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comparison trips_bam_to_sqlite/trips_bam_to_sqlite.xml @ 2:c8d8675697c6 draft

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author jackcurragh
date Wed, 20 Apr 2022 15:18:00 +0000
parents 3ac12b611d7f
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1:3ac12b611d7f 2:c8d8675697c6
1 <tool id="bam_to_sqlite" name="BAM to Sqlite (TRIPS-Viz)" version="1.0"> 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> 2 <description>Convert BAM file to SQLITE for TRIPS-Viz</description>
3 <requirements> 3 <requirements>
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="1.7.0">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 $input1 $input2 $input3 9 python $__tool_directory__/bam_to_sqlite.py $input1 $input2 $input3 $output1
10 ]]></command> 10 ]]></command>
11 <inputs> 11 <inputs>
12 <param name="input1" type="data" format="bam" label="Sorted (samtools -n) 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="text" label="Description of this sample" /> 14 <param name="input3" type="text" label="Description of this sample" />