Mercurial > repos > iuc > bam2fastx
changeset 1:7f7f2ee03430 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit c2e67f103e2b83fd0fb9757ea6b75984d4fd9b64
| author | iuc |
|---|---|
| date | Mon, 25 Mar 2024 17:50:00 +0000 |
| parents | 61a6b93ee6e1 |
| children | |
| files | bam2fastx.xml |
| diffstat | 1 files changed, 11 insertions(+), 11 deletions(-) [+] |
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--- a/bam2fastx.xml Tue Mar 12 15:42:13 2024 +0000 +++ b/bam2fastx.xml Mon Mar 25 17:50:00 2024 +0000 @@ -2,7 +2,7 @@ <description>PacBio BAM to Fastx</description> <macros> <token name="@TOOL_VERSION@">3.1.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">pbtk</requirement> @@ -18,9 +18,9 @@ #end if input.bam --num-threads "\${GALAXY_SLOTS:-1}" && -#if $output_format == "fasta": +#if $output_format == "fasta_gz": mv output.fasta.gz '$output_fasta_gz' -#elif $output_format == "fastq": +#elif $output_format == "fastq_gz": mv output.fastq.gz '$output_fastq_gz' #end if ]]></command> @@ -33,28 +33,28 @@ </inputs> <outputs> <data name="output_fasta_gz" format="fasta.gz" label="${tool.name} on ${on_string}: Fasta"> - <filter>output_format == "fasta"</filter> + <filter>output_format == "fasta_gz"</filter> </data> <data name="output_fastq_gz" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Fastq"> - <filter>output_format == "fastq"</filter> + <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"> + <param name="output_format" value="fastq.gz" /> + <output name="output_fastq_gz" decompress="true"> <assert_contents> - <has_size min="9000" /> + <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" > + <param name="output_format" value="fasta.gz" /> + <output name="output_fasta_gz" decompress="true"> <assert_contents> - <has_size min="9000" /> + <has_text text="AATGCCTTATTAAGTTAAGAAATGGTTTTTTTTAAACTTACAGATGGAA" /> </assert_contents> </output> </test>