add draft batch wrapper

wrapper/wrapper_batch.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+rmthis=`ls`
+echo ${rmthis}
+
+ARGS="${refgen} ${indpre} ${refann} ${input1} ${input2} ${input3} ${input3} ${input4} ${input5} ${input6} ${input7} ${input8} ${maskfile_links} ${maskfile_diff} ${insertsize} ${stdev} ${discalign} ${mixalign} ${libtype} ${sensitivity} ${fastqscale} ${minanchor} ${minintron_tophat} ${maxintron_tophat} ${maxalign} ${minreadlength} ${usegtf} ${userescue} ${lab1} ${lab2} ${lab3} ${lab4} ${maxit} ${idpre} ${isofrac} ${intraintrtresh} ${maxintron_cufflinks} ${minintron_cufflinks} ${junctionalpha} ${anchfrac} ${mintransfrag} ${termexonmax} ${trimcovavg} ${trimfrac} ${transfraggap} ${transfraggap} ${userescuecd} ${testalign} ${testfdr} ${normalhits} "
+INPUTS="${refgen} ${refann} ${input1} ${input2} ${input3} ${input4} ${input5} ${input6} ${input7} ${input8} ${maskfile_links} ${maskfile_diff}"
+
+echo ${ARGS};
+
+docker run cyverseuk/tuxedo ${ARGS};
+
+rmthis=`echo ${rmthis} | sed s/.*\.out// -`
+rmthis=`echo ${rmthis} | sed s/.*\.err// -`
+rm --verbose ${rmthis}