# HG changeset patch
# User jackcurragh
# Date 1653651225 0
# Node ID 3aa9416cc3b315b69a9b64bd4cd64c37c1052017
# Parent 79c0c6042954ed5bfb1c0703231efacd376638ee
Uploaded
diff -r 79c0c6042954 -r 3aa9416cc3b3 bedtools_genomecov/genomeCoverageBed.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bedtools_genomecov/genomeCoverageBed.xml Fri May 27 11:33:45 2022 +0000
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+ Compute Read Coverage Over An Entire Genome
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+ macros.xml
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+ '$output'
+ ]]>
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diff -r 79c0c6042954 -r 3aa9416cc3b3 bedtools_genomecov/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bedtools_genomecov/macros.xml Fri May 27 11:33:45 2022 +0000
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+ bedtools
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+ bedtools
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+ 2.30.0
+ 1.9
+ bed,bedgraph,gff,vcf,encodepeak
+ BED/bedGraph/GFF/VCF/EncodePeak
+ 20.05
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+ bedtools --version
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+#if $genome_file_opts.genome
+ -g
+ #if $genome_file_opts.genome_file_opts_selector == "loc":
+ '$genome_file_opts.genome.fields.len_path'
+ #elif $genome_file_opts.genome_file_opts_selector == "hist":
+ '$genome_file_opts.genome'
+ #end if
+#end if
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+
+#if $type.type_select == "genome":
+ #if $type.genome_file_opts.genome_file_opts_selector == "loc":
+ -g '$type.genome_file_opts.genome.fields.len_path'
+ #elif $type.genome_file_opts.genome_file_opts_selector == "hist":
+ -g '$type.genome_file_opts.genome'
+ #end if
+#end if
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+
+#if $empty.empty_selector == "-empty":
+ #if $empty.genome_file_opts.genome_file_opts_selector == "loc":
+ -g '$empty.genome_file_opts.genome.fields.len_path'
+ #elif $empty.genome_file_opts.genome_file_opts_selector == "hist":
+ -g '$empty.genome_file_opts.genome'
+ #end if
+#end if
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+
+#if $input_type.input_type_select == "bam":
+ -ibam '$input_type.input'
+#else:
+ -i '$input_type.input'
+ #if $input_type.genome_file_opts.genome_file_opts_selector == "loc":
+ -g '$input_type.genome_file_opts.genome.fields.len_path'
+ #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist":
+ -g '$input_type.genome_file_opts.genome'
+ #end if
+#end if
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+ #set $col = list()
+ #set $op = list()
+ #for $item in $c_and_o_argument_repeat:
+ #silent $col.append( str($item.col) )
+ #silent $op.append( str($item.operation) )
+ #end for
+ #if $col:
+ -c #echo ','.join($col)#
+ -o #echo ','.join($op)#
+ #end if
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+`_
+]]>
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+ 10.1093/bioinformatics/btq033
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diff -r 79c0c6042954 -r 3aa9416cc3b3 bedtools_genomecov/test-data/genomeCoverageBed1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bedtools_genomecov/test-data/genomeCoverageBed1.bed Fri May 27 11:33:45 2022 +0000
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+chr1 10 20
+chr1 20 30
+chr2 0 500
diff -r 79c0c6042954 -r 3aa9416cc3b3 bedtools_genomecov/test-data/genomeCoverageBed1.len
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bedtools_genomecov/test-data/genomeCoverageBed1.len Fri May 27 11:33:45 2022 +0000
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+chr1 1000
+chr2 500
diff -r 79c0c6042954 -r 3aa9416cc3b3 bedtools_genomecov/test-data/genomeCoverageBed_result1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bedtools_genomecov/test-data/genomeCoverageBed_result1.bed Fri May 27 11:33:45 2022 +0000
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+chr1 0 1000 1000 1
+chr2 0 500 500 1
+genome 0 1500 1500 1
diff -r 79c0c6042954 -r 3aa9416cc3b3 bedtools_genomecov/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bedtools_genomecov/tool_data_table_conf.xml.sample Fri May 27 11:33:45 2022 +0000
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+ value, dbkey, name, path
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+ value, dbkey, name, path
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+ value, name, len_path
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diff -r 79c0c6042954 -r 3aa9416cc3b3 bedtools_genomecov/tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bedtools_genomecov/tool_data_table_conf.xml.test Fri May 27 11:33:45 2022 +0000
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+ value, dbkey, name, path
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+ value, dbkey, name, path
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+ value, name, len_path
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