Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite
comparison trips_bam_to_sqlite/trips_bam_to_sqlite.xml @ 0:fef356fa1802 draft
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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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1 <tool id="bam_to_sqlite" name="BAM to Sqlite (TRIPS-Viz)" version="1.0"> | |
2 <description>Convert BAM file to SQLITE for TRIPS-Viz</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.19.0">pysam</requirement> | |
5 <requirement type="package" version="2.0.0">sqlitedict</requirement> | |
6 <requirement type="package" version="3.37.1">sqlite</requirement> | |
7 </requirements> | |
8 <command><![CDATA[ | |
9 python $__tool_directory__/bam_to_sqlite.py <path_to_bam_file> <path_to_organism.sqlite> <file_description (optional)> | |
10 ]]></command> | |
11 <inputs> | |
12 <param name="input1" type="data" format="bam" label="BAM file" /> | |
13 <param name="input2" type="data" format="sqlite" label="Path to organism SQLITE annotation file" /> | |
14 <param name="input3" type="data" format="text" label="Description of this sample" /> | |
15 </inputs> | |
16 <outputs> | |
17 <data name="output1" format="sqlite"/> | |
18 </outputs> | |
19 <tests> | |
20 <test> | |
21 <param name="input1" value="test.bam" ftype="bam"/> | |
22 <param name="input2" value="test.sqlite" ftype="sqlite"/> | |
23 <param name="input3" value="TEST DESCRIPTION" ftype="text"/> | |
24 <output name="output1" file="test.bam.sqlite" ftype="sqlite" lines_diff="4" /> | |
25 </test> | |
26 </tests> | |
27 <help> | |
28 **What it does** | |
29 | |
30 Process your transcriptome read alignments for TRIPS-Viz | |
31 | |
32 Prerequisites: | |
33 - name-sorted bam file (samtools sort -n) | |
34 - TRIPS-Viz annotation file in SQLITE format. | |
35 </help> | |
36 <citations/> | |
37 </tool> |