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comparison overlapping_reads.xml @ 12:aa5e2c64dff8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a
author artbio
date Sat, 22 Oct 2022 23:49:52 +0000
parents 8d3ca9652a5b
children 124f404b0fe7
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11:8d3ca9652a5b 12:aa5e2c64dff8
1 <tool id="overlapping_reads" name="Get overlapping reads" version="3.3"> 1 <tool id="overlapping_reads" name="Get overlapping reads" version="3.4.1">
2 <description /> 2 <description />
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.16.0.1=py37h45aed0b_3">pysam</requirement> 4 <requirement type="package" version="0.18.0">pysam</requirement>
5 <requirement type="package" version="1.13=h8c37831_0">samtools</requirement>
6 </requirements> 5 </requirements>
7 <stdio> 6 <stdio>
8 <exit_code range="1:" level="fatal" description="Tool exception" /> 7 <exit_code range="1:" level="fatal" description="Tool exception" />
9 </stdio> 8 </stdio>
10 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
11 samtools index '$input' && 10 ln -f -s $input.metadata.bam_index input.bam.bai &&
11 ln -s $input input.bam &&
12 python '$__tool_directory__'/overlapping_reads.py 12 python '$__tool_directory__'/overlapping_reads.py
13 --input '$input' 13 --input input.bam
14 --minquery '$minquery' 14 --minquery '$minquery'
15 --maxquery '$maxquery' 15 --maxquery '$maxquery'
16 --mintarget '$mintarget' 16 --mintarget '$mintarget'
17 --maxtarget '$maxtarget' 17 --maxtarget '$maxtarget'
18 --overlap '$overlap' 18 --overlap '$overlap'