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1 <tool id="bam_to_sqlite" name="BAM to Sqlite (TRIPS-Viz)" version="1.0">
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2 <description>Convert BAM file to SQLITE for TRIPS-Viz</description>
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3 <requirements>
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4 <requirement type="package" version="0.19.0">pysam</requirement>
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5 <requirement type="package" version="1.7.0">sqlitedict</requirement>
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6 <requirement type="package" version="3.37.1">sqlite</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 python $__tool_directory__/bam_to_sqlite.py $input1 $input2 $input3 $output1
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10 ]]></command>
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11 <inputs>
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12 <param name="input1" type="data" format="bam" label="Sorted (samtools -n) BAM file" />
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13 <param name="input2" type="data" format="sqlite" label="Path to organism SQLITE annotation file" />
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14 <param name="input3" type="text" label="Description of this sample" />
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15 </inputs>
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16 <outputs>
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17 <data name="output1" format="sqlite"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input1" value="test_n_sorted.bam" ftype="bam"/>
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22 <param name="input2" value="test_org.sqlite" ftype="sqlite"/>
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23 <param name="input3" value="TEST DESCRIPTION"/>
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24 <output name="output1" file="test_n_sorted.bamv2.sqlite" ftype="sqlite" lines_diff="4" />
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25 </test>
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26 </tests>
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27 <help>
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28 **What it does**
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29
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30 Process your transcriptome read alignments for TRIPS-Viz
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31
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32 Prerequisites:
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33 - name-sorted bam file (samtools sort -n)
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34 - TRIPS-Viz annotation file in SQLITE format.
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35 </help>
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36 <citations/>
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37 </tool>
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