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<tool id="knitrtest" name="testing knitr" version="0.0.1">
     Additional info: wrapper compatible with versions ..... 
    <description>
		for R scripts plugins.
    </description>
    
	<requirements>
		<requirement type="package" version="2.12">biocbasics</requirement>
		<requirement type="package" version="3.0.1">package_r3</requirement>
	</requirements>
    
    <command interpreter="sh">
		/usr/local/bin/R CMD BATCH ${runme}
    </command> 
   
    <inputs>
		<param format="tabular" name="counttable" type="data" label="Count table" help="Count table generated by HTSeq-count" /> 
		<param name="title" type="text" value="edgeR" size="80" label="Title for job outputs" help="Supply a meaningful name here to remind you what the outputs contain">
			<sanitizer invalid_char="">
				<valid initial="string.letters,string.digits"><add value="_" /> </valid>
			</sanitizer>
		</param>
		<param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
		<param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="counttable" numerical="True" 
         multiple="true" use_header_names="true" size="120" display="checkboxes">
			<validator type="no_options" message="Please select at least one column."/>
		</param>
		<param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
		<param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="counttable" numerical="True" 
         multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">
		</param>
		<param name="subjectids" type="text" optional="true" size="120" value = ""
       label="IF SUBJECTS NOT ALL INDEPENDENT! Enter integers to indicate sample pairing for every column in count table"
       help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter '1,2,1,2'">
			<sanitizer>
				<valid initial="string.digits"><add value="," /> </valid>
			</sanitizer>
		</param>
		<param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs"
			help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/>
		<param name="useNDF" type="boolean" truevalue="T" checked='false' falsevalue="" size="1" label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples"
			help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/>
		<param name="priordf" type="integer" value="20" size="3" label="prior.df for tagwise dispersion - lower value = more emphasis on each tag's variance. Replaces prior.n  and prior.df = prior.n * residual.df"
			help="Zero = Use edgeR default. Use a small value to 'smooth' small samples. See edgeR docs and note below"/>
		<param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
			help="Conventional default value of 0.05 recommended"/>
		<param name="fdrtype" type="select" label="FDR (Type II error) control method" 
			help="Use fdr or bh typically to control for the number of tests in a reliable way">
            <option value="fdr" selected="true">fdr</option>
            <option value="BH">Benjamini Hochberg</option>
            <option value="BY">Benjamini Yukateli</option>
            <option value="bonferroni">Bonferroni</option>
            <option value="hochberg">Hochberg</option>
            <option value="holm">Holm</option>
            <option value="hommel">Hommel</option>
            <option value="none">no control for multiple tests</option>
		</param>
    </inputs>

    <outputs>
		<data format="tabular" name="outtab" label="${title}.xls"/>
		<data format="html" name="html_file" label="${title}.html"/>		
    </outputs>

<configfiles>
	<configfile name="inputscript">	
Differential expression analysis
================================

Loading the R environment
```{r}
# Original edgeR code by: S.Lunke and A.Kaspi
reallybig = log10(.Machine\$double.xmax)
reallysmall = log10(.Machine\$double.xmin)
library('stringr')
library('gplots')
library('DESeq')
library('edgeR')
```

Reading count table from parameters
```{r}
filename="$counttable"
raw_counts = read.csv(filename, header=TRUE, stringsAsFactors=F)
```

And printing the count table
```{r}
head(raw_counts)
```

End of markdown script.
	</configfile>
	<configfile name="runme">
		require(knitr)
		require(markdown)
		knit("${inputscript}", "test.md")
		markdownToHTML("test.md", "${html_file}")
	</configfile>
</configfiles> 

    <tests>
    </tests>

    <help>
**knitr test**
Testing whether two config files can be nested.
    </help>
</tool>