Mercurial > repos > iuc > metaeuk_easy_predict
annotate metaeuk_easy_predict.xml @ 0:5f6ebc3103ee draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
author | iuc |
---|---|
date | Tue, 04 Aug 2020 15:43:31 -0400 |
parents | |
children | f91548912113 |
rev | line source |
---|---|
0
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
1 <tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy0"> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
2 <description>High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</description> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
3 <macros> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
4 <token name="@TOOL_VERSION@">2.ddf2742</token> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
5 </macros> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
6 <requirements> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
7 <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
8 </requirements> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
9 <command detect_errors="aggressive"><![CDATA[ |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
10 mkdir -p ./tmp && |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
11 metaeuk easy-predict |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
12 '$contigs' |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
13 '$query' |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
14 output.fasta |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
15 "./tmp/metaeuk_working" |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
16 --threads \${GALAXY_SLOTS:-1} |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
17 --min-length '${min_length}' |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
18 -e '${segment_eval}' |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
19 --metaeuk-eval '${metaeuk_eval}' |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
20 --metaeuk-tcov '${metaeuk_tcov}' |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
21 #if $adv.adv_options == "yes" |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
22 --max-intron '${adv.max_intron}' |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
23 --min-intron '${adv.min_intron}' |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
24 #end if |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
25 && mv output.fasta '$output' |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
26 ]]></command> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
27 <inputs> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
28 <param name="contigs" type="data" format="fasta" label="Contigs to search again" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
29 <param name="query" type="data" format="fasta" label="Proteins to search against contigs" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
30 <param argument="-e" name="segment_eval" type="float" value="100" label="Maximum e-value of individual match segment" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
31 <param argument="--min-length" name="min_length" type="integer" value="15" label="Minimum number of codons in predicted open reading frame" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
32 <param argument="--metaeuk-eval" name="metaeuk_eval" type="float" value="0.001" label="Maximum e-value of combined exon set" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
33 <param argument="--metaeuk-tcov" name="metaeuk_tcov" type="float" value="0.5" label="Minimum length ratio of combined exon set to target" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
34 <conditional name="adv"> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
35 <param type="select" name="adv_options" label="Show advanced options"> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
36 <option value="yes">Yes</option> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
37 <option value="no" selected="true">No</option> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
38 </param> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
39 <when value="yes"> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
40 <param argument="--max-intron" name="max_intron" value="10000" type="integer" label="Maximum intron size" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
41 <param argument="--min-intron" name="min_intron" value="15" type="integer" label="Minimum intron size" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
42 </when> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
43 <when value="no"> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
44 </when> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
45 </conditional> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
46 </inputs> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
47 <outputs> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
48 <data name="output" format="fasta" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
49 </outputs> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
50 |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
51 <tests> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
52 <test> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
53 <param name="contigs" ftype="fasta" value="contigs.fna" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
54 <param name="query" ftype="fasta" value="proteins.faa" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
55 <output name="output" ftype="fasta" value="output.fasta" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
56 </test> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
57 <test> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
58 <param name="contigs" ftype="fasta" value="contigs.fna" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
59 <param name="query" ftype="fasta" value="proteins.faa" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
60 <conditional name="adv"> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
61 <param name="adv_options" value="yes" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
62 <param name="max_intron" value="1000" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
63 </conditional> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
64 <assert_command> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
65 <has_text text="--max-intron '1000'" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
66 </assert_command> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
67 <output name="output" ftype="fasta" value="output.fasta" /> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
68 </test> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
69 </tests> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
70 <help><![CDATA[ |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
71 |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
72 MetaEuk_ is a modular toolkit designed for large-scale gene discovery and |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
73 annotation in eukaryotic metagenomic contigs. Metaeuk combines the fast and |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
74 sensitive homology search capabilities of MMseqs2_ with a dynamic programming |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
75 procedure to recover optimal exons sets. It reduces redundancies in multiple |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
76 discoveries of the same gene and resolves conflicting gene predictions on |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
77 the same strand. |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
78 |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
79 This tool implements the easy-predict command from metaeuk, which combines |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
80 metaeuk modules into a pipeline for protein alignment prediction. Input is |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
81 the contigs you want to search for protein hits and the proteins you want |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
82 to search against those contigs. Output is FASTA format predicted ORFs, with |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
83 exons annotated in the header according to the metaeuk header format_. |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
84 |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
85 .. _MetaEuk: https://github.com/soedinglab/metaeuk |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
86 .. _MMseqs2: https://github.com/soedinglab/MMseqs2 |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
87 .. _format: https://github.com/soedinglab/metaeuk#the-metaeuk-header |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
88 ]]></help> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
89 <citations> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
90 <citation type="doi">10.1186/s40168-020-00808-x</citation> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
91 </citations> |
5f6ebc3103ee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit a1b87b5a34d0f3971f0110a89f5e87a5937dc8d2"
iuc
parents:
diff
changeset
|
92 </tool> |