# HG changeset patch # User jackcurragh # Date 1653650754 0 # Node ID cb676890d6f871dbb110f5de8082ab0bd6e57179 # Parent a48ca51cb2de8ac270f0310a319bd46cdd010238 Deleted selected files diff -r a48ca51cb2de -r cb676890d6f8 bedtools_genomecov/genomeCoverageBed.xml --- a/bedtools_genomecov/genomeCoverageBed.xml Fri May 27 10:04:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,170 +0,0 @@ - - Compute Read Coverage Over An Entire Genome - - macros.xml - - - - - '$output' - ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r a48ca51cb2de -r cb676890d6f8 bedtools_genomecov/macros.xml --- a/bedtools_genomecov/macros.xml Fri May 27 10:04:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,266 +0,0 @@ - - - - bedtools - - - - - - bedtools - - - 2.30.0 - 1.9 - bed,bedgraph,gff,vcf,encodepeak - BED/bedGraph/GFF/VCF/EncodePeak - 20.05 - - - - - - - - - - bedtools --version - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -#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 - - -#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 - - -#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 - - -#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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -`_ -]]> - - - - 10.1093/bioinformatics/btq033 - - - - diff -r a48ca51cb2de -r cb676890d6f8 bedtools_genomecov/test-data/genomeCoverageBed1.bed --- a/bedtools_genomecov/test-data/genomeCoverageBed1.bed Fri May 27 10:04:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -chr1 10 20 -chr1 20 30 -chr2 0 500 diff -r a48ca51cb2de -r cb676890d6f8 bedtools_genomecov/test-data/genomeCoverageBed1.len --- a/bedtools_genomecov/test-data/genomeCoverageBed1.len Fri May 27 10:04:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -chr1 1000 -chr2 500 diff -r a48ca51cb2de -r cb676890d6f8 bedtools_genomecov/test-data/genomeCoverageBed_result1.bed --- a/bedtools_genomecov/test-data/genomeCoverageBed_result1.bed Fri May 27 10:04:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -chr1 0 1000 1000 1 -chr2 0 500 500 1 -genome 0 1500 1500 1 diff -r a48ca51cb2de -r cb676890d6f8 bedtools_genomecov/tool_data_table_conf.xml.sample --- a/bedtools_genomecov/tool_data_table_conf.xml.sample Fri May 27 10:04:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ - - - - value, dbkey, name, path - -
- - - value, dbkey, name, path - -
- - - value, name, len_path - -
-
diff -r a48ca51cb2de -r cb676890d6f8 bedtools_genomecov/tool_data_table_conf.xml.test --- a/bedtools_genomecov/tool_data_table_conf.xml.test Fri May 27 10:04:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ - - - - value, dbkey, name, path - -
- - - value, dbkey, name, path - -
- - - value, name, len_path - -
-