changeset 0:3856a1590a11 draft default tip

"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
author qfabrepo
date Mon, 14 Sep 2020 08:02:08 +0000
parents
children
files phyloseq_abundance_factor.r phyloseq_abundance_factor.xml test-data/abundace_factor.html test-data/biom_out.html test-data/metadata.txt test-data/test.biom
diffstat 6 files changed, 237 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_abundance_factor.r	Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,91 @@
+
+library('getopt')
+suppressPackageStartupMessages(library('phyloseq'))
+Sys.setenv("DISPLAY"=":1")
+
+
+cmd_args <- commandArgs(TRUE)
+options(warn=-1)
+option_specification = matrix(c(
+   'biomfile','b',2,'character',
+   'metafile','m',2,'character',
+     'xcolumn','x',2,'numeric',
+     'lcolumn','l',2,'numeric',
+     'factor1','f1',2,'numeric',
+     'factor2','f2',1,'numeric',
+     'outdir','o',2,'character',
+   'htmlfile','h',2,'character'
+),byrow=TRUE,ncol=4);
+
+
+options <- getopt(option_specification);
+options(bitmapType="cairo")
+
+
+
+if (!is.null(options$outdir)) {
+  # Create the directory
+  dir.create(options$outdir,FALSE)
+}
+
+
+galaxy_biom <- import_biom(options$biomfile)
+galaxy_map <- import_qiime_sample_data(options$metafile)
+
+
+tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
+tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
+
+number.of.tax.rank<-length(colnames(tax_table(galaxy_biom)))
+
+if( number.of.tax.rank == 7){
+colnames(tax_table(galaxy_biom)) <- tax_col_norm
+}else{
+colnames(tax_table(galaxy_biom)) <- tax_col_extra
+}
+
+
+AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map)
+
+
+pdffile <- gsub("[ ]+", "", paste(options$outdir,"/abundance.pdf"))
+pngfile_abundance <- gsub("[ ]+", "", paste(options$outdir,"/abundance.png"))
+htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
+
+
+###### To obtain the column name in metadata ################
+x.selectedColumn<-colnames(galaxy_map)[options$xcolumn]
+l.selectedColumn<-colnames(galaxy_map)[options$lcolumn]
+f1.selectedColumn<-colnames(galaxy_map)[options$factor1]
+
+factor.var <- f1.selectedColumn
+
+if(!is.null(options$factor2)){
+f2.selectedColumn<-colnames(galaxy_map)[options$factor2]
+factor.var <- paste(f1.selectedColumn,f2.selectedColumn,sep="+")
+}
+
+
+# Produce PDF file
+pdf(pdffile);
+plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', factor.var),fill=l.selectedColumn)
+garbage<-dev.off();
+
+#png('abundance_1.png')
+bitmap(pngfile_abundance,"png16m")
+plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', factor.var),fill=l.selectedColumn)
+garbage<-dev.off()
+
+# Produce the HTML file
+htmlfile_handle <- file(htmlfile)
+html_output = c('<html><body>',
+	            '<table align="center">',
+		        '<tr>',
+		        '<td valign="middle" style="vertical-align:middle;">',
+                '<a href="abundance.pdf"><img src="abundance.png"/></a>',
+		        '</td>',
+		        '</tr>',
+		        '</table>',
+                '</html></body>');
+writeLines(html_output, htmlfile_handle);
+close(htmlfile_handle);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_abundance_factor.xml	Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,108 @@
+<tool id="phyloseq_abundance" name="Phyloseq Abundance plot" version="1.22.3.3" hidden="false">
+  <description>Phyloseq Abundance Plot with the factors of choice</description>
+    <requirements>
+       <requirement type="package" version="3.4.1">r-base</requirement>
+	   <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
+	   <requirement type="package" version="1.20.0">r-getopt</requirement>
+	   <requirement type="package" version="9.18">ghostscript</requirement>
+	</requirements>
+  <version_command><![CDATA[
+          echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+  ]]></version_command>
+  <command detect_errors="exit_code"><![CDATA[
+  	Rscript '${__tool_directory__}/phyloseq_abundance_factor.r'
+    #if str($factor.type) == "one":
+    	--biomfile=$biom_input 
+		--metafile=$metadata_input 
+		--xcolumn="${xaxis_column}" 
+		--lcolumn="${legend_column}" 
+		--factor1="${factor.factor_column1}" 
+		--outdir="$htmlfile.files_path" 
+		--htmlfile='$htmlfile'
+    #else if str($factor.type) == "two":
+        --biomfile='$biom_input' 
+		--metafile='$metadata_input' 
+		--xcolumn="${xaxis_column}" 
+		--lcolumn="${legend_column}" 
+		--factor1="${factor.factor_column1}" 
+		--factor2="${factor.factor_column2}" 
+		--outdir="$htmlfile.files_path" 
+		--htmlfile='$htmlfile'
+    #end if
+ ]]> </command>
+
+ 
+  <inputs>
+
+    <param format="biom1" name="biom_input" type="data" label="BIOM file"/>
+    <param format="tabular" name="metadata_input" type="data" label="Metadata file"/>
+    <param name="xaxis_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used for X-axis"/>
+    <param name="legend_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as legend"/>
+    <conditional name="factor">
+      <param name="type" type="select" label="Is this one factor or two factor">
+              <option value="one">1</option>
+              <option value="two">2</option>
+      </param>
+      <when value="one">
+				<param name="factor_column1" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as factor 1"/>
+      </when>
+      <when value="two">
+				<param name="factor_column1" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as factor 1"/>
+				<param name="factor_column2" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as factor 2"/>
+      </when>
+    </conditional>
+
+  </inputs>
+ 
+  <outputs>
+        <data format="html" name="htmlfile" label="${tool.name}.html"/>
+  </outputs>
+
+  <tests>
+	 <test>
+	    <param name="biom_input" value="test.biom" ftype="biom1" />
+		<param name="metadata_input" value="metadata.txt"/>
+		<param name="xaxis_column" value="5" />
+		<param name="legend_column" value="3" />
+		<param name="type" value="1" />
+		<param name="factor_column1" value="4"/>
+		<output name="htmlfile" ftype="html" file="abundace_factor.html" />
+	</test>
+  </tests>
+
+  <help>
+**What it does**
+Creates an abundance barplot using an R package called phyloseq_.
+
+.. _phyloseq: https://joey711.github.io/phyloseq/plot_bar-examples.html
+
+-----
+
+**Input**
+
+
+- **BIOM file** - this is a BIOM_ file format
+- **Metadata file** - this is a metadata file of the experiment design
+- **Column used for X-axis** - The horizontal x-axis display on the barplot.
+- **Column used as legend** - select a group from the metadata to fill color to represent the group it belongs to.
+- **Is this one factor or two factor** - This is the facet_grid feature of phyloseq's plot_bar to allow plotting with two factors (e.g, facet_grid=~protein + allergy)
+- **Column used as factor 1** - select the first factor for facet_grid feature from the metadata file
+
+.. _BIOM: http://biom-format.org/
+
+-----
+
+=========
+Resources
+=========
+
+**Wrapper Authors**
+
+QFAB Bioinformatics (support@qfab.org)
+
+  </help>
+   <citations>
+	   <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
+	   <citation type="doi">doi:10.1186/2047-217X-1-7</citation>
+   </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abundace_factor.html	Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,9 @@
+<html><body>
+<table align="center">
+<tr>
+<td valign="middle" style="vertical-align:middle;">
+<a href="abundance.pdf"><img src="abundance.png"/></a>
+</td>
+</tr>
+</table>
+</html></body>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biom_out.html	Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,9 @@
+<html><body>
+<table align="center">
+<tr>
+<td valign="middle" style="vertical-align:middle;">
+<a href="pdffile.pdf"><img src="nmds.png" width="800" height="800"/></a>
+</td>
+</tr>
+</table>
+</html></body>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metadata.txt	Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,19 @@
+#SampleID	dpw	time	Food	Replicate_Group
+F3D0	0	Early	None	Group1
+F3D1	1	Early	None	Group1
+F3D2	2	Early	None	Group1
+F3D3	3	Early	Cheddar	Group2
+F3D5	5	Early	Cheddar	Group2
+F3D6	6	Early	Cheddar	Group2
+F3D7	7	Early	Swiss	Group3
+F3D8	8	Early	Swiss	Group3
+F3D9	9	Early	Swiss	Group3
+F3D141	141	Late	Cheddar	Group4
+F3D142	142	Late	Cheddar	Group4
+F3D143	143	Late	Cheddar	Group4
+F3D144	144	Late	None	Group5
+F3D145	145	Late	None	Group5
+F3D146	146	Late	None	Group5
+F3D147	147	Late	Swiss	Group6
+F3D148	148	Late	Swiss	Group6
+F3D149	149	Late	Swiss	Group6
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.biom	Mon Sep 14 08:02:08 2020 +0000
@@ -0,0 +1,1 @@
+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-09-08T01:49:15.647451","type": "OTU table","matrix_element_type": "float","shape": [5339, 18],"data": 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