amplicon_analysis_pipeline: amplicon_analysis

annotate amplicon_analysis_pipeline.xml @ 4:86a12d75ebe4 draft default tip

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8

author	pjbriggs
date	Fri, 20 Dec 2019 06:59:49 -0500
parents	3ab198df8f3f
children

rev	line source
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	1 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.3.6.0">
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	2 <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	3 <requirements>
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	4 <requirement type="package" version="1.3.6">amplicon_analysis_pipeline</requirement>
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	5 </requirements>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	6 <stdio>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	7 <exit_code range="1:" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	8 </stdio>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	9 <command><![CDATA[
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	10
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	11 ## Convenience variable for pipeline name
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	12 #set $pipeline_name = $pipeline.pipeline_name
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	13
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	14 ## Set the reference database name
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	15 #if str( $pipeline_name ) == "DADA2"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	16 #set reference_database_name = "silva"
1 1c1902e12caf Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	17 #else
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	18 #set reference_database = $pipeline.reference_database
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	19 #if $reference_database == "-S"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	20 #set reference_database_name = "silva"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	21 #else if $reference_database == "-H"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	22 #set reference_database_name = "homd"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	23 #else
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	24 #set reference_database_name = "gg"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	25 #end if
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	26 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	27
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	28 ## Run the amplicon analysis pipeline wrapper
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	29 python $__tool_directory__/amplicon_analysis_pipeline.py
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	30 ## Set options
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	31 #if str( $forward_pcr_primer ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	32 -g "$forward_pcr_primer"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	33 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	34 #if str( $reverse_pcr_primer ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	35 -G "$reverse_pcr_primer"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	36 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	37 #if str( $trimming_threshold ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	38 -q $trimming_threshold
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	39 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	40 #if str( $sliding_window_length ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	41 -l $sliding_window_length
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	42 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	43 #if str( $minimum_overlap ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	44 -O $minimum_overlap
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	45 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	46 #if str( $minimum_length ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	47 -L $minimum_length
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	48 #end if
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	49 -P $pipeline_name
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	50 -r \${AMPLICON_ANALYSIS_REF_DATA_PATH-ReferenceData}
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	51 #if str( $pipeline_name ) != "DADA2"
1 1c1902e12caf Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	52 ${reference_database}
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	53 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	54 #if str($categories_file_in) != 'None'
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	55 -c "${categories_file_in}"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	56 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	57 ## Input files
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	58 "${metatable_file_in}"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	59 ## FASTQ pairs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	60 #if str($input_type.pairs_or_collection) == "collection"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	61 #set fastq_pairs = $input_type.fastq_collection
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	62 #else
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	63 #set fastq_pairs = $input_type.fastq_pairs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	64 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	65 #for $fq_pair in $fastq_pairs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	66 "${fq_pair.name}" "${fq_pair.forward}" "${fq_pair.reverse}"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	67 #end for
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	68 &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	69
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	70 ## Collect outputs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	71 cp Metatable_log/Metatable_mod.txt "${metatable_mod}" &&
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	72 #if str( $pipeline_name ) == "Vsearch"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	73 ## Vsearch-specific
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	74 cp ${pipeline_name}_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	75 cp Multiplexed_files/${pipeline_name}_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta "${dereplicated_nonchimera_otus_fasta}" &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	76 cp QUALITY_CONTROL/Reads_count.txt "$read_counts_out" &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	77 #else
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	78 ## DADA2-specific
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	79 cp ${pipeline_name}_OTU_tables/DADA2_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	80 cp ${pipeline_name}_OTU_tables/seqs.fa "${dereplicated_nonchimera_otus_fasta}" &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	81 #end if
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	82 cp ${pipeline_name}_OTU_tables/otus.tre "${otus_tre_file}" &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	83 cp RESULTS/${pipeline_name}_${reference_database_name}/OTUs_count.txt "${otus_count_file}" &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	84 cp RESULTS/${pipeline_name}_${reference_database_name}/table_summary.txt "${table_summary_file}" &&
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	85 cp fastqc_quality_boxplots.html "${fastqc_quality_boxplots_html}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	86
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	87 ## OTU table heatmap
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	88 cp RESULTS/${pipeline_name}_${reference_database_name}/Heatmap.pdf "${heatmap_otu_table_pdf}" &&
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	89
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	90 ## HTML outputs
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	91
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	92 ## Phylum genus barcharts
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	93 mkdir $phylum_genus_dist_barcharts_html.files_path &&
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	94 cp -r RESULTS/${pipeline_name}_${reference_database_name}/phylum_genus_charts/charts $phylum_genus_dist_barcharts_html.files_path &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	95 cp -r RESULTS/${pipeline_name}_${reference_database_name}/phylum_genus_charts/raw_data $phylum_genus_dist_barcharts_html.files_path &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	96 cp RESULTS/${pipeline_name}_${reference_database_name}/phylum_genus_charts/bar_charts.html "${phylum_genus_dist_barcharts_html}" &&
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	97
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	98 ## Beta diversity weighted 2d plots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	99 mkdir $beta_div_even_weighted_2d_plots.files_path &&
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	100 cp -r RESULTS/${pipeline_name}_${reference_database_name}/beta_div_even/weighted_2d_plot/* $beta_div_even_weighted_2d_plots.files_path &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	101 cp RESULTS/${pipeline_name}_${reference_database_name}/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_weighted_2d_plots}" &&
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	102
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	103 ## Beta diversity unweighted 2d plots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	104 mkdir $beta_div_even_unweighted_2d_plots.files_path &&
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	105 cp -r RESULTS/${pipeline_name}_${reference_database_name}/beta_div_even/unweighted_2d_plot/* $beta_div_even_unweighted_2d_plots.files_path &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	106 cp RESULTS/${pipeline_name}_${reference_database_name}/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_unweighted_2d_plots}" &&
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	107
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	108 ## Alpha diversity rarefaction plots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	109 mkdir $alpha_div_rarefaction_plots.files_path &&
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	110 cp RESULTS/${pipeline_name}_${reference_database_name}/Alpha_diversity/rarefaction_curves/rarefaction_plots.html $alpha_div_rarefaction_plots &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	111 cp -r RESULTS/${pipeline_name}_${reference_database_name}/Alpha_diversity/rarefaction_curves/average_plots $alpha_div_rarefaction_plots.files_path &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	112
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	113 ## DADA2 error rate plots
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	114 #if str($pipeline_name) == "DADA2"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	115 mkdir $dada2_error_rate_plots.files_path &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	116 cp DADA2_OTU_tables/Error_rate_plots/error_rate_plots.html $dada2_error_rate_plots &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	117 cp -r DADA2_OTU_tables/Error_rate_plots/*.pdf $dada2_error_rate_plots.files_path &&
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	118 #end if
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	119
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	120 ## Categories data
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	121 #if str($categories_file_in) != 'None'
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	122 ## Alpha diversity boxplots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	123 mkdir $alpha_div_boxplots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	124 cp alpha_diversity_boxplots.html "$alpha_div_boxplots" &&
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	125 cp RESULTS/${pipeline_name}_${reference_database_name}/Alpha_diversity/Alpha_diversity_boxplot/Categories_shannon/*.pdf $alpha_div_boxplots.files_path &&
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	126 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	127
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	128 ## Pipeline outputs (log files etc)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	129 mkdir $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	130 cp Amplicon_analysis_pipeline.log $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	131 cp pipeline.log $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	132 cp Pipeline_outputs.txt $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	133 cp Metatable_log/Metatable.html $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	134 cp pipeline_outputs.html "$log_files"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	135 ]]></command>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	136 <inputs>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	137 <param name="title" type="text" value="test" size="25"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	138 label="Title" help="Optional text that will be added to the output dataset names" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	139 <param type="data" name="metatable_file_in" format="tabular"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	140 label="Input Metatable.txt file" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	141 <param type="data" name="categories_file_in" format="txt"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	142 label="Input Categories.txt file" optional="true"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	143 help="(optional)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	144 <conditional name="input_type">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	145 <param name="pairs_or_collection" type="select"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	146 label="Input FASTQ type">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	147 <option value="pairs_of_files">Pairs of datasets</option>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	148 <option value="collection" selected="true">Dataset pairs in a collection</option>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	149 </param>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	150 <when value="collection">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	151 <param name="fastq_collection" type="data_collection"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	152 format="fastqsanger,fastq" collection_type="list:paired"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	153 label="Collection of FASTQ forward and reverse (R1/R2) pairs"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	154 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 " />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	155 </when>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	156 <when value="pairs_of_files">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	157 <repeat name="fastq_pairs" title="Input fastq pairs" min="1">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	158 <param type="text" name="name" value=""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	159 label="Final name for FASTQ pair" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	160 <param type="data" name="fastq_r1" format="fastqsanger,fastq"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	161 label="FASTQ with forward reads (R1)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	162 <param type="data" name="fastq_r2" format="fastqsanger,fastq"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	163 label="FASTQ with reverse reads (R2)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	164 </repeat>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	165 </when>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	166 </conditional>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	167 <param type="text" name="forward_pcr_primer" value=""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	168 label="Forward PCR primer sequence"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	169 help="Optional; must not include barcode or adapter sequence (-g)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	170 <param type="text" name="reverse_pcr_primer" value=""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	171 label="Reverse PCR primer sequence"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	172 help="Optional; must not include barcode or adapter sequence (-G)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	173 <param type="integer" name="trimming_threshold" value="20"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	174 label="Threshold quality below which read will be trimmed"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	175 help="Phred score; default is 20 (-q)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	176 <param type="integer" name="minimum_overlap" value="10"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	177 label="Minimum overlap in bp between forward and reverse reads"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	178 help="Default is 10 (-O)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	179 <param type="integer" name="minimum_length" value="200"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	180 label="Minimum length in bp to keep sequence after overlapping"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	181 help="Default is 200 (-L)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	182 <param type="integer" name="sliding_window_length" value="10"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	183 label="Minimum length in bp to retain a read after trimming"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	184 help="Supplied to Sickle; default is 10 (-l)" />
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	185 <conditional name="pipeline">
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	186 <param type="select" name="pipeline_name"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	187 label="Pipeline to use for analysis">
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	188 <option value="Vsearch" selected="true" >Vsearch</option>
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	189 <option value="DADA2">DADA2</option>
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	190 </param>
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	191 <when value="Vsearch">
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	192 <param type="select" name="reference_database"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	193 label="Reference database">
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	194 <option value="" selected="true">GreenGenes</option>
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	195 <option value="-S">Silva</option>
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	196 <option value="-H">Human Oral Microbiome Database (HOMD)</option>
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	197 </param>
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	198 </when>
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	199 <when value="DADA2">
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	200 </when>
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	201 </conditional>
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	202 </inputs>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	203 <outputs>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	204 <data format="tabular" name="metatable_mod"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	205 label="${tool.name}:${title} Metatable_mod.txt" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	206 <data format="tabular" name="read_counts_out"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	207 label="${tool.name} (${pipeline.pipeline_name}):${title} read counts">
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	208 <filter>pipeline['pipeline_name'] == 'Vsearch'</filter>
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	209 </data>
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	210 <data format="biom" name="tax_otu_table_biom_file"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	211 label="${tool.name} (${pipeline.pipeline_name}):${title} tax OTU table (biom format)" />
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	212 <data format="tabular" name="otus_tre_file"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	213 label="${tool.name} (${pipeline.pipeline_name}):${title} otus.tre" />
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	214 <data format="html" name="phylum_genus_dist_barcharts_html"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	215 label="${tool.name} (${pipeline.pipeline_name}):${title} phylum genus dist barcharts HTML" />
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	216 <data format="tabular" name="otus_count_file"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	217 label="${tool.name} (${pipeline.pipeline_name}):${title} OTUs count file" />
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	218 <data format="tabular" name="table_summary_file"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	219 label="${tool.name} (${pipeline.pipeline_name}):${title} table summary file" />
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	220 <data format="fasta" name="dereplicated_nonchimera_otus_fasta"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	221 label="${tool.name} (${pipeline.pipeline_name}):${title} multiplexed linearized dereplicated mc2 repset nonchimeras OTUs FASTA" />
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	222 <data format="html" name="fastqc_quality_boxplots_html"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	223 label="${tool.name} (${pipeline.pipeline_name}):${title} FastQC per-base quality boxplots HTML" />
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	224 <data format="pdf" name="heatmap_otu_table_pdf"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	225 label="${tool.name} (${pipeline.pipeline_name}):${title} heatmap OTU table PDF" />
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	226 <data format="html" name="beta_div_even_weighted_2d_plots"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	227 label="${tool.name} (${pipeline.pipeline_name}):${title} beta diversity weighted 2D plots HTML" />
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	228 <data format="html" name="beta_div_even_unweighted_2d_plots"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	229 label="${tool.name} (${pipeline.pipeline_name}):${title} beta diversity unweighted 2D plots HTML" />
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	230 <data format="html" name="alpha_div_rarefaction_plots"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	231 label="${tool.name} (${pipeline.pipeline_name}):${title} alpha diversity rarefaction plots HTML" />
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	232 <data format="html" name="dada2_error_rate_plots"
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	233 label="${tool.name} (${pipeline.pipeline_name}):${title} DADA2 error rate plots">
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	234 <filter>pipeline['pipeline_name'] == 'DADA2'</filter>
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	235 </data>
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	236 <data format="html" name="alpha_div_boxplots"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	237 label="${tool.name} (${pipeline.pipeline_name}):${title} alpha diversity boxplots">
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	238 <filter>categories_file_in is not None</filter>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	239 </data>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	240 <data format="html" name="log_files"
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	241 label="${tool.name} (${pipeline.pipeline_name}):${title} log files" />
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	242 </outputs>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	243 <tests>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	244 </tests>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	245 <help><![CDATA[
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	246
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	247 What it does
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	248 ------------
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	249
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	250 This pipeline has been designed for the analysis of 16S rRNA data from
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	251 Illumina Miseq (Casava >= 1.8) paired-end reads.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	252
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	253 Usage
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	254 -----
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	255
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	256 1. Preparation of the mapping file and format of unique sample id
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	257 *****************************************************************
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	258
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	259 Before using the amplicon analysis pipeline it would be necessary to
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	260 follow the steps as below to avoid analysis failures and ensure samples
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	261 are labelled appropriately. Sample names for the labelling are derived
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	262 from the fastq files names that are generated from the sequencing. The
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	263 labels will include everything between the beginning of the name and
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	264 the sample number (from C11 to S19 in Fig. 1)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	265
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	266 .. image:: Pipeline_description_Fig1.png
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	267 :height: 46
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	268 :width: 382
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	269
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	270 Figure 1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	271
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	272 If analysing 16S data from multiple runs:
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	273
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	274 The samples from different runs may have identical IDs. For example,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	275 when sequencing the same samples twice, by chance, these could be at
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	276 the same position in both the runs. This would cause the fastq files
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	277 to have exactly the same IDs (Fig. 2).
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	278
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	279 .. image:: Pipeline_description_Fig2.png
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	280 :height: 100
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	281 :width: 463
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	282
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	283 Figure 2
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	284
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	285 In case of identical sample IDs the pipeline will fail to run and
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	286 generate an error at the beginning of the analysis.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	287
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	288 To avoid having to change the file names, before uploading the files,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	289 ensure that the samples IDs are not repeated.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	290
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	291 2. To upload the file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	292 *********************
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	293
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	294 Click on Get Data/Upload File from the Galaxy tool panel on the
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	295 left hand side.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	296
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	297 From the pop-up window, choose how to upload the file. The
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	298 Choose local file option can be used for files up to 4Gb. Fastq files
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	299 from Illumina MiSeq will rarely be bigger than 4Gb and this option is
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	300 recommended.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	301
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	302 After choosing the files click Start to begin the upload. The window can
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	303 now be closed and the files will be uploaded onto the Galaxy server. You
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	304 will see the progress on the ``HISTORY`` panel on the right
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	305 side of the screen. The colour will change from grey (queuing), to yellow
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	306 (uploading) and finally green (uploaded).
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	307
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	308 Once all the files are uploaded, click on the operations on multiple
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	309 datasets icon and select the fastq files that need to be analysed.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	310 Click on the tab For all selected... and on the option
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	311 Build List of Dataset pairs (Fig. 3).
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	312
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	313 .. image:: Pipeline_description_Fig3.png
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	314 :height: 247
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	315 :width: 586
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	316
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	317 Figure 3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	318
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	319 Change the filter parameter ``_1`` and ``_2`` to be ``_R1`` and ``_R2``.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	320 The fastq files forward R1 and reverse R2 should now appear in the
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	321 corresponding columns.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	322
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	323 Select Autopair. This creates a collection of paired fastq files for
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	324 the forward and reverse reads for each sample. The name of the pairs will
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	325 be the ones used by the pipeline. You are free to change the names at this
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	326 point as long as they are the same used in the Metatable file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	327 (see section 3).
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	328
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	329 Name the collection and click on create list. This reduces the time
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	330 required to input the forward and reverse reads for each individual sample.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	331
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	332 3. Create the Metatable files
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	333 *****************************
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	334
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	335 Metatable.txt
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	336 ~~~~~~~~~~~~~
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	337
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	338 Click on the list of pairs you just created to see the name of the single
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	339 pairs. The name of the pairs will be the ones used by the pipeline,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	340 therefore, these are the names that need to be used in the Metatable file.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	341
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	342 The Metatable file has to be in QIIME format. You can find a description
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	343 of it on QIIME website http://qiime.org/documentation/file_formats.html
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	344
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	345 EXAMPLE::
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	346
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	347 #SampleID BarcodeSequence LinkerPrimerSequence Disease Gender Description
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	348 Mock-RUN1 TAAGGCGAGCGTAAGA PsA Male Control
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	349 Mock-RUN2 CGTACTAGGCGTAAGA PsA Male Control
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	350 Mock-RUN3 AGGCAGAAGCGTAAGA PsC Female Control
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	351
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	352 Briefly: the column ``LinkerPrimerSequence`` is empty but it cannot be
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	353 deleted. The header is very important. ``#SampleID``, ``Barcode``,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	354 ``LinkerPrimerSequence`` and ``Description`` are mandatory. Between
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	355 ``LinkerPrimerSequence`` and ``Description`` you can add as many columns
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	356 as you want. For every column a PCoA plot will be created (see
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	357 Results section). You can create this file in Excel and it will have
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	358 to be saved as ``Text(Tab delimited)``.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	359
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	360 During the analysis the Metatable.txt will be checked to ensure that the
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	361 file has the correct format. If necessary, this will be modified and will
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	362 be available as Metatable_corrected.txt in the history panel. If you are
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	363 going to use the metatable file for any other statistical analyses,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	364 remember to use the ``Metatable_mod.txt`` one, otherwise the sample
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	365 names might not match!
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	366
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	367 Categories.txt (optional)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	368 ~~~~~~~~~~~~~~~~~~~~~~~~~
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	369
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	370 This file is required if you want to get box plots for comparison of
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	371 alpha diversity indices (see Results section). The file is a list
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	372 (without header and IN ONE COLUMN) of categories present in the
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	373 Metatable.txt file. THE NAMES YOU ARE USING HAVE TO BE THE SAME AS THE
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	374 ONES USED IN THE METATABLE.TXT. You can create this file in Excel and
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	375 will have to be saved as ``Text(Tab delimited)``.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	376
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	377 EXAMPLE::
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	378
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	379 Disease
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	380 Gender
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	381
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	382 Metatable and categories files can be uploaded using Get Data as done
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	383 with the fatsq files.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	384
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	385 4. Analysis
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	386 ***********
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	387
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	388 Under Amplicon_Analysis_Pipeline
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	389
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	390 * Title Name to distinguish between the runs. It will be shown at
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	391 the beginning of each output file name.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	392
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	393 * Input Metatable.txt file Select the Metatable.txt file related to
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	394 this analysis
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	395
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	396 * Input Categories.txt file (Optional) Select the Categories.txt file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	397 related to this analysis
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	398
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	399 * Input FASTQ type select Dataset pairs in a collection and, then,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	400 the collection of pairs you created earlier.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	401
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	402 * Forward/Reverse PCR primer sequence if the PCR primer sequences
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	403 have not been removed from the MiSeq during the fastq creation, they
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	404 have to be removed before the analysis. Insert the PCR primer sequence
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	405 in the corresponding field. DO NOT include any barcode or adapter
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	406 sequence. If the PCR primers have been already trimmed by the MiSeq,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	407 and you include the sequence in this field, this would lead to an error.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	408 Only include the sequences if still present in the fastq files.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	409
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	410 * Threshold quality below which reads will be trimmed Choose the
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	411 Phred score used by Sickle to trim the reads at the 3’ end.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	412
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	413 * Minimum length to retain a read after trimming If the read length
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	414 after trimming is shorter than a user defined length, the read, along
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	415 with the corresponding read pair, will be discarded.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	416
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	417 * Minimum overlap in bp between forward and reverse reads Choose the
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	418 minimum basepair overlap used by Pandaseq to assemble the reads.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	419 Default is 10.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	420
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	421 * Minimum length in bp to keep a sequence after overlapping Choose the
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	422 minimum sequence length used by Pandaseq to keep a sequence after the
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	423 overlapping. This depends on the expected amplicon length. Default is
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	424 380 (used for V3-V4 16S sequencing; expected length ~440bp)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	425
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	426 * Pipeline to use for analysis Choose the pipeline to use for OTU
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	427 clustering and chimera removal. The Galaxy tool supports the ``Vsearch``
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	428 and ``DADA2`` pipelines.
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	429
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	430 * Reference database Choose between ``GreenGenes``, ``Silva`` or
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	431 ``HOMD`` (Human Oral Microbiome Database) for taxa assignment.
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	432
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	433 Click on Execute to start the analysis.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	434
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	435 5. Results
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	436 **********
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	437
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	438 Results are entirely generated using QIIME scripts. The results will
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	439 appear in the History panel when the analysis is completed.
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	440
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	441 The following outputs are captured:
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	442
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	443 * Vsearch_tax_OTU_table.biom\|DADA2_tax_OTU_table.biom (biom format)
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	444 The OTU table in BIOM format (http://biom-format.org/)
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	445
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	446 * otus.tre Phylogenetic tree constructed using ``make_phylogeny.py``
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	447 (fasttree) QIIME script (http://qiime.org/scripts/make_phylogeny.html)
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	448
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	449 * Phylum_genus_dist_barcharts_HTML HTML file with bar charts at
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	450 Phylum, Genus and Species level
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	451 (http://qiime.org/scripts/summarize_taxa.html and
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	452 http://qiime.org/scripts/plot_taxa_summary.html)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	453
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	454 * OTUs_count_file Summary of OTU counts per sample
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	455 (http://biom-format.org/documentation/summarizing_biom_tables.html)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	456
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	457 * Table_summary_file Summary of sequences counts per sample
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	458 (http://biom-format.org/documentation/summarizing_biom_tables.html)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	459
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	460 * multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta\|seqs.fa
86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	461 Fasta file with OTU sequences (Vsearch\|DADA2)
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	462
4 86a12d75ebe4 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 7be61b7ed35ca3deaad68d2eae384c8cd365bcb8 pjbriggs parents: 3 diff changeset	463 * Heatmap_PDF OTU heatmap in PDF format
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	464 (http://qiime.org/1.8.0/scripts/make_otu_heatmap_html.html )
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	465
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	466 * Vsearch_beta_diversity_weighted_2D_plots_HTML PCoA plots in HTML
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	467 format using weighted Unifrac distance measure. Samples are grouped
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	468 by the column names present in the Metatable file. The samples are
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	469 firstly rarefied to the minimum sequencing depth
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	470 (http://qiime.org/scripts/beta_diversity_through_plots.html )
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	471
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	472 * Vsearch_beta_diversity_unweighted_2D_plots_HTML PCoA plots in HTML
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	473 format using Unweighted Unifrac distance measure. Samples are grouped
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	474 by the column names present in the Metatable file. The samples are
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	475 firstly rarefied to the minimum sequencing depth
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	476 (http://qiime.org/scripts/beta_diversity_through_plots.html )
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	477
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	478 Code availability
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	479 -----------------
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	480
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	481 Code is available at https://github.com/MTutino/Amplicon_analysis
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	482
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	483 Credits
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	484 -------
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	485
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	486 Pipeline author: Mauro Tutino
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	487
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	488 Galaxy tool: Peter Briggs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	489
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	490 ]]></help>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	491 <citations>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	492 <citation type="bibtex">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	493 @misc{githubAmplicon_analysis,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	494 author = {Tutino, Mauro},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	495 year = {2017},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	496 title = {Amplicon Analysis Pipeline},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	497 publisher = {GitHub},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	498 journal = {GitHub repository},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	499 url = {https://github.com/MTutino/Amplicon_analysis},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	500 }</citation>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	501 </citations>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	502 </tool>

Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate amplicon_analysis_pipeline.xml @ 4:86a12d75ebe4 draft default tip