Mercurial > repos > chrisw > bamcount_test
changeset 0:f02b4483eda2 draft
Uploaded
author | chrisw |
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date | Tue, 12 Feb 2019 12:51:34 -0500 |
parents | |
children | cb4c1efac7af |
files | .shed.yml README.rst tool_dependencies.xml |
diffstat | 3 files changed, 89 insertions(+), 0 deletions(-) [+] |
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--- /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
--- /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 +==================================
--- /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>