Mercurial > repos > iuc > bam2fastx
changeset 0:56d9933d2737 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
| author | iuc |
|---|---|
| date | Wed, 06 Nov 2024 22:22:21 +0000 |
| parents | |
| children | df0fa70d83e5 |
| files | bam2fastx.xml test-data/sample.bam |
| diffstat | 2 files changed, 77 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bam2fastx.xml Wed Nov 06 22:22:21 2024 +0000 @@ -0,0 +1,77 @@ +<tool id="bam2fastx" name="PacBio bam2fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> + <description>PacBio BAM to Fastx</description> + <macros> + <token name="@TOOL_VERSION@">3.4.0</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pbtk</requirement> + </requirements> + <command><![CDATA[ +mkdir -p output_files/ && +ln -s '$input_bam' input.bam && +pbindex input.bam && +#if $output_format == "fasta_gz": + bam2fasta -o output +#elif $output_format == "fastq_gz": + bam2fastq -o output +#end if +input.bam +--num-threads "\${GALAXY_SLOTS:-1}" && +#if $output_format == "fasta_gz": + mv output.fasta.gz '$output_fasta_gz' +#elif $output_format == "fastq_gz": + mv output.fastq.gz '$output_fastq_gz' +#end if + ]]></command> + <inputs> + <param name="input_bam" type="data" format="unsorted.bam" label="PacBio Bam file "/> + <param name="output_format" type="select" label="Output Format" help="Output a fasta.gz or fastq.gz"> + <option value="fastq_gz">fastq.gz</option> + <option value="fasta_gz">fasta.gz</option> + </param> + </inputs> + <outputs> + <data name="output_fasta_gz" format="fasta.gz" label="${tool.name} on ${on_string}: Fasta"> + <filter>output_format == "fasta_gz"</filter> + </data> + <data name="output_fastq_gz" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Fastq"> + <filter>output_format == "fastq_gz"</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_bam" ftype="unsorted.bam" value="sample.bam"/> + <param name="output_format" value="fastq.gz" /> + <output name="output_fastq_gz" decompress="true"> + <assert_contents> + <has_text text="AATGCCTTATTAAGTTAAGAAATGGTTTTTTTTAAACTTACAGATGGAA" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <param name="input_bam" ftype="bam" value="sample.bam"/> + <param name="output_format" value="fasta.gz" /> + <output name="output_fasta_gz" decompress="true"> + <assert_contents> + <has_text text="AATGCCTTATTAAGTTAAGAAATGGTTTTTTTTAAACTTACAGATGGAA" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +Convert a PacBio BAM file to Fastq or Fasta file. + ]]></help> + <citations> + <citation type="bibtex"> + @misc{githubpbtk, + author = {}, + year = {2024}, + title = {pbtk}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/PacificBiosciences/pbtk}, + } + </citation> + </citations> + </tool>