Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite
comparison trips_bam_to_sqlite/trips_bam_to_sqlite.xml @ 1:3ac12b611d7f draft
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author | jackcurragh |
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date | Sun, 17 Apr 2022 08:44:20 +0000 |
parents | fef356fa1802 |
children | c8d8675697c6 |
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0:fef356fa1802 | 1:3ac12b611d7f |
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4 <requirement type="package" version="0.19.0">pysam</requirement> | 4 <requirement type="package" version="0.19.0">pysam</requirement> |
5 <requirement type="package" version="2.0.0">sqlitedict</requirement> | 5 <requirement type="package" version="2.0.0">sqlitedict</requirement> |
6 <requirement type="package" version="3.37.1">sqlite</requirement> | 6 <requirement type="package" version="3.37.1">sqlite</requirement> |
7 </requirements> | 7 </requirements> |
8 <command><![CDATA[ | 8 <command><![CDATA[ |
9 python $__tool_directory__/bam_to_sqlite.py <path_to_bam_file> <path_to_organism.sqlite> <file_description (optional)> | 9 python $__tool_directory__/bam_to_sqlite.py $input1 $input2 $input3 |
10 ]]></command> | 10 ]]></command> |
11 <inputs> | 11 <inputs> |
12 <param name="input1" type="data" format="bam" label="BAM file" /> | 12 <param name="input1" type="data" format="bam" label="Sorted (samtools -n) BAM file" /> |
13 <param name="input2" type="data" format="sqlite" label="Path to organism SQLITE annotation 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" /> | 14 <param name="input3" type="text" label="Description of this sample" /> |
15 </inputs> | 15 </inputs> |
16 <outputs> | 16 <outputs> |
17 <data name="output1" format="sqlite"/> | 17 <data name="output1" format="sqlite"/> |
18 </outputs> | 18 </outputs> |
19 <tests> | 19 <tests> |
20 <test> | 20 <test> |
21 <param name="input1" value="test.bam" ftype="bam"/> | 21 <param name="input1" value="test_n_sorted.bam" ftype="bam"/> |
22 <param name="input2" value="test.sqlite" ftype="sqlite"/> | 22 <param name="input2" value="test_org.sqlite" ftype="sqlite"/> |
23 <param name="input3" value="TEST DESCRIPTION" ftype="text"/> | 23 <param name="input3" value="TEST DESCRIPTION"/> |
24 <output name="output1" file="test.bam.sqlite" ftype="sqlite" lines_diff="4" /> | 24 <output name="output1" file="test_n_sorted.bamv2.sqlite" ftype="sqlite" lines_diff="4" /> |
25 </test> | 25 </test> |
26 </tests> | 26 </tests> |
27 <help> | 27 <help> |
28 **What it does** | 28 **What it does** |
29 | 29 |