Mercurial > repos > iuc > metaeuk_easy_predict

annotate metaeuk_easy_predict.xml @ 2:24cca965e8df draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:37:08 +0000
parents 8138cfb92ba3
children 578bb60dcc94
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d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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1 <tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy0">
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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2 <description>High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</description>
2
24cca965e8df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <xrefs>
24cca965e8df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <xref type="bio.tools">MetaEuk</xref>
24cca965e8df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 </xrefs>
0
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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6 <macros>
1
8138cfb92ba3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit 36466f52394655b92d07a3a26ec3259bd30b89a2"
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7 <token name="@TOOL_VERSION@">4.a0f584d</token>
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d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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8 </macros>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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9 <requirements>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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10 <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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11 </requirements>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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12 <command detect_errors="aggressive"><![CDATA[
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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13 mkdir -p ./tmp &&
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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14 metaeuk easy-predict
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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15 '$contigs'
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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16 '$query'
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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17 output.fasta
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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18 "./tmp/metaeuk_working"
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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19 --threads \${GALAXY_SLOTS:-1}
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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20 --min-length '${min_length}'
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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21 -e '${segment_eval}'
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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22 --metaeuk-eval '${metaeuk_eval}'
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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23 --metaeuk-tcov '${metaeuk_tcov}'
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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24 #if $adv.adv_options == "yes"
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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25 --max-intron '${adv.max_intron}'
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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26 --min-intron '${adv.min_intron}'
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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27 #end if
1
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28 && mv output.fasta.codon.fas '$output'
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29 ]]></command>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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30 <inputs>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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31 <param name="contigs" type="data" format="fasta" label="Contigs to search again" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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32 <param name="query" type="data" format="fasta" label="Proteins to search against contigs" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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33 <param argument="-e" name="segment_eval" type="float" value="100" label="Maximum e-value of individual match segment" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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34 <param argument="--min-length" name="min_length" type="integer" value="15" label="Minimum number of codons in predicted open reading frame" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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35 <param argument="--metaeuk-eval" name="metaeuk_eval" type="float" value="0.001" label="Maximum e-value of combined exon set" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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36 <param argument="--metaeuk-tcov" name="metaeuk_tcov" type="float" value="0.5" label="Minimum length ratio of combined exon set to target" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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37 <conditional name="adv">
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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38 <param type="select" name="adv_options" label="Show advanced options">
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39 <option value="yes">Yes</option>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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40 <option value="no" selected="true">No</option>
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41 </param>
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42 <when value="yes">
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43 <param argument="--max-intron" name="max_intron" value="10000" type="integer" label="Maximum intron size" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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44 <param argument="--min-intron" name="min_intron" value="15" type="integer" label="Minimum intron size" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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45 </when>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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46 <when value="no">
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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47 </when>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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48 </conditional>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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49 </inputs>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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50 <outputs>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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51 <data name="output" format="fasta" />
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52 </outputs>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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53
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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54 <tests>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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55 <test>
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56 <param name="contigs" ftype="fasta" value="contigs.fna" />
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57 <param name="query" ftype="fasta" value="proteins.faa" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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58 <output name="output" ftype="fasta" value="output.fasta" />
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59 </test>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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60 <test>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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61 <param name="contigs" ftype="fasta" value="contigs.fna" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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62 <param name="query" ftype="fasta" value="proteins.faa" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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63 <conditional name="adv">
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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64 <param name="adv_options" value="yes" />
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65 <param name="max_intron" value="1000" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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66 </conditional>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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67 <assert_command>
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68 <has_text text="--max-intron '1000'" />
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69 </assert_command>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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70 <output name="output" ftype="fasta" value="output.fasta" />
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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71 </test>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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72 </tests>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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73 <help><![CDATA[
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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74
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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75 MetaEuk_ is a modular toolkit designed for large-scale gene discovery and
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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76 annotation in eukaryotic metagenomic contigs. Metaeuk combines the fast and
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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77 sensitive homology search capabilities of MMseqs2_ with a dynamic programming
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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78 procedure to recover optimal exons sets. It reduces redundancies in multiple
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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79 discoveries of the same gene and resolves conflicting gene predictions on
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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80 the same strand.
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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81
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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82 This tool implements the easy-predict command from metaeuk, which combines
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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83 metaeuk modules into a pipeline for protein alignment prediction. Input is
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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84 the contigs you want to search for protein hits and the proteins you want
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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85 to search against those contigs. Output is FASTA format predicted ORFs, with
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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86 exons annotated in the header according to the metaeuk header format_.
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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87
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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88 .. _MetaEuk: https://github.com/soedinglab/metaeuk
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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89 .. _MMseqs2: https://github.com/soedinglab/MMseqs2
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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90 .. _format: https://github.com/soedinglab/metaeuk#the-metaeuk-header
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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91 ]]></help>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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92 <citations>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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93 <citation type="doi">10.1186/s40168-020-00808-x</citation>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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94 </citations>
d8269f599799 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
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95 </tool>