 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	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 Code availability
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	464 -----------------
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	465
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	466 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	467
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	468 Credits
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	469 -------
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 Pipeline author: Mauro Tutino
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	472
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	473 Galaxy tool: Peter Briggs
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	474
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	475 ]]></help>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	476 <citations>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	477 <citation type="bibtex">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	478 @misc{githubAmplicon_analysis,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	479 author = {Tutino, Mauro},
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	480 year = {2017},
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	481 title = {Amplicon Analysis Pipeline},
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	482 publisher = {GitHub},
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	483 journal = {GitHub repository},
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	484 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	485 }</citation>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	486 </citations>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e pjbriggs parents: diff changeset	487 </tool>

Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate amplicon_analysis_pipeline.xml @ 4:013bf1e2cc8f draft