Mercurial > repos > mvdbeek > bam_readtagger
diff write_supplementary_fastq.xml @ 9:53b71263e2a2 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
author | mvdbeek |
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date | Wed, 08 Mar 2017 05:14:25 -0500 |
parents | |
children | c179d081b6ba |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/write_supplementary_fastq.xml Wed Mar 08 05:14:25 2017 -0500 @@ -0,0 +1,37 @@ +<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.5"> + <description>from SAM/BAM alignment files as FASTQ</description> + <requirements> + <requirement type="package" version="0.3.5">readtagger</requirement> + </requirements> + <version_command>write_supplementary_fastq --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + write_supplementary_fastq --input_path '$input' --output_path '$output' + ]]></command> + <inputs> + <param name="input" argument="--input_path" type="data" format="bam"/> + </inputs> + <outputs> + <data name="output" format="fastqsanger"/> + </outputs> + <tests> + <test> + <param name="input" value="supplementary.bam" ftype="bam"/> + <output name="output" file="supplementary.fastq" ftype="fastqsanger"/> + </test> + </tests> + <help><![CDATA[ +.. code-block:: + + Usage: write_supplementary_fastq [OPTIONS] + + Write all supplementary alignments in `input_path` to an output fastq file + at `output_path`. + + Options: + --input_path PATH Collect supplementary reads in this alignment file. + --output_path PATH Write supplementary reads to this FASTQ file. + --help Show this message and exit. + + + ]]></help> +</tool>