Mercurial > repos > peterjc > samtools_depad
view tools/samtools_depad/samtools_depad.xml @ 2:02572789ef6c draft
v0.0.4 Internal changes to command line handling
author | peterjc |
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date | Tue, 16 May 2017 09:29:05 -0400 |
parents | 01f8967ce1e0 |
children | 588c6ce25867 |
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<tool id="samtools_depad" name="Depad SAM/BAM file" version="0.0.4"> <description>samtools depad</description> <requirements> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> <version_command> python $__tool_directory__/samtools_depad.py --version </version_command> <command detect_errors="aggressive"> python $__tool_directory__/samtools_depad.py '$padded_ref' '$input_bam' '$input_bam.ext' '$output_bam' </command> <inputs> <param name="padded_ref" type="data" format="fasta" label="Padded FASTA file (with gap characters)" /> <param name="input_bam" type="data" format="sam,bam" label="Input SAM or BAM file (mapped against the padded FASTA)" /> </inputs> <outputs> <data name="output_bam" format="bam" label="$input_bam.name (depad)" /> </outputs> <tests> <test> <param name="padded_ref" value="sam_spec_padded.fasta" ftype="fasta" /> <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" /> <output name="output_bam" file="sam_spec_padded.depad.bam" ftype="bam" /> </test> <test> <param name="padded_ref" value="sam_spec_padded.fasta" ftype="fasta" /> <param name="input_bam" value="sam_spec_padded.sam" ftype="sam" /> <output name="output_bam" file="sam_spec_padded.depad.bam" ftype="bam" /> </test> </tests> <help> **What it does** This tool runs the ``samtools depad`` command in the SAMtools toolkit. Input is a *padded* FASTA file (with gaps represented by either ``*`` or ``-`` characters) and a SAM or BAM file mapped against this *padded* FASTA file. The output is a new BAM file mapped against the *unpadded* FASTA file created by removing all gap characters from the 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 depad command http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad 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_depad </help> <citations> <citation type="doi">10.1093/bioinformatics/btp352</citation> </citations> </tool>