annotate i-adhore.xml @ 15:0927e9c47b6e draft default tip

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 5fbff2ffc492ba5f6fbcbc05322dd47a8738ca6c-dirty

<tool id="i_adhore" name="i-adhore" version="0.1">
	<requirements>
		<requirement type="package" version="1.15.0.6-0">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>
		<requirement type="package" version="0.3.5">r-htmltools</requirement>
	</requirements>
	<description>Detect genomic homology</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>
	<help>
		This tool is a wrapper of the i-ADHoRe sofeware. To use this tool, you will need to have i-ADHoRe installed.
		This tool automatically detects genomic regions with statistically significant conserved gene content and order.
		Therefore, this tool can be used for analyses within one genome (to look for paralogous regions with duplicated
		genes) or for comparisons between genomes of different organisms (to look for colinearity). The algorithm was
		especially designed to cope with micro-rearrangements (events frequently observed within different plant
		lineages), since these greatly complicate the search for colinear regions.
	</help>
	<citations>
		<citation type="bibtex">
			@article{proost2011adhore,
			title={i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets},
			author={Proost, Sebastian and Fostier, Jan and De Witte, Dieter and Dhoedt, Bart and Demeester, Piet and Van de Peer, Yves and Vandepoele, Klaas},
			journal={Nucleic acids research},
			volume={40},
			number={2},
			pages={e11--e11},
			year={2011},
			publisher={Oxford University Press}
			}
		</citation>
		<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>
	</citations>
</tool>