Mercurial > repos > kevyin > homer
changeset 12:1bce61936d45 draft
Uploaded
| author | kevyin |
|---|---|
| date | Thu, 01 Nov 2012 23:05:53 -0400 |
| parents | 31b95602305d |
| children | 106c7c3720aa |
| files | annotatePeaks.xml |
| diffstat | 1 files changed, 41 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annotatePeaks.xml Thu Nov 01 23:05:53 2012 -0400 @@ -0,0 +1,41 @@ +<tool id="homer-annotate-peaks" name="annotate-peaks" version="0.0.1"> + <requirements> + <requirement type="package">homer</requirement> + </requirements> + <description></description> + <!--<version_command></version_command>--> + <command> + annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated + 2> $out_log || echo "Error running annotatePeaks." >&2 + </command> + <inputs> + <param format="tabular,bed" name="input_bed" type="data" label="Intervals in BED format" /> + <param name="genome_selector" type="select" label="Genome version"> + <option value="hg19" selected="true">hg19</option> + </param> + </inputs> + <outputs> + <!--<data format="html" name="html_outfile" label="index" />--> + <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> + <data format="csv" name="out_annotated" label="Annotated" /> + <data format="txt" name="out_log" label="homer_annotatePeaks.log" /> + </outputs> + <tests> + <test> + <!--<param name="input_file" value="extract_genomic_dna.fa" />--> + <!--<output name="html_file" file="sample_output.html" ftype="html" />--> + </test> + </tests> + + <help> + + .. class:: infomark + + **Homer annoatePeaks** + More information on accepted formats + http://biowhat.ucsd.edu/homer/ngs/annotation.html + + + </help> +</tool> +