<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>