Mercurial > repos > iuc > trimns
comparison TrimNs.xml @ 0:30178a68af68 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
| author | iuc |
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| date | Mon, 01 Feb 2021 19:46:34 +0000 |
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| -1:000000000000 | 0:30178a68af68 |
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| 1 <tool id="trimns" name="TrimN" version="0.1.0" profile="20.01"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="1.0">trimns_vgp</requirement> | |
| 4 </requirements> | |
| 5 <command detect_errors="exit_code"><![CDATA[ | |
| 6 remove_fake_cut_sites_DNAnexus.py '$fasta_in' step1_out.fasta step1.log | |
| 7 && trim_Ns_DNAnexus.py '$fasta_in' step2_out.list | |
| 8 && clip_regions_DNAnexus.py step1_out.fasta step2_out.list final_out.fasta | |
| 9 ]]></command> | |
| 10 <inputs> | |
| 11 <param name="fasta_in" type="data" format="fasta" label="Fasta file input" help="Fasta file to trim, and from which to remove Ns and fake cut sites."/> | |
| 12 </inputs> | |
| 13 <outputs> | |
| 14 <data name="trimmed_out" format="fasta" from_work_dir="final_out.fasta" label="${tool.name} on ${on_string}: trimmed fasta file" /> | |
| 15 </outputs> | |
| 16 <tests> | |
| 17 <test> | |
| 18 <param name="fasta_in" value="in.fasta"/> | |
| 19 <output name="trimmed_out" value="out.fasta" ftype="fasta"/> | |
| 20 </test> | |
| 21 </tests> | |
| 22 <help><![CDATA[ | |
| 23 .. class:: infomark | |
| 24 | |
| 25 **What it does** | |
| 26 | |
| 27 TrimNs is part of the VGP pipeline, and is made of a series of python scripts which trim off large stretches of N bases and to | |
| 28 remove fake cut sites that sometimes get inserted at the end of bionano hybrid scaffolds. | |
| 29 | |
| 30 ]]></help> | |
| 31 <citations> | |
| 32 <citation type="doi">10.1101/2020.05.22.110833</citation> | |
| 33 <citation type="doi">10.1101/2020.06.30.177956</citation> | |
| 34 </citations> | |
| 35 </tool> |