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author | jackcurragh |
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date | Mon, 04 Apr 2022 09:48:32 +0000 |
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children | 3ac12b611d7f |
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<tool id="bam_to_sqlite" name="BAM to Sqlite (TRIPS-Viz)" version="1.0"> <description>Convert BAM file to SQLITE for TRIPS-Viz</description> <requirements> <requirement type="package" version="0.19.0">pysam</requirement> <requirement type="package" version="2.0.0">sqlitedict</requirement> <requirement type="package" version="3.37.1">sqlite</requirement> </requirements> <command><![CDATA[ python $__tool_directory__/bam_to_sqlite.py <path_to_bam_file> <path_to_organism.sqlite> <file_description (optional)> ]]></command> <inputs> <param name="input1" type="data" format="bam" label="BAM file" /> <param name="input2" type="data" format="sqlite" label="Path to organism SQLITE annotation file" /> <param name="input3" type="data" format="text" label="Description of this sample" /> </inputs> <outputs> <data name="output1" format="sqlite"/> </outputs> <tests> <test> <param name="input1" value="test.bam" ftype="bam"/> <param name="input2" value="test.sqlite" ftype="sqlite"/> <param name="input3" value="TEST DESCRIPTION" ftype="text"/> <output name="output1" file="test.bam.sqlite" ftype="sqlite" lines_diff="4" /> </test> </tests> <help> **What it does** Process your transcriptome read alignments for TRIPS-Viz Prerequisites: - name-sorted bam file (samtools sort -n) - TRIPS-Viz annotation file in SQLITE format. </help> <citations/> </tool>