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comparison trips_bam_to_sqlite_builtin/trips_bam_to_sqlite.xml @ 13:df4bb52b226d draft

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author jackcurragh
date Thu, 03 Nov 2022 12:25:58 +0000
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12:02874b1b2015 13:df4bb52b226d
1 <tool id="bam_to_sqlite" name="BAM to Sqlite" version="1.1.1">
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="1.7.0">sqlitedict</requirement>
6 <requirement type="package" version="3.37.1">sqlite</requirement>
7 <requirement type="package" version="1.15.1">samtools</requirement>
8
9 </requirements>
10 <command>
11 #if $refGenomeSource.genomeSource == "builtin":
12 python $__tool_directory__/bam_to_sqlite.py $input1 ${refGenomeSource.input2_builtin.fields.path} $input3 $output1
13 #else:
14 python $__tool_directory__/bam_to_sqlite.py $input1 ${refGenomeSource.input2_file} $input3 $output1
15 #end if
16
17 </command>
18 <inputs>
19 <param name="input1" type="data" format="bam" label="Sorted (samtools -n) BAM file" />
20 <conditional name="refGenomeSource">
21 <param name="genomeSource" type="select" label="Will you select an annotation file from your history or use a built-in option?">
22 <option value="builtin">Use a built-in SQLITE</option>
23 <option value="history">Use one from the history</option>
24 </param>
25 <when value="builtin">
26 <param name="input2_builtin" type="select" format="sqlite" label="Select a SQLITE" help="if your organism of interest is not listed - contact RiboGalaxy team">
27 <options from_data_table="sqlites">
28 <filter type="sort_by" column="2" />
29 <validator type="no_options" message="No built-ins are available" />
30 </options>
31 </param>
32 </when>
33 <when value="history">
34 <param name="input2_file" type="data" format="sqlite" label="SQLITE File" />
35 </when>
36 </conditional>
37
38 <param name="input3" type="text" label="Description of this sample" />
39 </inputs>
40 <outputs>
41 <data name="output1" format="sqlite"/>
42 </outputs>
43 <tests>
44 <test>
45 <param name="input1" value="test_n_sorted.bam" ftype="bam"/>
46 <param name="input2" value="test_org.sqlite" ftype="sqlite"/>
47 <param name="input3" value="TEST DESCRIPTION"/>
48 <output name="output1" file="test_n_sorted.bamv2.sqlite" ftype="sqlite" lines_diff="4" />
49 </test>
50 </tests>
51 <help>
52 **What it does**
53
54 Process your transcriptome read alignments for TRIPS-Viz
55
56 Prerequisites:
57 - name-sorted bam file (samtools sort -n)
58 - TRIPS-Viz annotation file in SQLITE format.
59 </help>
60 <citations/>
61 </tool>
62