Mercurial > repos > peterjc > samtools_bam2fq
changeset 2:27135d7637b6 draft
Uploaded v0.0.1b, now includes -n and -O options.
| author | peterjc |
|---|---|
| date | Tue, 04 Nov 2014 06:07:53 -0500 |
| parents | 03adf9de156e |
| children | 14ff32f355f0 |
| files | test-data/sam_spec_padded.bam2fq_no_suf.fastq tools/samtools_bam2fq/README.rst tools/samtools_bam2fq/samtools_bam2fq.xml |
| diffstat | 3 files changed, 33 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sam_spec_padded.bam2fq_no_suf.fastq Tue Nov 04 06:07:53 2014 -0500 @@ -0,0 +1,12 @@ +>ref +AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT +>r001 +TTAGATAAAGGATACTG +>r002 +AAAAGATAAGGATA +>r003 +AGCTAA +>r004 +ATAGCTTCAGC +>r001 +ATGCCGCTG
--- a/tools/samtools_bam2fq/README.rst Mon Nov 03 11:44:44 2014 -0500 +++ b/tools/samtools_bam2fq/README.rst Tue Nov 04 06:07:53 2014 -0500 @@ -61,7 +61,7 @@ For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder:: - $ tar -czf samtools_bam2fq.tar.gz tools/samtools_bam2fq/README.rst tools/samtools_bam2fq/samtools_bam2fq.xml tools/samtools_bam2fq/tool_dependencies.xml test-data/sam_spec_padded.bam test-data/sam_spec_padded.sam test-data/sam_spec_padded.depad.bam test-data/sam_spec_padded.bam2fq.fastq + $ tar -czf samtools_bam2fq.tar.gz tools/samtools_bam2fq/README.rst tools/samtools_bam2fq/samtools_bam2fq.xml tools/samtools_bam2fq/tool_dependencies.xml test-data/sam_spec_padded.bam test-data/sam_spec_padded.sam test-data/sam_spec_padded.depad.bam test-data/sam_spec_padded.bam2fq.fastq test-data/sam_spec_padded.bam2fq_no_suf.fastq Check this worked:: @@ -73,6 +73,7 @@ test-data/sam_spec_padded.sam test-data/sam_spec_padded.depad.bam test-data/sam_spec_padded.bam2fq.fastq + test-data/sam_spec_padded.bam2fq_no_suf.fastq Licence (MIT)
--- a/tools/samtools_bam2fq/samtools_bam2fq.xml Mon Nov 03 11:44:44 2014 -0500 +++ b/tools/samtools_bam2fq/samtools_bam2fq.xml Tue Nov 04 06:07:53 2014 -0500 @@ -5,11 +5,15 @@ <requirement type="package" version="1.1">samtools</requirement> </requirements> <version_command>samtools 2>&1 | grep -i "Version:"</version_command> - <command>samtools bam2fq "$input_bam" > "$out_fastq"</command> + <command>samtools bam2fq $suffices $orig_qual "$input_bam" > "$out_fastq"</command> <inputs> <!-- Unlike other bits of samtools, this seems to autodetect SAM vs BAM --> <param name="input_bam" type="data" format="bam,sam" label="Input BAM file" /> - <!-- TODO - new options -n, -O and -s in samtools v1.1 --> + <param name="suffices" type="boolean" label="Add /1 and /2 suffices to paired reads?" + truevalue="" falsevalue="-n" checked="true" /> + <param name="orig_qual" type="boolean" label="Use original qualities (OQ tags) if present?" + truevalue="-O" falsevalue="" checked="false" /> + <!-- TODO - new option -s in samtools v1.1 --> </inputs> <outputs> <data name="out_fastq" format="fastqsanger" label="$input_bam.name (bam2fq)" /> @@ -22,6 +26,14 @@ <tests> <test> <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" /> + <param name="suffices" value="true" /> + <param name="orig_qual" value="false" /> + <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" /> + </test> + <test> + <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" /> + <param name="suffices" value="true" /> + <param name="orig_qual" value="true" /> <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" /> </test> <test> @@ -32,6 +44,11 @@ <param name="input_bam" value="sam_spec_padded.depad.bam" ftype="bam" /> <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" /> </test> + <test> + <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" /> + <param name="suffices" value="false"/> + <output name="out_fastq" file="sam_spec_padded.bam2fq_no_suf.fastq" ftype="fastqsanger" /> + </test> </tests> <help> **What it does**