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