Mercurial > repos > kevyin > homer
comparison annotatePeaks.xml @ 12:4356089c8e7f draft
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| author | kevyin |
|---|---|
| date | Mon, 17 Dec 2012 00:25:28 -0500 |
| parents | |
| children |
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| 11:83dffd6d7733 | 12:4356089c8e7f |
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| 1 <tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.4"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="4.1">homer</requirement> | |
| 4 </requirements> | |
| 5 <description></description> | |
| 6 <!--<version_command></version_command>--> | |
| 7 <command> | |
| 8 annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated | |
| 9 2> $out_log || echo "Error running annotatePeaks." >&2 | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param format="tabular,bed" name="input_bed" type="data" label="Homer peaks OR BED format"/> | |
| 13 <param name="genome_selector" type="select" label="Genome version"> | |
| 14 <option value="hg19" selected="true">hg19</option> | |
| 15 </param> | |
| 16 <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options"> | |
| 17 <sanitizer> | |
| 18 <valid initial="string.printable"> | |
| 19 <remove value="'"/> | |
| 20 <remove value="/"/> | |
| 21 </valid> | |
| 22 <mapping initial="none"> | |
| 23 <add source="'" target="__sq__"/> | |
| 24 </mapping> | |
| 25 </sanitizer> | |
| 26 </param> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <!--<data format="html" name="html_outfile" label="index" />--> | |
| 30 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> | |
| 31 <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" /> | |
| 32 <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.log" /> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 <test> | |
| 36 <!--<param name="input_file" value="extract_genomic_dna.fa" />--> | |
| 37 <!--<output name="html_file" file="sample_output.html" ftype="html" />--> | |
| 38 </test> | |
| 39 </tests> | |
| 40 | |
| 41 <help> | |
| 42 | |
| 43 .. class:: infomark | |
| 44 | |
| 45 **Homer annoatePeaks** | |
| 46 | |
| 47 More information on accepted formats and options | |
| 48 | |
| 49 http://biowhat.ucsd.edu/homer/ngs/annotation.html | |
| 50 | |
| 51 TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format. | |
| 52 | |
| 53 </help> | |
| 54 </tool> | |
| 55 |