Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite

comparison trips_bam_to_sqlite/trips_bam_to_sqlite.xml @ 0:fef356fa1802 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jackcurragh
date Mon, 04 Apr 2022 09:48:32 +0000
parents
children 3ac12b611d7f
comparison
equal deleted inserted replaced
-1:000000000000 0:fef356fa1802
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>