Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate amplicon_analysis_pipeline.xml @ 24:fe354f5dd0ee draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730
author pjbriggs
date Thu, 30 Aug 2018 08:13:55 -0400
parents 545f23776953
children b5e43dfe07ac
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1 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.2.1">
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 <!-- non-bioconda dependencies -->
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5 <requirement type="package" version="1.2.2">amplicon_analysis_pipeline</requirement>
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6 <requirement type="package" version="2010-04-29">microbiomeutil-chimeraslayer</requirement>
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7 <requirement type="package" version="1.2.22">uclust-qiime</requirement>
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8 <!-- bioconda dependencies -->
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9 <requirement type="package" version="2.7">python</requirement>
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10 <requirement type="package" version="1.11">cutadapt</requirement>
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11 <requirement type="package" version="1.33">sickle-trim</requirement>
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12 <requirement type="package" version="1.0">bioawk</requirement>
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13 <requirement type="package" version="2.8.1">pandaseq</requirement>
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14 <requirement type="package" version="3.5.0">spades</requirement>
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15 <requirement type="package" version="0.11.3">fastqc</requirement>
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16 <requirement type="package" version="1.8.0">qiime</requirement>
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17 <requirement type="package" version="2.2.26">blast-legacy</requirement>
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18 <requirement type="package" version="0.2.4">fasta-splitter</requirement>
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19 <requirement type="package" version="2.2">rdp_classifier</requirement>
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20 <requirement type="package" version="1.1.3">vsearch</requirement>
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21 <requirement type="package" version="3.2.1">R</requirement>
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22 </requirements>
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23 <stdio>
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24 <exit_code range="1:" />
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25 </stdio>
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26 <command><![CDATA[
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27 ## Set the reference database name
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28 #if $reference_database == "-S"
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29 #set reference_database_name = "silva"
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30 #else if $reference_database == "-H"
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31 #set reference_database_name = "homd"
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32 #else
0
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33 #set reference_database_name = "gg"
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34 #end if
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35
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36 ## Run the amplicon analysis pipeline wrapper
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37 python $__tool_directory__/amplicon_analysis_pipeline.py
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38 ## Set options
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39 #if str( $forward_pcr_primer ) != ""
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40 -g "$forward_pcr_primer"
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41 #end if
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42 #if str( $reverse_pcr_primer ) != ""
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43 -G "$reverse_pcr_primer"
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44 #end if
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45 #if str( $trimming_threshold ) != ""
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46 -q $trimming_threshold
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47 #end if
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48 #if str( $sliding_window_length ) != ""
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49 -l $sliding_window_length
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50 #end if
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51 #if str( $minimum_overlap ) != ""
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52 -O $minimum_overlap
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53 #end if
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54 #if str( $minimum_length ) != ""
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55 -L $minimum_length
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56 #end if
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57 -P $pipeline
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58 -r \$AMPLICON_ANALYSIS_REF_DATA_PATH
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59 #if str( $reference_database ) != ""
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60 ${reference_database}
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61 #end if
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62 #if str($categories_file_in) != 'None'
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63 -c "${categories_file_in}"
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64 #end if
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65 ## Input files
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66 "${metatable_file_in}"
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67 ## FASTQ pairs
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68 #if str($input_type.pairs_or_collection) == "collection"
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69 #set fastq_pairs = $input_type.fastq_collection
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70 #else
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71 #set fastq_pairs = $input_type.fastq_pairs
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72 #end if
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73 #for $fq_pair in $fastq_pairs
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74 "${fq_pair.name}" "${fq_pair.forward}" "${fq_pair.reverse}"
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75 #end for
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76 &&
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77
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78 ## Collect outputs
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79 cp Metatable_log/Metatable_mod.txt "${metatable_mod}" &&
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80 cp ${pipeline}_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
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81 cp ${pipeline}_OTU_tables/otus.tre "${otus_tre_file}" &&
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82 cp RESULTS/${pipeline}_${reference_database_name}/OTUs_count.txt "${otus_count_file}" &&
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83 cp RESULTS/${pipeline}_${reference_database_name}/table_summary.txt "${table_summary_file}" &&
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84 cp Multiplexed_files/${pipeline}_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta "${dereplicated_nonchimera_otus_fasta}" &&
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85 cp QUALITY_CONTROL/Reads_count.txt "$read_counts_out" &&
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86 cp fastqc_quality_boxplots.html "${fastqc_quality_boxplots_html}" &&
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87
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88 ## HTML outputs
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89
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90 ## OTU table
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91 mkdir $heatmap_otu_table_html.files_path &&
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92 cp -r RESULTS/${pipeline}_${reference_database_name}/Heatmap/js $heatmap_otu_table_html.files_path &&
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93 cp RESULTS/${pipeline}_${reference_database_name}/Heatmap/otu_table.html "${heatmap_otu_table_html}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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94
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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95 ## Phylum genus barcharts
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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96 mkdir $phylum_genus_dist_barcharts_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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97 cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/charts $phylum_genus_dist_barcharts_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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98 cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/raw_data $phylum_genus_dist_barcharts_html.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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99 cp RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/bar_charts.html "${phylum_genus_dist_barcharts_html}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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100
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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101 ## Beta diversity weighted 2d plots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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102 mkdir $beta_div_even_weighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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103 cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/* $beta_div_even_weighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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104 cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_weighted_2d_plots}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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105
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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106 ## Beta diversity unweighted 2d plots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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107 mkdir $beta_div_even_unweighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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108 cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/* $beta_div_even_unweighted_2d_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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109 cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_unweighted_2d_plots}" &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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110
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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111 ## Alpha diversity rarefaction plots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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112 mkdir $alpha_div_rarefaction_plots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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113 cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/rarefaction_plots.html $alpha_div_rarefaction_plots &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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114 cp -r RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/average_plots $alpha_div_rarefaction_plots.files_path &&
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115
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116 ## Categories data
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117 #if str($categories_file_in) != 'None'
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118 ## Alpha diversity boxplots
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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119 mkdir $alpha_div_boxplots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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120 cp alpha_diversity_boxplots.html "$alpha_div_boxplots" &&
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121 cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/Alpha_diversity_boxplot/Categories_shannon/*.pdf $alpha_div_boxplots.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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122 #end if
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123
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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124 ## Pipeline outputs (log files etc)
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125 mkdir $log_files.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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126 cp Amplicon_analysis_pipeline.log $log_files.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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127 cp pipeline.log $log_files.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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128 cp Pipeline_outputs.txt $log_files.files_path &&
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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129 cp Metatable_log/Metatable.html $log_files.files_path &&
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130 cp pipeline_outputs.html "$log_files"
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131 ]]></command>
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132 <inputs>
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133 <param name="title" type="text" value="test" size="25"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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134 label="Title" help="Optional text that will be added to the output dataset names" />
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135 <param type="data" name="metatable_file_in" format="tabular"
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136 label="Input Metatable.txt file" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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137 <param type="data" name="categories_file_in" format="txt"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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138 label="Input Categories.txt file" optional="true"
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139 help="(optional)" />
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140 <conditional name="input_type">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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141 <param name="pairs_or_collection" type="select"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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142 label="Input FASTQ type">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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143 <option value="pairs_of_files">Pairs of datasets</option>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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144 <option value="collection" selected="true">Dataset pairs in a collection</option>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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145 </param>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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146 <when value="collection">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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147 <param name="fastq_collection" type="data_collection"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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148 format="fastqsanger,fastq" collection_type="list:paired"
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149 label="Collection of FASTQ forward and reverse (R1/R2) pairs"
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150 help="Each FASTQ pair will be treated as one sample; the name of each sample will be taken from the first column of the Metatable file " />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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151 </when>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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152 <when value="pairs_of_files">
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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153 <repeat name="fastq_pairs" title="Input fastq pairs" min="1">
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154 <param type="text" name="name" value=""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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155 label="Final name for FASTQ pair" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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156 <param type="data" name="fastq_r1" format="fastqsanger,fastq"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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157 label="FASTQ with forward reads (R1)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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158 <param type="data" name="fastq_r2" format="fastqsanger,fastq"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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159 label="FASTQ with reverse reads (R2)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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160 </repeat>
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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161 </when>
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162 </conditional>
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163 <param type="text" name="forward_pcr_primer" value=""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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164 label="Forward PCR primer sequence"
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165 help="Optional; must not include barcode or adapter sequence (-g)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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166 <param type="text" name="reverse_pcr_primer" value=""
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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167 label="Reverse PCR primer sequence"
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168 help="Optional; must not include barcode or adapter sequence (-G)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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169 <param type="integer" name="trimming_threshold" value="20"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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170 label="Threshold quality below which read will be trimmed"
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171 help="Phred score; default is 20 (-q)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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172 <param type="integer" name="minimum_overlap" value="10"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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173 label="Minimum overlap in bp between forward and reverse reads"
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174 help="Default is 10 (-O)" />
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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175 <param type="integer" name="minimum_length" value="200"
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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176 label="Minimum length in bp to keep sequence after overlapping"
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177 help="Default is 200 (-L)" />
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178 <param type="integer" name="sliding_window_length" value="10"
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179 label="Minimum length in bp to retain a read after trimming"
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180 help="Supplied to Sickle; default is 10 (-l)" />
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181 <param type="select" name="pipeline"
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182 label="Pipeline to use for analysis">
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183 <option value="Vsearch" selected="true" >Vsearch</option>
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184 <!--
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185 Remove the QIIME and Uparse options for now
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186 <option value="QIIME">QIIME</option>
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187 <option value="Uparse">Uparse</option>
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188 -->
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189 </param>
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190 <param type="select" name="reference_database"
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191 label="Reference database">
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192 <option value="" selected="true">GreenGenes</option>
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193 <option value="-S">Silva</option>
2
a898ee628343 Updated to version 1.2.1.0
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194 <option value="-H">Human Oral Microbiome Database (HOMD)</option>
0
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195 </param>
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196 </inputs>
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197 <outputs>
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198 <data format="tabular" name="metatable_mod"
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199 label="${tool.name}:${title} Metatable_mod.txt" />
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200 <data format="tabular" name="read_counts_out"
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201 label="${tool.name} (${pipeline}):${title} read counts" />
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202 <data format="biom" name="tax_otu_table_biom_file"
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203 label="${tool.name} (${pipeline}):${title} tax OTU table (biom format)" />
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204 <data format="tabular" name="otus_tre_file"
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205 label="${tool.name} (${pipeline}):${title} otus.tre" />
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206 <data format="html" name="phylum_genus_dist_barcharts_html"
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207 label="${tool.name} (${pipeline}):${title} phylum genus dist barcharts HTML" />
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208 <data format="tabular" name="otus_count_file"
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209 label="${tool.name} (${pipeline}):${title} OTUs count file" />
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210 <data format="tabular" name="table_summary_file"
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211 label="${tool.name} (${pipeline}):${title} table summary file" />
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212 <data format="fasta" name="dereplicated_nonchimera_otus_fasta"
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213 label="${tool.name} (${pipeline}):${title} multiplexed linearized dereplicated mc2 repset nonchimeras OTUs FASTA" />
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214 <data format="html" name="fastqc_quality_boxplots_html"
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215 label="${tool.name} (${pipeline}):${title} FastQC per-base quality boxplots HTML" />
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216 <data format="html" name="heatmap_otu_table_html"
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217 label="${tool.name} (${pipeline}):${title} heatmap OTU table HTML" />
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218 <data format="html" name="beta_div_even_weighted_2d_plots"
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219 label="${tool.name} (${pipeline}):${title} beta diversity weighted 2D plots HTML" />
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220 <data format="html" name="beta_div_even_unweighted_2d_plots"
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221 label="${tool.name} (${pipeline}):${title} beta diversity unweighted 2D plots HTML" />
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222 <data format="html" name="alpha_div_rarefaction_plots"
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223 label="${tool.name} (${pipeline}):${title} alpha diversity rarefaction plots HTML" />
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224 <data format="html" name="alpha_div_boxplots"
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225 label="${tool.name} (${pipeline}):${title} alpha diversity boxplots">
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226 <filter>categories_file_in is not None</filter>
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227 </data>
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228 <data format="html" name="log_files"
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229 label="${tool.name} (${pipeline}):${title} log files" />
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230 </outputs>
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231 <tests>
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232 </tests>
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233 <help><![CDATA[
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234
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235 What it does
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236 ------------
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237
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238 This pipeline has been designed for the analysis of 16S rRNA data from
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
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239 Illumina Miseq (Casava >= 1.8) paired-end reads.
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240
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241 Usage
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242 -----
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243
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244 1. Preparation of the mapping file and format of unique sample id
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245 *****************************************************************
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246
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247 Before using the amplicon analysis pipeline it would be necessary to
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248 follow the steps as below to avoid analysis failures and ensure samples
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249 are labelled appropriately. Sample names for the labelling are derived
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250 from the fastq files names that are generated from the sequencing. The
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251 labels will include everything between the beginning of the name and
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252 the sample number (from C11 to S19 in Fig. 1)
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253
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254 .. image:: Pipeline_description_Fig1.png
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255 :height: 46
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256 :width: 382
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257
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258 **Figure 1**
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259
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260 If analysing 16S data from multiple runs:
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261
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262 The samples from different runs may have identical IDs. For example,
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263 when sequencing the same samples twice, by chance, these could be at
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264 the same position in both the runs. This would cause the fastq files
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265 to have exactly the same IDs (Fig. 2).
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266
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267 .. image:: Pipeline_description_Fig2.png
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268 :height: 100
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269 :width: 463
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270
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271 **Figure 2**
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272
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273 In case of identical sample IDs the pipeline will fail to run and
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274 generate an error at the beginning of the analysis.
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275
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276 To avoid having to change the file names, before uploading the files,
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277 ensure that the samples IDs are not repeated.
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278
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279 2. To upload the file
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280 *********************
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281
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282 Click on **Get Data/Upload File** from the Galaxy tool panel on the
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283 left hand side.
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284
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285 From the pop-up window, choose how to upload the file. The
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286 **Choose local file** option can be used for files up to 4Gb. Fastq files
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287 from Illumina MiSeq will rarely be bigger than 4Gb and this option is
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288 recommended.
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289
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290 After choosing the files click **Start** to begin the upload. The window can
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291 now be closed and the files will be uploaded onto the Galaxy server. You
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292 will see the progress on the ``HISTORY`` panel on the right
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293 side of the screen. The colour will change from grey (queuing), to yellow
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294 (uploading) and finally green (uploaded).
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295
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296 Once all the files are uploaded, click on the operations on multiple
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297 datasets icon and select the fastq files that need to be analysed.
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298 Click on the tab **For all selected...** and on the option
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299 **Build List of Dataset pairs** (Fig. 3).
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300
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301 .. image:: Pipeline_description_Fig3.png
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302 :height: 247
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303 :width: 586
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304
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305 **Figure 3**
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306
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307 Change the filter parameter ``_1`` and ``_2`` to be ``_R1`` and ``_R2``.
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308 The fastq files forward R1 and reverse R2 should now appear in the
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309 corresponding columns.
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310
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311 Select **Autopair**. This creates a collection of paired fastq files for
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312 the forward and reverse reads for each sample. The name of the pairs will
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313 be the ones used by the pipeline. You are free to change the names at this
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314 point as long as they are the same used in the Metatable file
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315 (see section 3).
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316
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317 Name the collection and click on **create list**. This reduces the time
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318 required to input the forward and reverse reads for each individual sample.
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319
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320 3. Create the Metatable files
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321 *****************************
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322
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323 Metatable.txt
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324 ~~~~~~~~~~~~~
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325
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326 Click on the list of pairs you just created to see the name of the single
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327 pairs. The name of the pairs will be the ones used by the pipeline,
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328 therefore, these are the names that need to be used in the Metatable file.
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329
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330 The Metatable file has to be in QIIME format. You can find a description
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331 of it on QIIME website http://qiime.org/documentation/file_formats.html
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332
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333 EXAMPLE::
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334
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335 #SampleID BarcodeSequence LinkerPrimerSequence Disease Gender Description
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336 Mock-RUN1 TAAGGCGAGCGTAAGA PsA Male Control
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337 Mock-RUN2 CGTACTAGGCGTAAGA PsA Male Control
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338 Mock-RUN3 AGGCAGAAGCGTAAGA PsC Female Control
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339
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340 Briefly: the column ``LinkerPrimerSequence`` is empty but it cannot be
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341 deleted. The header is very important. ``#SampleID``, ``Barcode``,
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342 ``LinkerPrimerSequence`` and ``Description`` are mandatory. Between
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343 ``LinkerPrimerSequence`` and ``Description`` you can add as many columns
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344 as you want. For every column a PCoA plot will be created (see
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345 **Results** section). You can create this file in Excel and it will have
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346 to be saved as ``Text(Tab delimited)``.
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347
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348 During the analysis the Metatable.txt will be checked to ensure that the
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349 file has the correct format. If necessary, this will be modified and will
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350 be available as Metatable_corrected.txt in the history panel. If you are
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351 going to use the metatable file for any other statistical analyses,
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352 remember to use the ``Metatable_mod.txt`` one, otherwise the sample
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353 names might not match!
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354
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355 Categories.txt (optional)
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356 ~~~~~~~~~~~~~~~~~~~~~~~~~
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357
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358 This file is required if you want to get box plots for comparison of
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359 alpha diversity indices (see **Results** section). The file is a list
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360 (without header and IN ONE COLUMN) of categories present in the
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361 Metatable.txt file. THE NAMES YOU ARE USING HAVE TO BE THE SAME AS THE
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362 ONES USED IN THE METATABLE.TXT. You can create this file in Excel and
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363 will have to be saved as ``Text(Tab delimited)``.
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364
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365 EXAMPLE::
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366
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367 Disease
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
368 Gender
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
369
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
370 Metatable and categories files can be uploaded using Get Data as done
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
371 with the fatsq files.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
372
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
373 4. Analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
374 ***********
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
375
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
376 Under **Amplicon_Analysis_Pipeline**
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
377
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
378 * **Title** Name to distinguish between the runs. It will be shown at
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
379 the beginning of each output file name.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
380
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
381 * **Input Metatable.txt file** Select the Metatable.txt file related to
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
382 this analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
383
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
384 * **Input Categories.txt file (Optional)** Select the Categories.txt file
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
385 related to this analysis
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
386
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
387 * **Input FASTQ type** select *Dataset pairs in a collection* and, then,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
388 the collection of pairs you created earlier.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
389
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
390 * **Forward/Reverse PCR primer sequence** if the PCR primer sequences
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
391 have not been removed from the MiSeq during the fastq creation, they
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
392 have to be removed before the analysis. Insert the PCR primer sequence
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
393 in the corresponding field. DO NOT include any barcode or adapter
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
394 sequence. If the PCR primers have been already trimmed by the MiSeq,
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
395 and you include the sequence in this field, this would lead to an error.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
396 Only include the sequences if still present in the fastq files.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
397
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
398 * **Threshold quality below which reads will be trimmed** Choose the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
399 Phred score used by Sickle to trim the reads at the 3’ end.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
400
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
401 * **Minimum length to retain a read after trimming** If the read length
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
402 after trimming is shorter than a user defined length, the read, along
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
403 with the corresponding read pair, will be discarded.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
404
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
405 * **Minimum overlap in bp between forward and reverse reads** Choose the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
406 minimum basepair overlap used by Pandaseq to assemble the reads.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
407 Default is 10.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
408
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
409 * **Minimum length in bp to keep a sequence after overlapping** Choose the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
410 minimum sequence length used by Pandaseq to keep a sequence after the
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
411 overlapping. This depends on the expected amplicon length. Default is
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
412 380 (used for V3-V4 16S sequencing; expected length ~440bp)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
413
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
414 * **Pipeline to use for analysis** Choose the pipeline to use for OTU
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
415 clustering and chimera removal. The Galaxy tool currently supports
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
416 ``Vsearch`` only. ``Uparse`` and ``QIIME`` are planned to be added
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
417 shortly (the tools are already available for the stand-alone pipeline).
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
418
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
419 * **Reference database** Choose between ``GreenGenes`` and ``Silva``
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
420 databases for taxa assignment.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
421
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
422 Click on **Execute** to start the analysis.
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
423
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
424 5. Results
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
425 **********
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
426
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
427 Results are entirely generated using QIIME scripts. The results will
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
428 appear in the History panel when the analysis is completed
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
429
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
430 * **Vsearch_tax_OTU_table (biom format)** The OTU table in BIOM format
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
431 (http://biom-format.org/)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
432
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
433 * **Vsearch_OTUs.tree** Phylogenetic tree constructed using
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
434 ``make_phylogeny.py`` (fasttree) QIIME script
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
435 (http://qiime.org/scripts/make_phylogeny.html)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
436
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
437 * **Vsearch_phylum_genus_dist_barcharts_HTML** HTML file with bar
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
438 charts at Phylum, Genus and Species level
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
439 (http://qiime.org/scripts/summarize_taxa.html and
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
440 http://qiime.org/scripts/plot_taxa_summary.html)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
441
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
442 * **Vsearch_OTUs_count_file** Summary of OTU counts per sample
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
443 (http://biom-format.org/documentation/summarizing_biom_tables.html)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
444
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
445 * **Vsearch_table_summary_file** Summary of sequences counts per sample
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
446 (http://biom-format.org/documentation/summarizing_biom_tables.html)
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
447
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
448 * **Vsearch_multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta**
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
449 Fasta file with OTU sequences
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
450
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
451 * **Vsearch_heatmap_OTU_table_HTML** Interactive OTU heatmap
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
452 (http://qiime.org/1.8.0/scripts/make_otu_heatmap_html.html )
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
453
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
454 * **Vsearch_beta_diversity_weighted_2D_plots_HTML** PCoA plots in HTML
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
455 format using weighted Unifrac distance measure. Samples are grouped
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
456 by the column names present in the Metatable file. The samples are
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
457 firstly rarefied to the minimum sequencing depth
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
458 (http://qiime.org/scripts/beta_diversity_through_plots.html )
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
459
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
460 * **Vsearch_beta_diversity_unweighted_2D_plots_HTML** PCoA plots in HTML
b433086738d6 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit ba3e5b591407db52a586361efb21927c8171ec0e
pjbriggs
parents:
diff changeset
461 format using Unweighted Unifrac distance measure. Samples are grouped
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462 by the column names present in the Metatable file. The samples are
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463 firstly rarefied to the minimum sequencing depth
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464 (http://qiime.org/scripts/beta_diversity_through_plots.html )
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465
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466 Code availability
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467 -----------------
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468
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469 **Code is available at** https://github.com/MTutino/Amplicon_analysis
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470
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471 Credits
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472 -------
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473
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474 Pipeline author: Mauro Tutino
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475
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476 Galaxy tool: Peter Briggs
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477
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478 ]]></help>
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479 <citations>
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480 <citation type="bibtex">
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481 @misc{githubAmplicon_analysis,
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482 author = {Tutino, Mauro},
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483 year = {2017},
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484 title = {Amplicon Analysis Pipeline},
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485 publisher = {GitHub},
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486 journal = {GitHub repository},
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487 url = {https://github.com/MTutino/Amplicon_analysis},
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488 }</citation>
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489 </citations>
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490 </tool>