Mercurial > repos > chrisw > bamcount_tool_test
changeset 0:1f0e3aaaba19 draft
Uploaded
| author | chrisw |
|---|---|
| date | Tue, 12 Feb 2019 13:42:37 -0500 |
| parents | |
| children | 78bca99736b0 |
| files | .shed.yml bamcount.xml test-data/test.bam tool_dependencies.xml |
| diffstat | 4 files changed, 101 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Feb 12 13:42:37 2019 -0500 @@ -0,0 +1,11 @@ +categories: +- Statistics +description: bamcount is a tools for efficiently summarizing coverage information from a BAM file +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: bamcount +owner: ChristoperWilks +remote_repository_url: https://github.com/ChristopherWilks/bamcount_galaxy +type: unrestricted
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamcount.xml Tue Feb 12 13:42:37 2019 -0500 @@ -0,0 +1,84 @@ +<tool id="bamcount" name="Summarize coverage from a BAM (bamcount)" version="0.1.0"> + <requirements> + <requirement type="package" version="0.2.6">bamcount</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + bamcount "$input1" --threads $threads --coverage --no-head --require-mdz --min-unique-qual $min_uniq_qual --frag-dist bc --bigwig bc --annotation $annotation bc --auc bc --alts bc + ]]></command> + <inputs> + <param type="data" name="input1" format="bam" /> + </inputs> + <outputs> + <data name="output1" format="auc.tsv" from_work_dir="bc.auc.tsv" /> + </outputs> + <tests> + <test> + <param name="input1" value="test.bam"/> + <output name="output1" file="bc.auc.tsv"/> + </test> + </tests> + <help><![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) + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubbamcount, + author = {Wilks, Christopher}, + year = {2019}, + title = {bamcount}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/BenLangmead/bamcount}, +}</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Feb 12 13:42:37 2019 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bamcount" version="0.2.6"> + <repository changeset_revision="f02b4483eda2" name="bamcount_test" owner="chrisw" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>