Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite
comparison trips_bam_to_sqlite_builtin/trips_bam_to_sqlite.xml @ 13:df4bb52b226d draft
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author | jackcurragh |
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date | Thu, 03 Nov 2022 12:25:58 +0000 |
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12:02874b1b2015 | 13:df4bb52b226d |
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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 |