# HG changeset patch
# User chrisw
# Date 1574132142 0
# Node ID cb4c1efac7afee504904eb83e0fe29e5fbff91aa
# Parent  f02b4483eda29d0f06c1378506d7c1f02e148d76
Uploaded

diff -r f02b4483eda2 -r cb4c1efac7af .shed.yml
--- a/.shed.yml	Tue Feb 12 12:51:34 2019 -0500
+++ b/.shed.yml	Tue Nov 19 02:55:42 2019 +0000
@@ -1,11 +1,11 @@
 categories:
 - Tool Dependency Packages
-description: Contains a tool dependency definition that downloads version 0.2.6 of bamcount
+description: Contains a tool dependency definition that downloads version 0.4.0 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
+name: package_bamcount_0_4_0
 owner: ChristoperWilks
 remote_repository_url: https://github.com/ChristopherWilks/bamcount_galaxy
 type: tool_dependency_definition
diff -r f02b4483eda2 -r cb4c1efac7af README.rst
--- a/README.rst	Tue Feb 12 12:51:34 2019 -0500
+++ b/README.rst	Tue Nov 19 02:55:42 2019 +0000
@@ -1,2 +1,2 @@
-bamcount Galaxy Dependency Package
-==================================
+bamcount Galaxy Tool Dependency Package
+=======================================
diff -r f02b4483eda2 -r cb4c1efac7af tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 12 12:51:34 2019 -0500
+++ b/tool_dependencies.xml	Tue Nov 19 02:55:42 2019 +0000
@@ -4,11 +4,11 @@
     <package name="htslib" version="1.9"/>
     <package name="libbigwig" version="0.4.2"/>
 -->
-    <package name="bamcount" version="0.2.6">
+    <package name="bamcount" version="0.4.0">
         <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="download_by_url">https://github.com/ChristopherWilks/bamcount/releases/download/0.4.0/bamcount-0.4.0.zip</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
@@ -20,7 +20,7 @@
             </actions_group>
         </install>
         <readme><![CDATA[
-bamcount 0.2.6
+bamcount 0.4.0
 
 BAM and BigWig utility.
 
@@ -32,16 +32,30 @@
   --version            Show version.
   --threads            # of threads to do BAM decompression
 
+Extract basic junction information from the BAM, including co-occurrence
+  --junctions <prefix> Extract jx coordinates, strand, and anchor length, per read
+                       Writes to a TSV file <prefix>.jxs.tsv
+
+Extract reads from BAM into FASTQ (exclusive of all other modes):
+  --bam2fastq <prefix> Extract all reads from the passed in BAM and output as FASTQs
+                       Uses prefix to name the fastq(s)
+  --filter-out         SAM bit flags to filter out
+  --filter-in          SAM bit flags to filter in
+  --re-reverse         If read is reversed in alignment, re-reverse it in output
+  --one-file           If you know file is not paired or just want all reads in one file
+
 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
+  --alts <prefix>              Print differing from ref per-base coverages
+                               Writes to a CSV file <prefix>.alts.tsv
+  --include-softclip <prefix>  Print a record to the alts CSV for soft-clipped bases
+                               Writes total counts to a separate TSV file <prefix>.softclip.tsv
+  --only-polya                 If --include-softclip, only print softclips which are mostly A's or T's
+  --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)
@@ -54,6 +68,8 @@
   --annotation <bed> <prefix>
                        Path to BED file containing list of regions to sum coverage over
                        (tab-delimited: chrm,start,end)
+  --keep-bam-order     Output annotation coverage in the order chromosomes appear in the BAM file.
+                       The default is to output annotation coverage in the order chromosomes appear in the BED file.
   --min-unique-qual <int>
                        Output second bigWig consisting built only from alignments
                        with at least this mapping quality.  --bigwig must be specified.
@@ -71,6 +87,7 @@
                        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>
+  --test-polya         Lower Poly-A filter minimums for testing (only useful for debugging/testing)
+]]></readme>
     </package>
 </tool_dependency>