Mercurial > repos > peterjc > samtools_bam2fq
diff tools/samtools_bam2fq/samtools_bam2fq.xml @ 0:c961d16801e4 draft default tip
Uploaded v0.0.2
| author | peterjc |
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| date | Tue, 04 Nov 2014 07:15:50 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/samtools_bam2fq/samtools_bam2fq.xml Tue Nov 04 07:15:50 2014 -0500 @@ -0,0 +1,137 @@ +<tool id="samtools_bam2fq" name="Convert BAM to FASTQ" version="0.0.2"> + <description>samtools bam2fq</description> + <requirements> + <requirement type="binary">samtools</requirement> + <requirement type="package" version="1.1">samtools</requirement> + </requirements> + <version_command>samtools 2>&1 | grep -i "Version:"</version_command> + <command> + #if $action_mode.mode == "pairs": + ## Sort by name for pair-aware output (should give nice interlaced FASTQ) + ## Galaxy has a tendancy to automatically apply co-ordindate sorting, + ## so just do this every time. If it was name sorted, pay an IO overhead. + ## Note requiring -T is samtools issue 295 + samtools sort -n -O bam -T TEMP_SORT "$input_bam" | samtools bam2fq -s "$singletons_fastq" - > "$pairs_fastq" + #else + ## Naive conversion using order in the input file + samtools bam2fq $suffices $orig_qual "$input_bam" > "$out_fastq" + #end if + </command> + <inputs> + <!-- Unlike samtools 0.1.x, samtools 1.1 will autodetect SAM vs BAM --> + <param name="input_bam" type="data" format="bam,sam" label="Input SAM/BAM file" /> + <param name="suffices" type="boolean" label="Add /1 and /2 suffices to paired reads?" + truevalue="" falsevalue="-n" checked="true" /> + <param name="orig_qual" type="boolean" label="Use original qualities (OQ tags) if present?" + truevalue="-O" falsevalue="" checked="false" /> + <!-- Using a condition here to allow different output files; default to paired mode --> + <conditional name="action_mode"> + <param name="mode" type="select" label="Mode of action"> + <option value="pairs" selected="true">Sort by name, then divide into paired and singletons (two FASTQ files)</option> + <option value="naive">No pre-sorting, all reads in a single FASTQ file</option> + </param> + </conditional> + </inputs> + <outputs> + <data name="pairs_fastq" format="fastqsanger" label="$input_bam.name (bam2fq pairs)"> + <filter>(action_mode['mode'] == 'pairs')</filter> + </data> + <data name="singletons_fastq" format="fastqsanger" label="$input_bam.name (bam2fq singletons)"> + <filter>(action_mode['mode'] == 'pairs')</filter> + </data> + <data name="out_fastq" format="fastqsanger" label="$input_bam.name (bam2fq)"> + <filter>(action_mode['mode'] == 'naive')</filter> + </data> + </outputs> + <stdio> + <!-- Assume anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <tests> + <test> + <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" /> + <param name="suffices" value="true" /> + <param name="orig_qual" value="false" /> + <param name="mode" value="naive" /> + <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" /> + <param name="mode" value="naive" /> + <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" /> + </test> + <test> + <param name="input_bam" value="sam_spec_padded.sam" ftype="sam" /> + <param name="mode" value="naive" /> + <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" /> + </test> + <test> + <param name="input_bam" value="sam_spec_padded.depad.bam" ftype="bam" /> + <param name="mode" value="naive" /> + <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"/> + <param name="mode" value="naive" /> + <output name="out_fastq" file="sam_spec_padded.bam2fq_no_suf.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="false" /> + <param name="mode" value="pairs" /> + <output name="pairs_fastq" file="sam_spec_padded.bam2fq_pairs.fastq" ftype="fastqsanger" /> + <output name="singletons_fastq" file="sam_spec_padded.bam2fq_singles.fastq" ftype="fastqsanger" /> + </test> + <test> + <param name="input_bam" value="sam_spec_padded.sam" ftype="sam" /> + <param name="suffices" value="true" /> + <param name="orig_qual" value="false" /> + <param name="mode" value="pairs" /> + <output name="pairs_fastq" file="sam_spec_padded.bam2fq_pairs.fastq" ftype="fastqsanger" /> + <output name="singletons_fastq" file="sam_spec_padded.bam2fq_singles.fastq" ftype="fastqsanger" /> + </test> + </tests> + <help> +**What it does** + +This tool runs the ``samtools bam2fq`` command in the SAMtools toolkit. + +By default this will pre-sort your SAM/BAM file by read name and split your +reads into an interlaced FASTQ file for paired reads, and a separate FASTQ +file for singleton reads. A naive conversion is also offered which gives a +single FASTQ file with the reads ordered as in the input SAM/BAM file. + +It is quite common to wish to remap high-throughput sequencing data. If you +only have the mapped reads in SAM/BAM format, this tool can "unmap" them to +recover FASTQ format reads to input into an alternative mapping tool. + +BAM files can hold both aligned reads and unaligned reads, so another example +usage would be to filter your BAM file to get only the unaligned reads, and +turn those back in FASTQ using this tool ready for *de novo* assembly, or to +try mapping against another reference sequence. + + +**Citation** + +If you use this Galaxy tool in work leading to a scientific publication please +cite: + +Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools. +Bioinformatics 25(16), 2078-9. +http://dx.doi.org/10.1093/bioinformatics/btp352 + +Peter J.A. Cock (2014), Galaxy wrapper for the samtools bam2fq command +http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + </citations> +</tool>