amplicon_analysis_pipeline: amplicon_analysis

annotate amplicon_analysis_pipeline.xml @ 3:3ab198df8f3f draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 15390f18b91d838880d952eb2714f689bbd8a042

author	pjbriggs
date	Thu, 18 Oct 2018 09:18:04 -0400
parents	43d6f81bc667
children	86a12d75ebe4

rev	line source
3 3ab198df8f3f planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 15390f18b91d838880d952eb2714f689bbd8a042 pjbriggs parents: 2 diff changeset	1 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.3.0">
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>
3 3ab198df8f3f planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 15390f18b91d838880d952eb2714f689bbd8a042 pjbriggs parents: 2 diff changeset	4 <requirement type="package" version="1.2.3">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[
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	10 ## Set the reference database name
1 1c1902e12caf Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	11 #if $reference_database == "-S"
1c1902e12caf Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	12 #set reference_database_name = "silva"
1c1902e12caf Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	13 #else if $reference_database == "-H"
1c1902e12caf Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	14 #set reference_database_name = "homd"
1c1902e12caf Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	15 #else
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	16 #set reference_database_name = "gg"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	17 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	18
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	19 ## Run the amplicon analysis pipeline wrapper
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	20 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	21 ## Set options
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	22 #if str( $forward_pcr_primer ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	23 -g "$forward_pcr_primer"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	24 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	25 #if str( $reverse_pcr_primer ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	26 -G "$reverse_pcr_primer"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	27 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	28 #if str( $trimming_threshold ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	29 -q $trimming_threshold
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	30 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	31 #if str( $sliding_window_length ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	32 -l $sliding_window_length
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( $minimum_overlap ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	35 -O $minimum_overlap
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( $minimum_length ) != ""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	38 -L $minimum_length
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 -P $pipeline
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	41 -r \$AMPLICON_ANALYSIS_REF_DATA_PATH
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	42 #if str( $reference_database ) != ""
1 1c1902e12caf Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	43 ${reference_database}
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	44 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	45 #if str($categories_file_in) != 'None'
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	46 -c "${categories_file_in}"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	47 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	48 ## Input files
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	49 "${metatable_file_in}"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	50 ## FASTQ pairs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	51 #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	52 #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	53 #else
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	54 #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	55 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	56 #for $fq_pair in $fastq_pairs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	57 "${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	58 #end for
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	59 &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	60
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	61 ## Collect outputs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	62 cp Metatable_log/Metatable_mod.txt "${metatable_mod}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	63 cp ${pipeline}_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	64 cp ${pipeline}_OTU_tables/otus.tre "${otus_tre_file}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	65 cp RESULTS/${pipeline}_${reference_database_name}/OTUs_count.txt "${otus_count_file}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	66 cp RESULTS/${pipeline}_${reference_database_name}/table_summary.txt "${table_summary_file}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	67 cp Multiplexed_files/${pipeline}_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta "${dereplicated_nonchimera_otus_fasta}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	68 cp QUALITY_CONTROL/Reads_count.txt "$read_counts_out" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	69 cp fastqc_quality_boxplots.html "${fastqc_quality_boxplots_html}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	70
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	71 ## HTML outputs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	72
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	73 ## OTU table
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	74 mkdir $heatmap_otu_table_html.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	75 cp -r RESULTS/${pipeline}_${reference_database_name}/Heatmap/js $heatmap_otu_table_html.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	76 cp RESULTS/${pipeline}_${reference_database_name}/Heatmap/otu_table.html "${heatmap_otu_table_html}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	77
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	78 ## Phylum genus barcharts
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	79 mkdir $phylum_genus_dist_barcharts_html.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	80 cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/charts $phylum_genus_dist_barcharts_html.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	81 cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/raw_data $phylum_genus_dist_barcharts_html.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	82 cp RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/bar_charts.html "${phylum_genus_dist_barcharts_html}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	83
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	84 ## Beta diversity weighted 2d plots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	85 mkdir $beta_div_even_weighted_2d_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	86 cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/* $beta_div_even_weighted_2d_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	87 cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_weighted_2d_plots}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	88
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	89 ## Beta diversity unweighted 2d plots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	90 mkdir $beta_div_even_unweighted_2d_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	91 cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/* $beta_div_even_unweighted_2d_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	92 cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_unweighted_2d_plots}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	93
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	94 ## Alpha diversity rarefaction plots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	95 mkdir $alpha_div_rarefaction_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	96 cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/rarefaction_plots.html $alpha_div_rarefaction_plots &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	97 cp -r RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/average_plots $alpha_div_rarefaction_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	98
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	99 ## Categories data
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	100 #if str($categories_file_in) != 'None'
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	101 ## Alpha diversity boxplots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	102 mkdir $alpha_div_boxplots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	103 cp alpha_diversity_boxplots.html "$alpha_div_boxplots" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	104 cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/Alpha_diversity_boxplot/Categories_shannon/*.pdf $alpha_div_boxplots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	105 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	106
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	107 ## Pipeline outputs (log files etc)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	108 mkdir $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	109 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	110 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	111 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	112 cp Metatable_log/Metatable.html $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	113 cp pipeline_outputs.html "$log_files"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	114 ]]></command>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	115 <inputs>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	116 <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	117 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	118 <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	119 label="Input Metatable.txt file" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	120 <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	121 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	122 help="(optional)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	123 <conditional name="input_type">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	124 <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	125 label="Input FASTQ type">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	126 <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	127 <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	128 </param>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	129 <when value="collection">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	130 <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	131 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	132 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	133 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	134 </when>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	135 <when value="pairs_of_files">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	136 <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	137 <param type="text" name="name" value=""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	138 label="Final name for FASTQ pair" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	139 <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	140 label="FASTQ with forward reads (R1)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	141 <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	142 label="FASTQ with reverse reads (R2)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	143 </repeat>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	144 </when>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	145 </conditional>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	146 <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	147 label="Forward PCR primer sequence"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	148 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	149 <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	150 label="Reverse PCR primer sequence"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	151 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	152 <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	153 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	154 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	155 <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	156 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	157 help="Default is 10 (-O)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	158 <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	159 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	160 help="Default is 200 (-L)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	161 <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	162 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	163 help="Supplied to Sickle; default is 10 (-l)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	164 <param type="select" name="pipeline"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	165 label="Pipeline to use for analysis">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	166 <option value="Vsearch" selected="true" >Vsearch</option>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	167 <!--
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	168 Remove the QIIME and Uparse options for now
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	169 <option value="QIIME">QIIME</option>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	170 <option value="Uparse">Uparse</option>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	171 -->
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	172 </param>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	173 <param type="select" name="reference_database"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	174 label="Reference database">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	175 <option value="" selected="true">GreenGenes</option>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	176 <option value="-S">Silva</option>
1 1c1902e12caf Updated to version 1.2.1.0 pjbriggs parents: 0 diff changeset	177 <option value="-H">Human Oral Microbiome Database (HOMD)</option>
0 47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	178 </param>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	179 </inputs>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	180 <outputs>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	181 <data format="tabular" name="metatable_mod"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	182 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	183 <data format="tabular" name="read_counts_out"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	184 label="${tool.name} (${pipeline}):${title} read counts" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	185 <data format="biom" name="tax_otu_table_biom_file"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	186 label="${tool.name} (${pipeline}):${title} tax OTU table (biom format)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	187 <data format="tabular" name="otus_tre_file"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	188 label="${tool.name} (${pipeline}):${title} otus.tre" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	189 <data format="html" name="phylum_genus_dist_barcharts_html"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	190 label="${tool.name} (${pipeline}):${title} phylum genus dist barcharts HTML" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	191 <data format="tabular" name="otus_count_file"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	192 label="${tool.name} (${pipeline}):${title} OTUs count file" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	193 <data format="tabular" name="table_summary_file"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	194 label="${tool.name} (${pipeline}):${title} table summary file" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	195 <data format="fasta" name="dereplicated_nonchimera_otus_fasta"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	196 label="${tool.name} (${pipeline}):${title} multiplexed linearized dereplicated mc2 repset nonchimeras OTUs FASTA" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	197 <data format="html" name="fastqc_quality_boxplots_html"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	198 label="${tool.name} (${pipeline}):${title} FastQC per-base quality boxplots HTML" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	199 <data format="html" name="heatmap_otu_table_html"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	200 label="${tool.name} (${pipeline}):${title} heatmap OTU table HTML" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	201 <data format="html" name="beta_div_even_weighted_2d_plots"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	202 label="${tool.name} (${pipeline}):${title} beta diversity weighted 2D plots HTML" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	203 <data format="html" name="beta_div_even_unweighted_2d_plots"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	204 label="${tool.name} (${pipeline}):${title} beta diversity unweighted 2D plots HTML" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	205 <data format="html" name="alpha_div_rarefaction_plots"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	206 label="${tool.name} (${pipeline}):${title} alpha diversity rarefaction plots HTML" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	207 <data format="html" name="alpha_div_boxplots"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	208 label="${tool.name} (${pipeline}):${title} alpha diversity boxplots">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	209 <filter>categories_file_in is not None</filter>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	210 </data>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	211 <data format="html" name="log_files"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	212 label="${tool.name} (${pipeline}):${title} log files" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	213 </outputs>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	214 <tests>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	215 </tests>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	216 <help><![CDATA[
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	217
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	218 What it does
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	219 ------------
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	220
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	221 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	222 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	223
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	224 Usage
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	225 -----
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	226
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	227 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	228 *****************************************************************
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	229
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	230 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	231 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	232 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	233 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	234 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	235 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	236
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	237 .. image:: Pipeline_description_Fig1.png
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	238 :height: 46
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	239 :width: 382
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	240
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	241 Figure 1
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	242
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	243 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	244
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	245 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	246 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	247 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	248 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	249
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	250 .. image:: Pipeline_description_Fig2.png
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	251 :height: 100
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	252 :width: 463
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	253
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	254 Figure 2
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 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	257 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	258
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	259 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	260 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	261
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	262 2. To upload the file
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	263 *********************
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	264
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	265 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	266 left hand side.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	267
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	268 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	269 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	270 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	271 recommended.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	272
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	273 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	274 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	275 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	276 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	277 (uploading) and finally green (uploaded).
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 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	280 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	281 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	282 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	283
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	284 .. image:: Pipeline_description_Fig3.png
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	285 :height: 247
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	286 :width: 586
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 Figure 3
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	289
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	290 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	291 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	292 corresponding columns.
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 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	295 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	296 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	297 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	298 (see section 3).
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	299
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	300 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	301 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	302
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	303 3. Create the Metatable files
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	304 *****************************
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	305
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	306 Metatable.txt
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
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	309 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	310 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	311 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	312
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	313 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	314 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	315
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	316 EXAMPLE::
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	317
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	318 #SampleID BarcodeSequence LinkerPrimerSequence Disease Gender Description
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	319 Mock-RUN1 TAAGGCGAGCGTAAGA PsA Male Control
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	320 Mock-RUN2 CGTACTAGGCGTAAGA PsA Male Control
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	321 Mock-RUN3 AGGCAGAAGCGTAAGA PsC Female Control
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 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	324 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	325 ``LinkerPrimerSequence`` and ``Description`` are mandatory. Between
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	326 ``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	327 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	328 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	329 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	330
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	331 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	332 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	333 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	334 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	335 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	336 names might not match!
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 Categories.txt (optional)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	339 ~~~~~~~~~~~~~~~~~~~~~~~~~
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	340
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	341 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	342 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	343 (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	344 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	345 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	346 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	347
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	348 EXAMPLE::
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	349
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	350 Disease
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	351 Gender
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	352
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	353 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	354 with the fatsq files.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	355
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	356 4. Analysis
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	357 ***********
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	358
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	359 Under Amplicon_Analysis_Pipeline
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	360
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	361 * 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	362 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	363
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	364 * 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	365 this analysis
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 * 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	368 related to this analysis
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 * 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	371 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	372
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	373 * 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	374 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	375 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	376 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	377 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	378 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	379 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	380
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	381 * 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	382 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	383
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	384 * 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	385 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	386 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	387
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	388 * 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	389 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	390 Default is 10.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	391
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	392 * 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	393 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	394 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	395 380 (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	396
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	397 * Pipeline to use for analysis Choose the pipeline to use for OTU
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	398 clustering and chimera removal. The Galaxy tool currently supports
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	399 ``Vsearch`` only. ``Uparse`` and ``QIIME`` are planned to be added
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	400 shortly (the tools are already available for the stand-alone pipeline).
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 * Reference database Choose between ``GreenGenes`` and ``Silva``
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	403 databases for taxa assignment.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	404
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	405 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	406
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	407 5. Results
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	408 **********
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 Results are entirely generated using QIIME scripts. The results will
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	411 appear in the History panel when the analysis is completed
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 * Vsearch_tax_OTU_table (biom format) The OTU table in BIOM format
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	414 (http://biom-format.org/)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	415
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	416 * Vsearch_OTUs.tree Phylogenetic tree constructed using
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	417 ``make_phylogeny.py`` (fasttree) QIIME script
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	418 (http://qiime.org/scripts/make_phylogeny.html)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	419
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	420 * Vsearch_phylum_genus_dist_barcharts_HTML HTML file with bar
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	421 charts at Phylum, Genus and Species level
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	422 (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	423 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	424
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	425 * Vsearch_OTUs_count_file Summary of OTU counts per sample
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	426 (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	427
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	428 * Vsearch_table_summary_file Summary of sequences counts per sample
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	429 (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	430
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	431 * Vsearch_multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	432 Fasta file with OTU sequences
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	433
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	434 * Vsearch_heatmap_OTU_table_HTML Interactive OTU heatmap
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	435 (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	436
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	437 * 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	438 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	439 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	440 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	441 (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	442
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	443 * 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	444 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	445 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	446 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	447 (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	448
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	449 Code availability
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	450 -----------------
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	451
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	452 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	453
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	454 Credits
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	455 -------
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	456
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	457 Pipeline author: Mauro Tutino
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	458
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	459 Galaxy tool: Peter Briggs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	460
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	461 ]]></help>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	462 <citations>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	463 <citation type="bibtex">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	464 @misc{githubAmplicon_analysis,
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	465 author = {Tutino, Mauro},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	466 year = {2017},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	467 title = {Amplicon Analysis Pipeline},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	468 publisher = {GitHub},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	469 journal = {GitHub repository},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	470 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	471 }</citation>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	472 </citations>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92 pjbriggs parents: diff changeset	473 </tool>

Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate amplicon_analysis_pipeline.xml @ 3:3ab198df8f3f draft