amplicon_analysis_pipeline: amplicon_analysis

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

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

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

comparison

equal deleted inserted replaced

-:3ab198df8f3f
+:86a12d75ebe4
-<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.3.0">
+<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.3.6.0">
 <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
 <requirements>
-<requirement type="package" version="1.2.3">amplicon_analysis_pipeline</requirement>
+<requirement type="package" version="1.3.6">amplicon_analysis_pipeline</requirement>
 </requirements>
 <stdio>
 <exit_code range="1:" />
 </stdio>
 <command><![CDATA[
+## Convenience variable for pipeline name
+#set $pipeline_name = $pipeline.pipeline_name
 ## Set the reference database name
-#if $reference_database == "-S"
+#if str( $pipeline_name ) == "DADA2"
 #set reference_database_name = "silva"
-#else if $reference_database == "-H"
-#set reference_database_name = "homd"
 #else
-#set reference_database_name = "gg"
+#set reference_database = $pipeline.reference_database
+#if $reference_database == "-S"
+#set reference_database_name = "silva"
+#else if $reference_database == "-H"
+#set reference_database_name = "homd"
+#else
+#set reference_database_name = "gg"
+#end if
 #end if
 ## Run the amplicon analysis pipeline wrapper
 python $__tool_directory__/amplicon_analysis_pipeline.py
 ## Set options
 -O $minimum_overlap
 #end if
 #if str( $minimum_length ) != ""
 -L $minimum_length
 #end if
--P $pipeline
+-P $pipeline_name
--r \$AMPLICON_ANALYSIS_REF_DATA_PATH
+-r \${AMPLICON_ANALYSIS_REF_DATA_PATH-ReferenceData}
-#if str( $reference_database ) != ""
+#if str( $pipeline_name ) != "DADA2"
 ${reference_database}
 #end if
 #if str($categories_file_in) != 'None'
 -c "${categories_file_in}"
 #end if
 #end for
 &&
 ## Collect outputs
 cp Metatable_log/Metatable_mod.txt "${metatable_mod}" &&
-cp ${pipeline}_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
+#if str( $pipeline_name ) == "Vsearch"
-cp ${pipeline}_OTU_tables/otus.tre "${otus_tre_file}" &&
+## Vsearch-specific
-cp RESULTS/${pipeline}_${reference_database_name}/OTUs_count.txt "${otus_count_file}" &&
+cp ${pipeline_name}_OTU_tables/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
-cp RESULTS/${pipeline}_${reference_database_name}/table_summary.txt "${table_summary_file}" &&
+cp Multiplexed_files/${pipeline_name}_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta "${dereplicated_nonchimera_otus_fasta}" &&
-cp Multiplexed_files/${pipeline}_pipeline/multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta "${dereplicated_nonchimera_otus_fasta}" &&
+cp QUALITY_CONTROL/Reads_count.txt "$read_counts_out" &&
-cp QUALITY_CONTROL/Reads_count.txt "$read_counts_out" &&
+#else
+## DADA2-specific
+cp ${pipeline_name}_OTU_tables/DADA2_tax_OTU_table.biom "${tax_otu_table_biom_file}" &&
+cp ${pipeline_name}_OTU_tables/seqs.fa "${dereplicated_nonchimera_otus_fasta}" &&
+#end if
+cp ${pipeline_name}_OTU_tables/otus.tre "${otus_tre_file}" &&
+cp RESULTS/${pipeline_name}_${reference_database_name}/OTUs_count.txt "${otus_count_file}" &&
+cp RESULTS/${pipeline_name}_${reference_database_name}/table_summary.txt "${table_summary_file}" &&
 cp fastqc_quality_boxplots.html "${fastqc_quality_boxplots_html}" &&
+## OTU table heatmap
+cp RESULTS/${pipeline_name}_${reference_database_name}/Heatmap.pdf "${heatmap_otu_table_pdf}" &&
 ## HTML outputs
-## OTU table
-mkdir $heatmap_otu_table_html.files_path &&
-cp -r RESULTS/${pipeline}_${reference_database_name}/Heatmap/js $heatmap_otu_table_html.files_path &&
-cp RESULTS/${pipeline}_${reference_database_name}/Heatmap/otu_table.html "${heatmap_otu_table_html}" &&
 ## Phylum genus barcharts
 mkdir $phylum_genus_dist_barcharts_html.files_path &&
-cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/charts $phylum_genus_dist_barcharts_html.files_path &&
+cp -r RESULTS/${pipeline_name}_${reference_database_name}/phylum_genus_charts/charts $phylum_genus_dist_barcharts_html.files_path &&
-cp -r RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/raw_data $phylum_genus_dist_barcharts_html.files_path &&
+cp -r RESULTS/${pipeline_name}_${reference_database_name}/phylum_genus_charts/raw_data $phylum_genus_dist_barcharts_html.files_path &&
-cp RESULTS/${pipeline}_${reference_database_name}/phylum_genus_charts/bar_charts.html "${phylum_genus_dist_barcharts_html}" &&
+cp RESULTS/${pipeline_name}_${reference_database_name}/phylum_genus_charts/bar_charts.html "${phylum_genus_dist_barcharts_html}" &&
 ## Beta diversity weighted 2d plots
 mkdir $beta_div_even_weighted_2d_plots.files_path &&
-cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/* $beta_div_even_weighted_2d_plots.files_path &&
+cp -r RESULTS/${pipeline_name}_${reference_database_name}/beta_div_even/weighted_2d_plot/* $beta_div_even_weighted_2d_plots.files_path &&
-cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_weighted_2d_plots}" &&
+cp RESULTS/${pipeline_name}_${reference_database_name}/beta_div_even/weighted_2d_plot/weighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_weighted_2d_plots}" &&
 ## Beta diversity unweighted 2d plots
 mkdir $beta_div_even_unweighted_2d_plots.files_path &&
-cp -r RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/* $beta_div_even_unweighted_2d_plots.files_path &&
+cp -r RESULTS/${pipeline_name}_${reference_database_name}/beta_div_even/unweighted_2d_plot/* $beta_div_even_unweighted_2d_plots.files_path &&
-cp RESULTS/${pipeline}_${reference_database_name}/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_unweighted_2d_plots}" &&
+cp RESULTS/${pipeline_name}_${reference_database_name}/beta_div_even/unweighted_2d_plot/unweighted_unifrac_pc_2D_PCoA_plots.html "${beta_div_even_unweighted_2d_plots}" &&
 ## Alpha diversity rarefaction plots
 mkdir $alpha_div_rarefaction_plots.files_path &&
-cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/rarefaction_plots.html $alpha_div_rarefaction_plots &&
+cp RESULTS/${pipeline_name}_${reference_database_name}/Alpha_diversity/rarefaction_curves/rarefaction_plots.html $alpha_div_rarefaction_plots &&
-cp -r RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/rarefaction_curves/average_plots $alpha_div_rarefaction_plots.files_path &&
+cp -r RESULTS/${pipeline_name}_${reference_database_name}/Alpha_diversity/rarefaction_curves/average_plots $alpha_div_rarefaction_plots.files_path &&
+## DADA2 error rate plots
+#if str($pipeline_name) == "DADA2"
+mkdir $dada2_error_rate_plots.files_path &&
+cp DADA2_OTU_tables/Error_rate_plots/error_rate_plots.html $dada2_error_rate_plots &&
+cp -r DADA2_OTU_tables/Error_rate_plots/*.pdf $dada2_error_rate_plots.files_path &&
+#end if
 ## Categories data
 #if str($categories_file_in) != 'None'
 ## Alpha diversity boxplots
 mkdir $alpha_div_boxplots.files_path &&
 cp alpha_diversity_boxplots.html "$alpha_div_boxplots" &&
-cp RESULTS/${pipeline}_${reference_database_name}/Alpha_diversity/Alpha_diversity_boxplot/Categories_shannon/*.pdf $alpha_div_boxplots.files_path &&
+cp RESULTS/${pipeline_name}_${reference_database_name}/Alpha_diversity/Alpha_diversity_boxplot/Categories_shannon/*.pdf $alpha_div_boxplots.files_path &&
 #end if
 ## Pipeline outputs (log files etc)
 mkdir $log_files.files_path &&
 cp Amplicon_analysis_pipeline.log $log_files.files_path &&
 	   label="Minimum length in bp to keep sequence after overlapping"
 	   help="Default is 200 (-L)" />
 <param type="integer" name="sliding_window_length" value="10"
 	   label="Minimum length in bp to retain a read after trimming"
 	   help="Supplied to Sickle; default is 10 (-l)" />
-<param type="select" name="pipeline"
+<conditional name="pipeline">
-	    label="Pipeline to use for analysis">
+<param type="select" name="pipeline_name"
-<option value="Vsearch" selected="true" >Vsearch</option>
+	     label="Pipeline to use for analysis">
-<!--
+	<option value="Vsearch" selected="true" >Vsearch</option>
-Remove the QIIME and Uparse options for now
+	<option value="DADA2">DADA2</option>
-<option value="QIIME">QIIME</option>
+</param>
-<option value="Uparse">Uparse</option>
+<when value="Vsearch">
--->
+	<param type="select" name="reference_database"
-</param>
+	       label="Reference database">
-<param type="select" name="reference_database"
+	  <option value="" selected="true">GreenGenes</option>
-	   label="Reference database">
+	  <option value="-S">Silva</option>
-<option value="" selected="true">GreenGenes</option>
+	  <option value="-H">Human Oral Microbiome Database (HOMD)</option>
-<option value="-S">Silva</option>
+	</param>
-<option value="-H">Human Oral Microbiome Database (HOMD)</option>
+</when>
-</param>
+<when value="DADA2">
+</when>
+</conditional>
 </inputs>
 <outputs>
 <data format="tabular" name="metatable_mod"
 	  label="${tool.name}:${title} Metatable_mod.txt" />
 <data format="tabular" name="read_counts_out"
-	  label="${tool.name} (${pipeline}):${title} read counts" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} read counts">
+<filter>pipeline['pipeline_name'] == 'Vsearch'</filter>
+</data>
 <data format="biom" name="tax_otu_table_biom_file"
-	  label="${tool.name} (${pipeline}):${title} tax OTU table (biom format)" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} tax OTU table (biom format)" />
 <data format="tabular" name="otus_tre_file"
-	  label="${tool.name} (${pipeline}):${title} otus.tre" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} otus.tre" />
 <data format="html" name="phylum_genus_dist_barcharts_html"
-	  label="${tool.name} (${pipeline}):${title} phylum genus dist barcharts HTML" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} phylum genus dist barcharts HTML" />
 <data format="tabular" name="otus_count_file"
-	  label="${tool.name} (${pipeline}):${title} OTUs count file" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} OTUs count file" />
 <data format="tabular" name="table_summary_file"
-	  label="${tool.name} (${pipeline}):${title} table summary file" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} table summary file" />
 <data format="fasta" name="dereplicated_nonchimera_otus_fasta"
-	  label="${tool.name} (${pipeline}):${title} multiplexed linearized dereplicated mc2 repset nonchimeras OTUs FASTA" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} multiplexed linearized dereplicated mc2 repset nonchimeras OTUs FASTA" />
 <data format="html" name="fastqc_quality_boxplots_html"
-	  label="${tool.name} (${pipeline}):${title} FastQC per-base quality boxplots HTML" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} FastQC per-base quality boxplots HTML" />
-<data format="html" name="heatmap_otu_table_html"
+<data format="pdf" name="heatmap_otu_table_pdf"
-	  label="${tool.name} (${pipeline}):${title} heatmap OTU table HTML" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} heatmap OTU table PDF" />
 <data format="html" name="beta_div_even_weighted_2d_plots"
-	  label="${tool.name} (${pipeline}):${title} beta diversity weighted 2D plots HTML" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} beta diversity weighted 2D plots HTML" />
 <data format="html" name="beta_div_even_unweighted_2d_plots"
-	  label="${tool.name} (${pipeline}):${title} beta diversity unweighted 2D plots HTML" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} beta diversity unweighted 2D plots HTML" />
 <data format="html" name="alpha_div_rarefaction_plots"
-	  label="${tool.name} (${pipeline}):${title} alpha diversity rarefaction plots HTML" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} alpha diversity rarefaction plots HTML" />
+<data format="html" name="dada2_error_rate_plots"
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} DADA2 error rate plots">
+<filter>pipeline['pipeline_name'] == 'DADA2'</filter>
+</data>
 <data format="html" name="alpha_div_boxplots"
-	  label="${tool.name} (${pipeline}):${title} alpha diversity boxplots">
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} alpha diversity boxplots">
 <filter>categories_file_in is not None</filter>
 </data>
 <data format="html" name="log_files"
-	  label="${tool.name} (${pipeline}):${title} log files" />
+	  label="${tool.name} (${pipeline.pipeline_name}):${title} log files" />
 </outputs>
 <tests>
 </tests>
 <help><![CDATA[
 minimum sequence length used by Pandaseq to keep a sequence after the
 overlapping. This depends on the expected amplicon length. Default is
 380 (used for V3-V4 16S sequencing; expected length ~440bp)
 * **Pipeline to use for analysis** Choose the pipeline to use for OTU
-clustering and chimera removal. The Galaxy tool currently supports
+clustering and chimera removal. The Galaxy tool supports the ``Vsearch``
-``Vsearch`` only. ``Uparse`` and ``QIIME`` are planned to be added
+and ``DADA2`` pipelines.
-shortly (the tools are already available for the stand-alone pipeline).
+* **Reference database** Choose between ``GreenGenes``, ``Silva`` or
-* **Reference database** Choose between ``GreenGenes`` and ``Silva``
+``HOMD`` (Human Oral Microbiome Database) for taxa assignment.
-databases for taxa assignment.
 Click on **Execute** to start the analysis.
 5. Results
 **********
 Results are entirely generated using QIIME scripts. The results will
-appear in the History panel when the analysis is completed
+appear in the History panel when the analysis is completed.
-* **Vsearch_tax_OTU_table (biom format)** The OTU table in BIOM format
+The following outputs are captured:
-(http://biom-format.org/)
+* **Vsearch_tax_OTU_table.biom|DADA2_tax_OTU_table.biom (biom format)**
-* **Vsearch_OTUs.tree** Phylogenetic tree constructed using
+The OTU table in BIOM format (http://biom-format.org/)
-``make_phylogeny.py`` (fasttree) QIIME script
-(http://qiime.org/scripts/make_phylogeny.html)
+* **otus.tre** Phylogenetic tree constructed using ``make_phylogeny.py``
+(fasttree) QIIME script (http://qiime.org/scripts/make_phylogeny.html)
-* **Vsearch_phylum_genus_dist_barcharts_HTML** HTML file with bar
-charts at Phylum, Genus and Species level
+* **Phylum_genus_dist_barcharts_HTML** HTML file with bar charts at
+Phylum, Genus and Species level
 (http://qiime.org/scripts/summarize_taxa.html and
 http://qiime.org/scripts/plot_taxa_summary.html)
-* **Vsearch_OTUs_count_file** Summary of OTU counts per sample
+* **OTUs_count_file** Summary of OTU counts per sample
 (http://biom-format.org/documentation/summarizing_biom_tables.html)
-* **Vsearch_table_summary_file** Summary of sequences counts per sample
+* **Table_summary_file** Summary of sequences counts per sample
 (http://biom-format.org/documentation/summarizing_biom_tables.html)
-* **Vsearch_multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta**
+* **multiplexed_linearized_dereplicated_mc2_repset_nonchimeras_OTUs.fasta|seqs.fa**
-Fasta file with OTU sequences
+Fasta file with OTU sequences (Vsearch|DADA2)
-* **Vsearch_heatmap_OTU_table_HTML** Interactive OTU heatmap
+* **Heatmap_PDF** OTU heatmap in PDF format
 (http://qiime.org/1.8.0/scripts/make_otu_heatmap_html.html )
 * **Vsearch_beta_diversity_weighted_2D_plots_HTML** PCoA plots in HTML
 format using weighted Unifrac distance measure. Samples are grouped
 by the column names present in the Metatable file. The samples are

Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

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