Mercurial > repos > iuc > macs2
diff macs2_predictd.xml @ 12:836578426f44 draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 24 Jan 2014 10:35:51 -0500 |
| parents | 97449a3c1f27 |
| children | d89001e78ee4 |
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--- a/macs2_predictd.xml Thu Jan 23 11:31:32 2014 -0500 +++ b/macs2_predictd.xml Fri Jan 24 10:35:51 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="macs2_predict" name="Predict" version="2.0.10.0"> - <description>d or fragment size from alignment results</description> +<tool id="macs2_predictd" name="MACS2 predictd" version="2.0.10.0"> + <description>Predict 'd' or fragment size from alignment results</description> <expand macro="requirements"> <requirement type="package" version="3.0.1">R_3_0_1</requirement> </expand> @@ -8,24 +8,19 @@ <import>macs2_macros.xml</import> </macros> <command> - macs2 predict - -i #echo ','.join($infiles)# + macs2 predictd + -i #echo ','.join( map( str, $infiles) )# --tsize $tsize @effective_genome_size@ --bw $band_width - --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi + --mfold $mfoldlo $mfoldhi > $outfile; Rscript predicted_model.R > $outfile_image </command> - <expand macro="stdio" /> + <expand macro="stdio" /> <inputs> - <repeat name="infiles" title="ChIP-seq alignment files" min="1" - help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command."> - - <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" /> - </repeat> - + <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" /> <expand macro="conditional_effective_genome_size" /> <expand macro="tag_size" /> @@ -55,12 +50,6 @@ Note that pair-end data is not supposed to work with this command. ------- - -**Citation** - -For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. - -Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org. +@citation@ </help> </tool>