Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite
diff trips_bam_to_sqlite/trips_bam_to_sqlite.xml @ 0:fef356fa1802 draft
Uploaded
author | jackcurragh |
---|---|
date | Mon, 04 Apr 2022 09:48:32 +0000 |
parents | |
children | 3ac12b611d7f |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trips_bam_to_sqlite/trips_bam_to_sqlite.xml Mon Apr 04 09:48:32 2022 +0000 @@ -0,0 +1,37 @@ +<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>