# HG changeset patch
# User chrisw
# Date 1549993894 18000
# Node ID f02b4483eda29d0f06c1378506d7c1f02e148d76

Uploaded

diff -r 000000000000 -r f02b4483eda2 .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Tue Feb 12 12:51:34 2019 -0500
@@ -0,0 +1,11 @@
+categories:
+- Tool Dependency Packages
+description: Contains a tool dependency definition that downloads version 0.2.6 of bamcount
+long_description: |
+    bamcount is a tool for efficiently computing coverage statistics over a DNA/RNA BAM file.
+    It is aligner agnostic and counts everything over only one pass through the BAM.
+    https://github.com/BenLangmead/bamcount
+name: package_bamcount_0_2_6
+owner: ChristoperWilks
+remote_repository_url: https://github.com/ChristopherWilks/bamcount_galaxy
+type: tool_dependency_definition
diff -r 000000000000 -r f02b4483eda2 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Tue Feb 12 12:51:34 2019 -0500
@@ -0,0 +1,2 @@
+bamcount Galaxy Dependency Package
+==================================
diff -r 000000000000 -r f02b4483eda2 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Feb 12 12:51:34 2019 -0500
@@ -0,0 +1,76 @@
+<?xml version="1.0"?>
+<tool_dependency>
+<!--
+    <package name="htslib" version="1.9"/>
+    <package name="libbigwig" version="0.4.2"/>
+-->
+    <package name="bamcount" version="0.2.6">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">https://github.com/BenLangmead/bamcount/releases/download/0.2.6/bamcount-0.2.6.zip</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme><![CDATA[
+bamcount 0.2.6
+
+BAM and BigWig utility.
+
+Usage:
+  bamcount <bam> [options]
+
+Options:
+  -h --help            Show this screen.
+  --version            Show version.
+  --threads            # of threads to do BAM decompression
+
+Non-reference summaries:
+  --alts <prefix>      Print differing from ref per-base coverages
+                       Writes to a CSV file <prefix>.alts.tsv
+  --include-softclip   Print a record for soft-clipped bases
+  --include-n          Print mismatch records when mismatched read base is N
+  --print-qual         Print quality values for mismatched bases
+  --delta              Print POS field as +/- delta from previous
+  --require-mdz        Quit with error unless MD:Z field exists everywhere it's
+                       expected
+  --no-head            Don't print sequence names and lengths in header
+
+Coverage and quantification:
+  --coverage           Print per-base coverage (slow but totally worth it)
+  --auc <prefix>       Print per-base area-under-coverage, will generate it for the genome
+                       and for the annotation if --annotation is also passed in
+                       Writes to a TSV file <prefix>.auc.tsv
+  --bigwig <prefix>    Output coverage as BigWig file(s).  Writes to <prefix>.all.bw
+                       (also <prefix>.unique.bw when --min-unique-qual is specified).
+                       Requires libBigWig.
+  --annotation <bed> <prefix>
+                       Path to BED file containing list of regions to sum coverage over
+                       (tab-delimited: chrm,start,end)
+  --min-unique-qual <int>
+                       Output second bigWig consisting built only from alignments
+                       with at least this mapping quality.  --bigwig must be specified.
+                       Also produces second set of annotation sums based on this coverage
+                       if --annotation is enabled
+  --double-count       Allow overlapping ends of PE read to count twice toward
+                       coverage
+  --num-bases          Report total sum of bases in alignments processed (that pass filters)
+
+Other outputs:
+  --read-ends          Print counts of read starts/ends, if --min-unique-qual is set
+                       then only the alignments that pass that filter will be counted here
+                       Writes to 2 TSV files: <prefix>.starts.tsv, <prefix>.ends.tsv
+  --frag-dist <prefix> Print fragment length distribution across the genome
+                       Writes to a TSV file <prefix>.frags.tsv
+  --echo-sam           Print a SAM record for each aligned read
+  --ends               Report end coordinate for each read (useful for debugging)
+        ]]></readme>
+    </package>
+</tool_dependency>