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comparison trips_bam_to_sqlite/trips_bam_to_sqlite.xml @ 1:3ac12b611d7f draft

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author jackcurragh
date Sun, 17 Apr 2022 08:44:20 +0000
parents fef356fa1802
children c8d8675697c6
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0:fef356fa1802 1:3ac12b611d7f
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