Mercurial > repos > dpryan79 > data_manager_star_index_builder

diff data_manager/macros.xml @ 7:6f9dd98d641a draft

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author dpryan79
date Tue, 18 Apr 2017 14:32:58 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/macros.xml	Tue Apr 18 14:32:58 2017 -0400
@@ -0,0 +1,20 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.5.2b">star</requirement>
+            <requirement type="package" version="0.1.19">samtools</requirement>
+        </requirements>
+    </xml>
+    <token name="@FASTQ_GZ_OPTION@">
+        --readFilesCommand zcat
+    </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/bts635</citation>
+        </citations>
+    </xml>
+    <xml name="@SJDBOPTIONS@">
+         <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="true" help="Exon junction information for mapping splices"/>
+         <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
+    </xml>
+</macros>