# HG changeset patch
# User chrisw
# Date 1574140999 0
# Node ID f84a4ffe8bd7d8345e7adcba4ba25db2aeeb040b
# Parent  8e9a8987581c21a58b2c3774d04ea087dbdfc977
Uploaded

diff -r 8e9a8987581c -r f84a4ffe8bd7 tool_dependencies.26.xml
--- a/tool_dependencies.26.xml	Tue Nov 19 05:21:33 2019 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-<?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>