Mercurial > repos > petr-novak > long_reads_sampling
annotate long2short.xml @ 3:9819570dc020 draft
planemo upload for repository https://github.com/kavonrtep/galaxy_tools commit 5cc98a80e4e99f2b4089b9a8de458035304a6319
author | petr-novak |
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date | Fri, 08 Dec 2023 11:24:06 +0000 |
parents | 5596bafd2119 |
children | 060fc04af21c |
rev | line source |
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3
9819570dc020
planemo upload for repository https://github.com/kavonrtep/galaxy_tools commit 5cc98a80e4e99f2b4089b9a8de458035304a6319
petr-novak
parents:
1
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changeset
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1 <tool id="long2short" name="Get pseudo short paired end reads from long reads" version="0.1.1"> |
1 | 2 <requirements> |
3 <requirement type="package">biopython</requirement> | |
4 <requirement type="package" version="3.6">python</requirement> | |
5 </requirements> | |
6 <command detect_errors="exit_code"><![CDATA[ | |
7 python3 $__tool_directory__/long2short.py -i "$input1" -o "$output1" -cov ${coverage} -L ${insert_length} -l ${read_length} | |
8 ]]></command> | |
9 <inputs> | |
10 <param type="data" name="input1" format="fasta" /> | |
11 <param type="integer" name="insert_length" value="1000" /> | |
12 <param type="integer" name="read_length" value="300" /> | |
13 <param type="float" name="coverage" value="0.1" min="0.0001" max="10"/> | |
14 </inputs> | |
15 <outputs> | |
16 <data name="output1" format="fasta" /> | |
17 </outputs> | |
18 <tests> | |
19 <test> | |
20 <param name="input1" value="read_10k_ALL_oxford_nanopore_sample" /> | |
21 <param name="cov" value="0.1" /> | |
22 <param name="insert_length" value="600" /> | |
23 <param name="read_length" value="100" /> | |
24 <output name="output1" file="pseudo_paired_end.fasta"/> | |
25 </test> | |
26 </tests> | |
27 <help><![CDATA[ Create pseudo short paired-edn reads from long read with | |
28 required read length, insert length and coverage. Original position on long | |
29 reads is kept as part of the read name ]]></help> | |
30 | |
31 </tool> |