<tool id="phyloseq_net" name="Phyloseq Network Plot" version="1.24.2" hidden="false">
  <description>Phyloseq Network Plot</description>
  <requirements>
        <requirement type="package" version="3.4.1">r-base</requirement>
        <requirement type="package" version="1.24.2">bioconductor-phyloseq</requirement>
		<requirement type="package" version="1.20.0">bioconductor-deseq2</requirement>
		<requirement type="package" version="1.10.4">r-data.table</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_net.r'
    #if str($file_source.file_source_selector) == "set_biom":
        --infile='$input' 
        --metafile='$metadata_input' 
        --biom="${file_source.file_source_selector}" 
        --xcolumn="${xaxis_column}" 
        --lcolumn="${legend_column}" 
        --outdir="$htmlfile.files_path" 
        --htmlfile='$htmlfile'
    #else:
        --infile='$input' 
        --metafile='$metadata_input' 
        --biom="${file_source.file_source_selector}" 
        --obsfile="${file_source.obstable}" 
        --norm="${file_source.norm_bool}" 
        --xcolumn="${xaxis_column}" 
        --lcolumn="${legend_column}" 
        --outdir="$htmlfile.files_path" 
        --htmlfile='$htmlfile'
    #end if
  ]]></command>
 
  <inputs>

    <conditional name="file_source">
      <param name="file_source_selector" type="select" label="Choose a file type">
	<option value="set_biom" selected="True"> BIOM File</option>
	<option value="set_table"> Count File </option>
      </param>
      <when value="set_biom">
	 <param format="biom1" name="input" type="data" label="Input File"/>

      </when>
      <when value="set_table">
	<param format="tabular" name="input" type="data" label="Input File"/>
	<param format="tabular" name="obstable" type="data" label="Observation file"/>
	<param name="norm_bool" type="boolean" truevalue="true" falsevalue="false" checked="false" label="is the data normalised?"/>
      </when>
    </conditional>
    <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="Select a group for distance matrix"/>
    <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>  <!-- Test #1: Test BIOM format input -->
	 		<!-- <conditional name="file_source"> -->
				<param name="file_source_selector" value="set_biom"/>
				<param name="input" value="GP.biom" ftype="biom1" />
				<param name="norm_bool" value="true"/>
				<param name="metadata_input" value="metadata.txt" ftype="tabular"/>
				<param name="xaxis_column" value="5" />
				<param name="legend_column" value="4" />
			<!-- </conditional>-->
			 <output name="htmlfile" ftype="html" file="biom_out.html" />
	 </test>
	 <test>  <!-- Test #2: Test TABULAR format inputs -->
	 		<!-- <conditional name="file_source"> -->
				 <param name="file_source_selector" value="set_table" />
				 <param name="input" value="count.txt" ftype="tabular" />
				 <param name="obstable" value="observation.txt" ftype="tabular" />
				 <param name="metadata_input" value="metadata.txt" ftype="tabular" />
				 <param name="norm_bool" value="true" />
				 <param name="xaxis_column" value="5" />
				 <param name="legend_column" value="4" />
			<!-- </conditional> -->
			<output name="htmlfile" ftype="html" file="test.html" />
	 </test>
  </tests>

  <help>
**What it does**
Creates a correlation network plot between samples using an R package called phyloseq_.

.. _phyloseq: https://joey711.github.io/phyloseq/plot_network-examples.html

-----

**Input**


- **Choose a file type** - choose the input file type (e.g., BIOM or count table)
- **Input file** - choose the input file
- **Observation** - appear only if the "count table" selected in "choose a file type"
- **is the data normalised** - appear only if the "count table" selected in "choose a file type"
- **Select a group for distance matrix** - This group will be used to calculate the distance matrix
- **Column used as legend** - select a group from the metadata for legend


.. _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="dio">doi:10.1186/2047-217X-1-7</citation>
  </citations>

</tool>