Mercurial > repos > avowinkel > gatk
comparison base_recalibrator.xml @ 0:b80ff7f43ad1 draft default tip
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
| author | avowinkel |
|---|---|
| date | Thu, 24 Sep 2015 12:10:01 -0400 |
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| children |
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| -1:000000000000 | 0:b80ff7f43ad1 |
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| 1 <macros> | |
| 2 <xml name="BaseRecalibratorParameters" tokens="tag"> | |
| 3 | |
| 4 <expand macro="macro_bam_input" tag="@TAG@" /> | |
| 5 | |
| 6 <param name="knownSites" type="data" format="vcf,bcf,bed,pileup,tabular,table" label="Database of known Sites (ROD files; e.g. VCF format)" multiple="true" title="A database of known polymorphic sites to skip over in the recalibration algorithm" help="-knownSites,‑‑knownSites &lt;knownSites&gt;" /> | |
| 7 | |
| 8 </xml> | |
| 9 | |
| 10 <xml name="BaseRecalibratorOutput"> | |
| 11 <data format="tabular" name="br_table" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (Table)"> | |
| 12 <yield /> | |
| 13 </data> | |
| 14 </xml> | |
| 15 | |
| 16 <template name="BaseRecalibratorPreprocessing"> | |
| 17 <![CDATA[ | |
| 18 @token_bam_input_pre@ | |
| 19 #for $i, $variant in enumerate($analysis_type.knownSites): | |
| 20 ln -s -f ${variant} variant_${i}.vcf && | |
| 21 #end for | |
| 22 ]]> | |
| 23 </template> | |
| 24 | |
| 25 <template name="BaseRecalibratorOptions"> | |
| 26 <![CDATA[ | |
| 27 --out ${br_table} | |
| 28 | |
| 29 @token_bam_input@ | |
| 30 | |
| 31 #for $i, $variant in enumerate($analysis_type.knownSites): | |
| 32 --knownSites variant_${i}.vcf | |
| 33 #end for | |
| 34 ]]> | |
| 35 </template> | |
| 36 </macros> | |
| 37 | |
| 38 |