# HG changeset patch
# User yating-l
# Date 1494961847 14400
# Node ID 4dfdf2090b35817233c23d257092edb7217f0cfa
planemo upload
diff -r 000000000000 -r 4dfdf2090b35 test-data/contigs.2bit
Binary file test-data/contigs.2bit has changed
diff -r 000000000000 -r 4dfdf2090b35 test-data/contigs_chromInfo.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs_chromInfo.tab Tue May 16 15:10:47 2017 -0400
@@ -0,0 +1,2 @@
+contig12 56019
+contig10 43013
diff -r 000000000000 -r 4dfdf2090b35 test-data/contigs_gaps.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs_gaps.bed Tue May 16 15:10:47 2017 -0400
@@ -0,0 +1,4 @@
+contig10 16942 16962 gap_0
+contig12 18710 18730 gap_1
+contig12 29582 29904 gap_2
+contig12 30821 30841 gap_3
diff -r 000000000000 -r 4dfdf2090b35 test-data/contigs_no_Ns_chromInfo.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs_no_Ns_chromInfo.tab Tue May 16 15:10:47 2017 -0400
@@ -0,0 +1,2 @@
+contig12 55657
+contig10 42993
diff -r 000000000000 -r 4dfdf2090b35 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue May 16 15:10:47 2017 -0400
@@ -0,0 +1,57 @@
+
+
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+ http://old-gep.wustl.edu/~wilson/packages/ucsc_twobit/ucsc_twobit_340_macOS_x86_64.tar.gz
+
+
+ bin
+ $INSTALL_DIR/bin
+
+
+
+
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+ http://old-gep.wustl.edu/~wilson/packages/ucsc_twobit/ucsc_twobit_340_linux_x86_64.tar.gz
+
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+ bin
+ $INSTALL_DIR/bin
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+
+
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+
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+ echo "ERROR: This package only supports 64-bit systems running macOS or Linux"
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+ false
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+
+
+
+ $INSTALL_DIR/bin
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+
+
+
+ `_.
+ The utilities were created by the
+ `Genome Bioinformatics Group `_
+ at the UCSC Genomics Institute.
+
+ The twoBit file format is designed to store genomic sequences and the
+ associated repeat masking information. The twoBit file is used by the
+ UCSC Genome Browser and by tools such as
+ `BLAT `_.
+ ]]>
+
+
+
diff -r 000000000000 -r 4dfdf2090b35 twobit_info.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/twobit_info.xml Tue May 16 15:10:47 2017 -0400
@@ -0,0 +1,94 @@
+
+
+ Get sequence information from a twoBit file
+
+
+ ucsc_macros.xml
+
+
+
+
+
+ "${output}"
+ #else:
+ twoBitInfo -nBed "${twobit_input}" stdout |
+ sort -k 1,1 -k 2,2n |
+ awk 'BEGIN { OFS = "\t" } { print $1, $2, $3, sprintf("gap_%d", idx++ ) }'
+ > "${output}"
+ #end if
+]]>
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diff -r 000000000000 -r 4dfdf2090b35 ucsc_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsc_macros.xml Tue May 16 15:10:47 2017 -0400
@@ -0,0 +1,44 @@
+
+
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+ ucsc_twobit
+
+
+
+
+
+
+ C
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+
+ @article{Kent01062002,
+author = {Kent, W. James and Sugnet, Charles W. and Furey, Terrence S. and Roskin, Krishna M. and Pringle, Tom H. and Zahler, Alan M. and Haussler, and David},
+title = {The Human Genome Browser at UCSC},
+volume = {12},
+number = {6},
+pages = {996-1006},
+year = {2002},
+doi = {10.1101/gr.229102},
+URL = {http://genome.cshlp.org/content/12/6/996.abstract},
+eprint = {http://genome.cshlp.org/content/12/6/996.full.pdf+html},
+journal = {Genome Research}
+}
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