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author | jackcurragh |
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date | Tue, 08 Aug 2023 11:00:26 +0000 |
parents | d8cc5dbc9fa8 |
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<tool id="bam_to_sqlite" name="BAM to Sqlite" version="1.7"> <description>Convert BAM file to SQLITE for Trips-Viz</description> <requirements> <requirement type="package" version="0.19.0">pysam</requirement> <requirement type="package" version="1.7.0">sqlitedict</requirement> <requirement type="package" version="3.37.1">sqlite</requirement> <requirement type="package" version="1.15.1">samtools</requirement> </requirements> <command> #if $refGenomeSource.genomeSource == "builtin": python $__tool_directory__/bam_to_sqlite.py $input1 ${refGenomeSource.input2_builtin.fields.path} $input3 $output1 #else: python $__tool_directory__/bam_to_sqlite.py $input1 ${refGenomeSource.input2_file} $input3 $output1 #end if </command> <inputs> <param name="input1" type="data" format="bam" label="Sorted (samtools -n) BAM file" /> <conditional name="refGenomeSource"> <param name="genomeSource" type="select" label="Will you select an annotation file from your history or use a built-in option?"> <option value="builtin">Use a built-in SQLITE</option> <option value="history">Use one from the history</option> </param> <when value="builtin"> <param name="input2_builtin" type="select" format="sqlite" label="Select a SQLITE" help="if your organism of interest is not listed - contact RiboGalaxy team"> <options from_data_table="sqlites"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No built-ins are available" /> </options> </param> </when> <when value="history"> <param name="input2_file" type="data" format="sqlite" label="SQLITE File" /> </when> </conditional> <param name="input3" type="text" label="Description of this sample (Required)"/> </inputs> <outputs> <data name="output1" format="sqlite"/> </outputs> <tests> <test> <param name="input1" value="test_n_sorted.bam" ftype="bam"/> <param name="input2" value="test_org.sqlite" ftype="sqlite"/> <param name="input3" value="TEST DESCRIPTION"/> <output name="output1" file="test_n_sorted.bamv2.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>