Mercurial > repos > iuc > macs2
diff macs2_filterdup.xml @ 5:beb902da6e5f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
author | iuc |
---|---|
date | Sat, 08 Apr 2017 08:28:57 -0400 |
parents | bfe57d6e0c4c |
children | acbd3fb47f90 |
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--- a/macs2_filterdup.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_filterdup.xml Sat Apr 08 08:28:57 2017 -0400 @@ -6,29 +6,26 @@ <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> - <command> + <command><![CDATA[ macs2 filterdup - -i "${ infile }" - -o temp_outfile - + -i '${ infile }' + -o '${ outfile }' --format '${ infile.extension.upper() }' @effective_genome_size@ @tag_size@ - --pvalue "${ pvalue }" + --pvalue '${ pvalue }' #if str( $keep_dup_options.keep_dup_options_selector ) == "user": - --keep-dup "${ keep_dup_options.user_keepdup }" + --keep-dup '${ keep_dup_options.user_keepdup }' #else - --keep-dup "${ keep_dup_options.keep_dup_options_selector }" + --keep-dup '${ keep_dup_options.keep_dup_options_selector }' #end if - ; - mv temp_outfile "${ outfile }" + ]]> </command> <inputs> <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> <expand macro="conditional_effective_genome_size" /> <expand macro="tag_size" /> - <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="default: 1e-5 (--pvalue)" /> - + <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" /> <expand macro="keep_duplicates" /> </inputs> @@ -46,12 +43,15 @@ </test> </tests> <help> +<![CDATA[ **What it does** -Remove duplicate reads at the same position, then convert acceptable format to BED format. -filterdup tool from macs2 +This is **filterdup** utility from the MACS2_ Package. It removes duplicate reads and converts results to BED format. + +.. _MACS2: https://github.com/taoliu/MACS @citation@ +]]> </help> <expand macro="citations" /> </tool>