# HG changeset patch
# User iuc
# Date 1611325923 0
# Node ID 6184cfc70e28aa71cf7816f9f6b5bf8d472297f0
# Parent 9919057a466c1d2408f163ffcde903e7fc8fec3d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
diff -r 9919057a466c -r 6184cfc70e28 filter.xml
--- a/filter.xml Thu Oct 29 20:50:57 2020 +0000
+++ b/filter.xml Fri Jan 22 14:32:03 2021 +0000
@@ -8,12 +8,12 @@
'sample.bcf.gz' &&
- bcftools index 'sample.bcf.gz' &&
+#if $input.is_of_type('vcf')
+ bcftools view -Ob '$input' > 'input.bcf.gz' &&
+ bcftools index 'input.bcf.gz' &&
#else
- ln -s '${samples}' 'sample.bcf.gz' &&
- ln -s '${samples.metadata.bcf_index}' 'sample.bcf.gz.csi' &&
+ ln -s '${input}' 'input.bcf.gz' &&
+ ln -s '${input.metadata.bcf_index}' 'input.bcf.gz.csi' &&
#end if
## run
@@ -31,38 +31,37 @@
--samples '$sv.mode_cond.samples'
--coverage $sv.mode_cond.coverage
--controlcontamination $sv.mode_cond.controlcontamination
-#end if
## germline options
-#if $sv.mode_cond.mode_sel == 'germline'
+#else if $sv.mode_cond.mode_sel == 'germline'
--gq $sv.mode_cond.gq
--rddel $sv.mode_cond.rddel
--rddup $sv.mode_cond.rddup
#end if
-## samples
-'sample.bcf.gz' ## input
+## input
+'input.bcf.gz'
## postprocessing
@LOG@
@VCF@
]]>
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@@ -72,23 +71,23 @@
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@@ -137,6 +136,11 @@
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@@ -200,6 +199,11 @@
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