Mercurial > repos > sanbi-uwc > shapeit_phase

comparison shapeit_phase.xml @ 10:03af7e3e3b2f draft

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planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
author sanbi-uwc
date Tue, 18 Sep 2018 01:54:33 -0400
parents 9f7a81693561
children f25ff17454f4
comparison
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9:9f7a81693561 10:03af7e3e3b2f
1 <tool id="shapeit_phase" name="shapeit_phase" version="0.8.0"> 1 <tool id="shapeit_phase" name="shapeit_phase" version="0.9.0">
2 <description>genomic data with or without reference panel</description> 2 <description>genomic data with or without reference panel</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.r837">shapeit</requirement> 5 <requirement type="package" version="2.r837">shapeit</requirement>
6 </requirements> 6 </requirements>
24 if [ -f "\$HAP" ] ; then 24 if [ -f "\$HAP" ] ; then
25 echo "Failed to find valid .hap file at \$HAP" >&2 && 25 echo "Failed to find valid .hap file at \$HAP" >&2 &&
26 exit 1 ; 26 exit 1 ;
27 fi && 27 fi &&
28 LEGEND="\${REF_DIR}/\${REF_PREFIX}\${PART}.legend.gz" && 28 LEGEND="\${REF_DIR}/\${REF_PREFIX}\${PART}.legend.gz" &&
29 if [ -f "\$LEGEND ] ; then 29 if [ -f "\$LEGEND" ] ; then
30 echo "Failed to find valid .legend file at \$LEGEND" >&2 && 30 echo "Failed to find valid .legend file at \$LEGEND" >&2 &&
31 exit 1 ; 31 exit 1 ;
32 fi && 32 fi &&
33 MAP_PREFIX='${use_genetic_map.genetic_map_from_table.map_from_table.fields.map_prefix}' && 33 MAP_PREFIX='${use_genetic_map.genetic_map_from_table.map_from_table.fields.map_prefix}' &&
34 MAP=`ls \${REF_DIR}/\${MAP_PREFIX}\${PART}_*` && 34 MAP=`ls \${REF_DIR}/\${MAP_PREFIX}\${PART}_*` &&