# HG changeset patch
# User iuc
# Date 1485884671 18000
# Node ID f6a06fcdebdc8b368050806db39d85690abdafe4
# Parent b8e20c8b4caad539c01ed2d297c97dba9e633aa9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
diff -r b8e20c8b4caa -r f6a06fcdebdc macros.xml
--- a/macros.xml Mon Oct 03 12:15:38 2016 -0400
+++ b/macros.xml Tue Jan 31 12:44:31 2017 -0500
@@ -14,14 +14,16 @@
bcftools
htslib
+
samtools
bcftools 2>&1 | grep 'Version:'
-
+
10.1093/bioinformatics/btp352
@@ -45,20 +47,20 @@
$input_vcf &&
bcftools index $input_vcf &&
-#elif $input_file.datatype.file_ext == 'vcf_bgzip'
+#elif $input_file.is_of_type('vcf_bgzip')
ln -s "$input_file" $input_vcf
-#elif $input_file.datatype.file_ext == 'bcf'
+#elif $input_file.is_of_type('bcf')
#set $input_vcf = 'input.bcf'
- ln -s "$input_file" $input_vcf &&
+ ln -s "$input_file" $input_vcf &&
#if $input_file.metadata.bcf_index:
ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
- #else
+ #else
bcftools index $input_vcf &&
#end if
-#elif $input_file.datatype.file_ext == 'bcf_bgzip'
+#elif $input_file.is_of_type('bcf_bgzip')
ln -s "$input_file" $input_vcf
#end if
]]>
@@ -77,21 +79,21 @@
#set $vcfs_list_file = 'vcfs_list'
#for (i,input_file) in enumerate($input_files):
#set $input_vcf = 'input' + str($i) + '.vcf.gz'
- #if $input_file.datatype.file_ext == 'vcf'
+ #if $input_file.is_of_type('vcf')
bgzip -c "$input_file" > $input_vcf &&
bcftools index $input_vcf &&
- #elif $input_file.datatype.file_ext == 'vcf_bgz'
+ #elif $input_file.is_of_type('vcf_bgz')
ln -s "$input_file" $input_vcf
- #elif $input_file.datatype.file_ext == 'bcf'
+ #elif $input_file.is_of_type('bcf')
#set $input_vcf = 'input' + str($i) + '.bcf.gz'
## bgzip -c "$input_file" > $input_vcf &&
ln -s "$input_file" $input_vcf &&
#if $input_file.metadata.bcf_index:
ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
- #else
+ #else
bcftools index $input_vcf &&
#end if
- #elif $input_file.datatype.file_ext == 'bcfvcf_bgz'
+ #elif $input_file.is_of_type('bcfvcf_bgz')
ln -s "$input_file" $input_vcf &&
#end if
echo '$input_vcf' >> $vcfs_list_file &&
@@ -225,7 +227,7 @@
-
^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$
@@ -272,7 +274,7 @@
-
^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$
@@ -299,7 +301,7 @@
$targets_path &&
@@ -331,7 +333,7 @@
-
^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$
@@ -358,15 +360,15 @@
-
^(\w+(,\w+)*)?$
-
-
-
@@ -416,7 +418,7 @@
-
^([^,]+(,[^,]+)*)?$
@@ -443,7 +445,7 @@
Output Type
-----------
-Output compressed BCF (b), or uncompressed VCF (v).
+Output compressed BCF (b), or uncompressed VCF (v).
Use the BCF option when piping between bcftools subcommands to speed up
performance by removing unecessary compression/decompression
and VCF<->BCF conversion.