Mercurial > repos > mvdbeek > bam_readtagger
comparison findcluster.xml @ 5:f002e5797570 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
| author | mvdbeek |
|---|---|
| date | Thu, 02 Mar 2017 09:02:15 -0500 |
| parents | |
| children | 7434aa9a8638 |
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| 4:e0b1919b6bd8 | 5:f002e5797570 |
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| 1 <tool id="findcluster" name="Find clusters of reads" version="0.3.0"> | |
| 2 <description>in bam files</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.3.0">readtagger</requirement> | |
| 5 </requirements> | |
| 6 <version_command>findcluster --version</version_command> | |
| 7 <command detect_errors="aggressive"><![CDATA[ | |
| 8 findcluster | |
| 9 --input_path '$input' | |
| 10 --output_bam '$output_bam' | |
| 11 --output_gff '$output_gff' | |
| 12 --sample_name '$input.element_identifier' | |
| 13 ]]></command> | |
| 14 <inputs> | |
| 15 <param name="input" argument="--input_path" type="data" format="bam"/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/> | |
| 19 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/> | |
| 24 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/> | |
| 25 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/> | |
| 26 </test> | |
| 27 </tests> | |
| 28 <help><![CDATA[ | |
| 29 .. code-block:: | |
| 30 | |
| 31 Find clusters of reads that support a TE insertion. | |
| 32 | |
| 33 optional arguments: | |
| 34 -h, --help show this help message and exit | |
| 35 --input_path INPUT_PATH | |
| 36 Find cluster in this BAM file. (default: None) | |
| 37 --output_bam OUTPUT_BAM | |
| 38 Write out BAM file with cluster information to this | |
| 39 path. Reads will have an additional "CD" tag to | |
| 40 indicate the cluster number (default: None) | |
| 41 --output_gff OUTPUT_GFF | |
| 42 Write out GFF file with cluster information to this | |
| 43 path. (default: None) | |
| 44 --version show program's version number and exit | |
| 45 | |
| 46 ]]></help> | |
| 47 </tool> |