diff phyloseq_richness.xml @ 0:0ab4501d805b draft

"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_richness.xml	Mon Sep 14 07:38:57 2020 +0000
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+<tool id="phyloseq_richness" name="Phyloseq Richness" version="1.22.3.2" hidden="false">
+  <description>Phyloseq Richness Plot</description>
+     <requirements>
+	         <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_richness.r' 
+			--biomfile='$biom_input' 
+			--metafile='$metadata_input' 
+			--xcolumn="${xaxis_column}" 
+			--lcolumn="${legend_column}" 
+			--outdir="$htmlfile.files_path" 
+			--htmlfile='$htmlfile'
+  ]]></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"/>
+  </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="4" />
+		<output name="htmlfile" ftype="html" file="biom_out.html" />
+	</test>
+ </tests>
+
+
+  <help>
+**What it does**
+Creates an alpha biodivesrsity abundance plot using an R package called phyloseq_.
+
+.. _phyloseq: https://joey711.github.io/phyloseq/plot_richness-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.
+
+.. _BIOM: http://biom-format.org/
+
+-----
+
+=========
+Resources
+=========
+
+**Wrapper Authors**
+
+QFAB Bioinformatics ([e-mail])
+ 
+  </help>
+    <citations>
+	    <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
+		<citation type="doi">doi:10.1186/2047-217X-1-7</citation>
+	</citations>
+ -----
+ 
+  </help>
+</tool>