<tool id="i_adhore" name="i-adhore" version="0.1">
	<requirements>
		<requirement type="package" version="1.19.2.1">pandoc</requirement>
		<requirement type="package" version="1.20.0">r-getopt</requirement>
		<requirement type="package" version="1.2">r-rmarkdown</requirement>
		<requirement type="package" version="1.8.4">r-plyr</requirement>
		<requirement type="package" version="0.5.0">r-dplyr</requirement>
	</requirements>
	<description>Generate i-adhore configure file</description>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command><![CDATA[

    	Rscript '${__tool_directory__}/i_adhore_configure_render.R'

    		## 1. input data
    		-e $echo

			#set $g_analysis_files = ''
			#for $g in $genomes
				#if str($g.genome_name)
					#set $analysis_files = []
					#for $file in $g.analysis_files.to_dataset_instances($g.analysis_files)
						#set $analysis_files += [$file.__str__]
					#end for
					#set g_analysis_files += str($g.genome_name) + ':' + ','.join($analysis_files) + ';'
				#end if
			#end for
			-G '$g_analysis_files'

    		-b $blast_table
    		-g $gap_size
    		-c $cluster_gap
    		-q $q_value
    		-p $prob_cutoff
    		-a $anchor_points
    		-m $alignment_method
    		-l $level2only
    		-T $table_type
    		-h $multi_hypothesis_correction

    		## 2. output report and file directory
    		-x $i_adhore_configure_txt
    		-o $i_adhore_configure
    		-d $i_adhore_configure.files_path

    		## 3. Rmd templates in the tool directory
    		-t '${__tool_directory__}/i_adhore_configure.Rmd'


    ]]></command>
	<inputs>
		<repeat name="genomes" title="genome" min="1">
			<param name="genome_name" type="text" value="" label="Specify genome name" />
			<param name="analysis_files" type="data" format="txt" multiple="true" label="analysis files (.lst or .txt files)" />
		</repeat>
		<param name="blast_table" type="data" format="csv" multiple="false" label="blast table (.csv file)" />
		<param name="gap_size" type="text" value="30" label="gap size" />
		<param name="cluster_gap" type="text" value="35" label="cluster gap" />
		<param name="q_value" type="text" value="0.75" label="q value" />
		<param name="prob_cutoff" type="text" value="0.01" label="probability cutoff" />
		<param name="anchor_points" type="text" value="3" label="anchor_points" />
		<param name="alignment_method" type="text" value="gg4" label="alignment method" />
		<param name="level2only" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="level 2 only" />
		<param name="table_type" type="text" value="family" label="table type" />
		<param name="multi_hypothesis_correction" type="text" value="FDR" label="multiple hypothesis correction" />

		<param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
	</inputs>
	<outputs>
		<data name="i_adhore_configure" format="html" label="i-adhore configure report" />
		<data name="i_adhore_configure_txt" format="txt" label="i-adhore configure file" />
	</outputs>
	<citations>
		<citation type="bibtex">
			@article{allaire2016rmarkdown,
			title={rmarkdown: Dynamic Documents for R, 2016},
			author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
			journal={R package version 0.9},
			volume={6},
			year={2016}
			}
		</citation>
		<citation type="bibtex">
			@book{xie2015dynamic,
			title={Dynamic Documents with R and knitr},
			author={Xie, Yihui},
			volume={29},
			year={2015},
			publisher={CRC Press}
			}
		</citation>
		<citation type="bibtex">
			@book{xie2015dynamic,
			title={Dynamic Documents with R and knitr},
			author={Xie, Yihui},
			volume={29},
			year={2015},
			publisher={CRC Press}
			}
		</citation>
	</citations>
</tool>