annotate amplicon_analysis_pipeline.xml @ 1:1c1902e12caf draft

Updated to version 1.2.1.0
author pjbriggs
date Wed, 25 Apr 2018 03:54:00 -0400
parents 47ec9c6f44b8
children 43d6f81bc667
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1 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.1.0">
0
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2 <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.1">amplicon_analysis_pipeline</requirement>
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5 <requirement type="package" version="1.11">cutadapt</requirement>
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6 <requirement type="package" version="1.33">sickle</requirement>
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7 <requirement type="package" version="27-08-2013">bioawk</requirement>
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8 <requirement type="package" version="2.8.1">pandaseq</requirement>
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9 <requirement type="package" version="3.5.0">spades</requirement>
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10 <requirement type="package" version="0.11.3">fastqc</requirement>
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11 <requirement type="package" version="1.8.0">qiime</requirement>
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12 <requirement type="package" version="2.2.26">blast</requirement>
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13 <requirement type="package" version="0.2.4">fasta-splitter</requirement>
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14 <requirement type="package" version="2.2">rdp-classifier</requirement>
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15 <requirement type="package" version="3.2.0">R</requirement>
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16 <requirement type="package" version="1.1.3">vsearch</requirement>
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17 <requirement type="package" version="2010-04-29">microbiomeutil</requirement>
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18 <requirement type="package">fasta_number</requirement>
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19 </requirements>
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20 <stdio>
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21 <exit_code range="1:" />
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22 </stdio>
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23 <command><![CDATA[
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24 ## Set the reference database name
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25 #if $reference_database == "-S"
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26 #set reference_database_name = "silva"
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27 #else if $reference_database == "-H"
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28 #set reference_database_name = "homd"
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29 #else
0
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30 #set reference_database_name = "gg"
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31 #end if
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32
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33 ## Run the amplicon analysis pipeline wrapper
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34 python $__tool_directory__/amplicon_analysis_pipeline.py
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35 ## Set options
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36 #if str( $forward_pcr_primer ) != ""
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37 -g "$forward_pcr_primer"
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38 #end if
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39 #if str( $reverse_pcr_primer ) != ""
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40 -G "$reverse_pcr_primer"
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41 #end if
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42 #if str( $trimming_threshold ) != ""
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43 -q $trimming_threshold
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44 #end if
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45 #if str( $sliding_window_length ) != ""
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46 -l $sliding_window_length
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47 #end if
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48 #if str( $minimum_overlap ) != ""
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49 -O $minimum_overlap
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50 #end if
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51 #if str( $minimum_length ) != ""
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52 -L $minimum_length
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53 #end if
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54 -P $pipeline
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55 -r \$AMPLICON_ANALYSIS_REF_DATA_PATH
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56 #if str( $reference_database ) != ""
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57 ${reference_database}
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58 #end if
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59 #if str($categories_file_in) != 'None'
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60 -c "${categories_file_in}"
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61 #end if
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62 ## Input files
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63 "${metatable_file_in}"
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64 ## FASTQ pairs
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65 #if str($input_type.pairs_or_collection) == "collection"
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66 #set fastq_pairs = $input_type.fastq_collection
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67 #else
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68 #set fastq_pairs = $input_type.fastq_pairs
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69 #end if
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70 #for $fq_pair in $fastq_pairs
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71 "${fq_pair.name}" "${fq_pair.forward}" "${fq_pair.reverse}"
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72 #end for
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73 &&
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74
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75 ## Collect outputs
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76 cp Metatable_log/Metatable_mod.txt "${metatable_mod}" &&
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77 cp ${pipeline}_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
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78 cp ${pipeline}_OTU_tables/otus.tre "${otus_tre_file}" &&
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79 cp RESULTS/${pipeline}_${reference_database_name}/OTUs_count.txt "${otus_count_file}" &&
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80 cp RESULTS/${pipeline}_${reference_database_name}/table_summary.txt "${table_summary_file}" &&
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81 cp Multiplexed_files/${pipeline}_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta "${dereplicated_nonchimera_otus_fasta}" &&
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82 cp QUALITY_CONTROL/Reads_count.txt "$read_counts_out" &&
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83 cp fastqc_quality_boxplots.html "${fastqc_quality_boxplots_html}" &&
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84
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85 ## HTML outputs
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86
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87 ## OTU table
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88 mkdir $heatmap_otu_table_html.files_path &&
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89 cp -r RESULTS/${pipeline}_${reference_database_name}/Heatmap/js $heatmap_otu_table_html.files_path &&
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90 cp RESULTS/${pipeline}_${reference_database_name}/Heatmap/otu_table.html "${heatmap_otu_table_html}" &&
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91
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92 ## Phylum genus barcharts
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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93 mkdir $phylum_genus_dist_barcharts_html.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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94 cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/charts $phylum_genus_dist_barcharts_html.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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95 cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/raw_data $phylum_genus_dist_barcharts_html.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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96 cp RESULTS/${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
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97
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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98 ## Beta diversity weighted 2d plots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
99 mkdir $beta_div_even_weighted_2d_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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100 cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/* $beta_div_even_weighted_2d_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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101 cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_weighted_2d_plots}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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102
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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103 ## Beta diversity unweighted 2d plots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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104 mkdir $beta_div_even_unweighted_2d_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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105 cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/* $beta_div_even_unweighted_2d_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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106 cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_unweighted_2d_plots}" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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107
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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108 ## Alpha diversity rarefaction plots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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109 mkdir $alpha_div_rarefaction_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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110 cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/rarefaction_plots.html $alpha_div_rarefaction_plots &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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111 cp -r RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/average_plots $alpha_div_rarefaction_plots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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112
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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113 ## Categories data
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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114 #if str($categories_file_in) != 'None'
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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115 ## Alpha diversity boxplots
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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116 mkdir $alpha_div_boxplots.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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117 cp alpha_diversity_boxplots.html "$alpha_div_boxplots" &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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118 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
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119 #end if
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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120
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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121 ## Pipeline outputs (log files etc)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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122 mkdir $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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123 cp Amplicon_analysis_pipeline.log $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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124 cp pipeline.log $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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125 cp Pipeline_outputs.txt $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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126 cp Metatable_log/Metatable.html $log_files.files_path &&
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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127 cp pipeline_outputs.html "$log_files"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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128 ]]></command>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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129 <inputs>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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130 <param name="title" type="text" value="test" size="25"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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131 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
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132 <param type="data" name="metatable_file_in" format="tabular"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
133 label="Input Metatable.txt file" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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134 <param type="data" name="categories_file_in" format="txt"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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135 label="Input Categories.txt file" optional="true"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
136 help="(optional)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
137 <conditional name="input_type">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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138 <param name="pairs_or_collection" type="select"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
139 label="Input FASTQ type">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
140 <option value="pairs_of_files">Pairs of datasets</option>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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141 <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
142 </param>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
143 <when value="collection">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
144 <param name="fastq_collection" type="data_collection"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
145 format="fastqsanger,fastq" collection_type="list:paired"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
146 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
147 help="Each FASTQ pair will be treated as one sample; the name of each sample will be taken from the first column of the Metatable file " />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
148 </when>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
149 <when value="pairs_of_files">
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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150 <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
151 <param type="text" name="name" value=""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
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152 label="Final name for FASTQ pair" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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153 <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
154 label="FASTQ with forward reads (R1)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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155 <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
156 label="FASTQ with reverse reads (R2)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
157 </repeat>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
158 </when>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
159 </conditional>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
160 <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
161 label="Forward PCR primer sequence"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
162 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
163 <param type="text" name="reverse_pcr_primer" value=""
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
164 label="Reverse PCR primer sequence"
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
165 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
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diff changeset
166 <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
167 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
168 help="Phred score; default is 20 (-q)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
169 <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
170 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
171 help="Default is 10 (-O)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
172 <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
173 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
174 help="Default is 200 (-L)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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diff changeset
175 <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
176 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
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177 help="Supplied to Sickle; default is 10 (-l)" />
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
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178 <param type="select" name="pipeline"
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179 label="Pipeline to use for analysis">
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180 <option value="Vsearch" selected="true" >Vsearch</option>
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181 <!--
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182 Remove the QIIME and Uparse options for now
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183 <option value="QIIME">QIIME</option>
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184 <option value="Uparse">Uparse</option>
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185 -->
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186 </param>
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187 <param type="select" name="reference_database"
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188 label="Reference database">
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189 <option value="" selected="true">GreenGenes</option>
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190 <option value="-S">Silva</option>
1
1c1902e12caf Updated to version 1.2.1.0
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191 <option value="-H">Human Oral Microbiome Database (HOMD)</option>
0
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192 </param>
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193 </inputs>
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194 <outputs>
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195 <data format="tabular" name="metatable_mod"
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196 label="${tool.name}:${title} Metatable_mod.txt" />
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197 <data format="tabular" name="read_counts_out"
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198 label="${tool.name} (${pipeline}):${title} read counts" />
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199 <data format="biom" name="tax_otu_table_biom_file"
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200 label="${tool.name} (${pipeline}):${title} tax OTU table (biom format)" />
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201 <data format="tabular" name="otus_tre_file"
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202 label="${tool.name} (${pipeline}):${title} otus.tre" />
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203 <data format="html" name="phylum_genus_dist_barcharts_html"
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204 label="${tool.name} (${pipeline}):${title} phylum genus dist barcharts HTML" />
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205 <data format="tabular" name="otus_count_file"
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206 label="${tool.name} (${pipeline}):${title} OTUs count file" />
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207 <data format="tabular" name="table_summary_file"
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208 label="${tool.name} (${pipeline}):${title} table summary file" />
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209 <data format="fasta" name="dereplicated_nonchimera_otus_fasta"
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210 label="${tool.name} (${pipeline}):${title} multiplexed linearized dereplicated mc2 repset nonchimeras OTUs FASTA" />
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211 <data format="html" name="fastqc_quality_boxplots_html"
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212 label="${tool.name} (${pipeline}):${title} FastQC per-base quality boxplots HTML" />
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213 <data format="html" name="heatmap_otu_table_html"
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214 label="${tool.name} (${pipeline}):${title} heatmap OTU table HTML" />
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215 <data format="html" name="beta_div_even_weighted_2d_plots"
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216 label="${tool.name} (${pipeline}):${title} beta diversity weighted 2D plots HTML" />
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217 <data format="html" name="beta_div_even_unweighted_2d_plots"
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218 label="${tool.name} (${pipeline}):${title} beta diversity unweighted 2D plots HTML" />
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219 <data format="html" name="alpha_div_rarefaction_plots"
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220 label="${tool.name} (${pipeline}):${title} alpha diversity rarefaction plots HTML" />
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221 <data format="html" name="alpha_div_boxplots"
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222 label="${tool.name} (${pipeline}):${title} alpha diversity boxplots">
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223 <filter>categories_file_in is not None</filter>
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224 </data>
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225 <data format="html" name="log_files"
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226 label="${tool.name} (${pipeline}):${title} log files" />
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227 </outputs>
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228 <tests>
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229 </tests>
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230 <help><![CDATA[
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231
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232 What it does
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233 ------------
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234
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235 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
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236 Illumina Miseq (Casava >= 1.8) paired-end reads.
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237
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238 Usage
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239 -----
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240
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241 1. Preparation of the mapping file and format of unique sample id
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242 *****************************************************************
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243
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244 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
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245 follow the steps as below to avoid analysis failures and ensure samples
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246 are labelled appropriately. Sample names for the labelling are derived
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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247 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
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248 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
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249 the sample number (from C11 to S19 in Fig. 1)
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250
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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251 .. image:: Pipeline_description_Fig1.png
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252 :height: 46
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253 :width: 382
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254
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255 **Figure 1**
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256
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257 If analysing 16S data from multiple runs:
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258
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259 The samples from different runs may have identical IDs. For example,
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260 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
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261 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
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262 to have exactly the same IDs (Fig. 2).
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263
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264 .. image:: Pipeline_description_Fig2.png
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265 :height: 100
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266 :width: 463
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267
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268 **Figure 2**
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269
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270 In case of identical sample IDs the pipeline will fail to run and
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271 generate an error at the beginning of the analysis.
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272
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273 To avoid having to change the file names, before uploading the files,
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274 ensure that the samples IDs are not repeated.
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275
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276 2. To upload the file
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277 *********************
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278
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279 Click on **Get Data/Upload File** from the Galaxy tool panel on the
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280 left hand side.
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281
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282 From the pop-up window, choose how to upload the file. The
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283 **Choose local file** option can be used for files up to 4Gb. Fastq files
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284 from Illumina MiSeq will rarely be bigger than 4Gb and this option is
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285 recommended.
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286
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287 After choosing the files click **Start** to begin the upload. The window can
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288 now be closed and the files will be uploaded onto the Galaxy server. You
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289 will see the progress on the ``HISTORY`` panel on the right
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290 side of the screen. The colour will change from grey (queuing), to yellow
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291 (uploading) and finally green (uploaded).
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292
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293 Once all the files are uploaded, click on the operations on multiple
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294 datasets icon and select the fastq files that need to be analysed.
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295 Click on the tab **For all selected...** and on the option
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296 **Build List of Dataset pairs** (Fig. 3).
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297
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298 .. image:: Pipeline_description_Fig3.png
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299 :height: 247
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300 :width: 586
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301
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302 **Figure 3**
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303
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304 Change the filter parameter ``_1`` and ``_2`` to be ``_R1`` and ``_R2``.
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305 The fastq files forward R1 and reverse R2 should now appear in the
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306 corresponding columns.
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307
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308 Select **Autopair**. This creates a collection of paired fastq files for
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309 the forward and reverse reads for each sample. The name of the pairs will
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310 be the ones used by the pipeline. You are free to change the names at this
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311 point as long as they are the same used in the Metatable file
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312 (see section 3).
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313
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314 Name the collection and click on **create list**. This reduces the time
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315 required to input the forward and reverse reads for each individual sample.
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316
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317 3. Create the Metatable files
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318 *****************************
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319
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320 Metatable.txt
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321 ~~~~~~~~~~~~~
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322
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323 Click on the list of pairs you just created to see the name of the single
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324 pairs. The name of the pairs will be the ones used by the pipeline,
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325 therefore, these are the names that need to be used in the Metatable file.
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326
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327 The Metatable file has to be in QIIME format. You can find a description
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328 of it on QIIME website http://qiime.org/documentation/file_formats.html
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329
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330 EXAMPLE::
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331
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332 #SampleID BarcodeSequence LinkerPrimerSequence Disease Gender Description
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333 Mock-RUN1 TAAGGCGAGCGTAAGA PsA Male Control
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334 Mock-RUN2 CGTACTAGGCGTAAGA PsA Male Control
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335 Mock-RUN3 AGGCAGAAGCGTAAGA PsC Female Control
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336
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337 Briefly: the column ``LinkerPrimerSequence`` is empty but it cannot be
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338 deleted. The header is very important. ``#SampleID``, ``Barcode``,
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339 ``LinkerPrimerSequence`` and ``Description`` are mandatory. Between
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340 ``LinkerPrimerSequence`` and ``Description`` you can add as many columns
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341 as you want. For every column a PCoA plot will be created (see
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342 **Results** section). You can create this file in Excel and it will have
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343 to be saved as ``Text(Tab delimited)``.
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344
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345 During the analysis the Metatable.txt will be checked to ensure that the
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346 file has the correct format. If necessary, this will be modified and will
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347 be available as Metatable_corrected.txt in the history panel. If you are
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348 going to use the metatable file for any other statistical analyses,
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349 remember to use the ``Metatable_mod.txt`` one, otherwise the sample
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350 names might not match!
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351
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352 Categories.txt (optional)
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353 ~~~~~~~~~~~~~~~~~~~~~~~~~
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354
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355 This file is required if you want to get box plots for comparison of
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356 alpha diversity indices (see **Results** section). The file is a list
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357 (without header and IN ONE COLUMN) of categories present in the
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358 Metatable.txt file. THE NAMES YOU ARE USING HAVE TO BE THE SAME AS THE
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359 ONES USED IN THE METATABLE.TXT. You can create this file in Excel and
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360 will have to be saved as ``Text(Tab delimited)``.
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361
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362 EXAMPLE::
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363
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
364 Disease
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
365 Gender
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 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
368 with the fatsq files.
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 4. Analysis
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
371 ***********
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 Under **Amplicon_Analysis_Pipeline**
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
374
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
375 * **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
376 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
377
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
378 * **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
379 this analysis
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 * **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
382 related to this analysis
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 * **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
385 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
386
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
387 * **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
388 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
389 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
390 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
391 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
392 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
393 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
394
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
395 * **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
396 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
397
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
398 * **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
399 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
400 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
401
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
402 * **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
403 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
404 Default is 10.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
405
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
406 * **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
407 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
408 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
409 380 (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
410
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
411 * **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
412 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
413 ``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
414 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
415
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
416 * **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
417 databases for taxa assignment.
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
418
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
419 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
420
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
421 5. Results
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
422 **********
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
423
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
424 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
425 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
426
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
427 * **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
428 (http://biom-format.org/)
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
429
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
430 * **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
431 ``make_phylogeny.py`` (fasttree) QIIME script
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
432 (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
433
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
434 * **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
435 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
436 (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
437 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
438
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
439 * **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
440 (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
441
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
442 * **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
443 (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
444
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
445 * **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
446 Fasta file with OTU sequences
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
447
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
448 * **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
449 (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
450
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
pjbriggs
parents:
diff changeset
451 * **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
452 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
453 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
454 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
455 (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
456
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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457 * **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
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458 format using Unweighted Unifrac distance measure. Samples are grouped
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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459 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
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460 firstly rarefied to the minimum sequencing depth
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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461 (http://qiime.org/scripts/beta_diversity_through_plots.html )
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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462
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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463 Code availability
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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464 -----------------
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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465
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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466 **Code is available at** https://github.com/MTutino/Amplicon_analysis
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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467
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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468 Credits
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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469 -------
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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470
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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471 Pipeline author: Mauro Tutino
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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472
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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473 Galaxy tool: Peter Briggs
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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474
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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475 ]]></help>
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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476 <citations>
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477 <citation type="bibtex">
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478 @misc{githubAmplicon_analysis,
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479 author = {Tutino, Mauro},
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480 year = {2017},
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481 title = {Amplicon Analysis Pipeline},
47ec9c6f44b8 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit b63924933a03255872077beb4d0fde49d77afa92
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482 publisher = {GitHub},
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483 journal = {GitHub repository},
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484 url = {https://github.com/MTutino/Amplicon_analysis},
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485 }</citation>
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486 </citations>
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487 </tool>