Mercurial > repos > iuc > metaeuk_easy_predict

comparison metaeuk_easy_predict.xml @ 3:578bb60dcc94 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit 3309bdde7b03c5c250a020b0aee221133d9ea79b"
author iuc
date Thu, 21 Oct 2021 16:09:42 +0000
parents 24cca965e8df
children ce703f4dfbd4
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2:24cca965e8df 3:578bb60dcc94
2 <description>High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</description> 2 <description>High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">MetaEuk</xref> 4 <xref type="bio.tools">MetaEuk</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
7 <token name="@TOOL_VERSION@">4.a0f584d</token> 7 <token name="@TOOL_VERSION@">5.34c21f2</token>
8 </macros> 8 </macros>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
23 --metaeuk-tcov '${metaeuk_tcov}' 23 --metaeuk-tcov '${metaeuk_tcov}'
24 #if $adv.adv_options == "yes" 24 #if $adv.adv_options == "yes"
25 --max-intron '${adv.max_intron}' 25 --max-intron '${adv.max_intron}'
26 --min-intron '${adv.min_intron}' 26 --min-intron '${adv.min_intron}'
27 #end if 27 #end if
28 --write-frag-coords $write_frag_coords
28 && mv output.fasta.codon.fas '$output' 29 && mv output.fasta.codon.fas '$output'
30 && mv output.fasta.gff '$gff_output'
29 ]]></command> 31 ]]></command>
30 <inputs> 32 <inputs>
31 <param name="contigs" type="data" format="fasta" label="Contigs to search again" /> 33 <param name="contigs" type="data" format="fasta" label="Contigs to search again" />
32 <param name="query" type="data" format="fasta" label="Proteins to search against contigs" /> 34 <param name="query" type="data" format="fasta" label="Proteins to search against contigs" />
33 <param argument="-e" name="segment_eval" type="float" value="100" label="Maximum e-value of individual match segment" /> 35 <param argument="-e" name="segment_eval" type="float" value="100" label="Maximum e-value of individual match segment" />
44 <param argument="--min-intron" name="min_intron" value="15" type="integer" label="Minimum intron size" /> 46 <param argument="--min-intron" name="min_intron" value="15" type="integer" label="Minimum intron size" />
45 </when> 47 </when>
46 <when value="no"> 48 <when value="no">
47 </when> 49 </when>
48 </conditional> 50 </conditional>
51 <param name="write_frag_coords" type="select" value="0" label="Write the contig coords of the stop-to-stop fragment in which putative exon lies" help="The fragment coordinates in square brackets refer to the original fragment in which the exon was found." >
52 <option value="0">Yes</option>
53 <option value="1">No</option>
54 </param>
49 </inputs> 55 </inputs>
50 <outputs> 56 <outputs>
51 <data name="output" format="fasta" /> 57 <data name="output" format="fasta" />
58 <data name="gff_output" format="gff" />
52 </outputs> 59 </outputs>
53 60
54 <tests> 61 <tests>
55 <test> 62 <test>
56 <param name="contigs" ftype="fasta" value="contigs.fna" /> 63 <param name="contigs" ftype="fasta" value="contigs.fna" />
57 <param name="query" ftype="fasta" value="proteins.faa" /> 64 <param name="query" ftype="fasta" value="proteins.faa" />
58 <output name="output" ftype="fasta" value="output.fasta" /> 65 <output name="output" ftype="fasta" value="output.fasta" />
66 <output name="gff_output" ftype="gff" value="output.gff" />
59 </test> 67 </test>
60 <test> 68 <test>
61 <param name="contigs" ftype="fasta" value="contigs.fna" /> 69 <param name="contigs" ftype="fasta" value="contigs.fna" />
62 <param name="query" ftype="fasta" value="proteins.faa" /> 70 <param name="query" ftype="fasta" value="proteins.faa" />
71 <param name="write_frag_coords" value="1" />
63 <conditional name="adv"> 72 <conditional name="adv">
64 <param name="adv_options" value="yes" /> 73 <param name="adv_options" value="yes" />
65 <param name="max_intron" value="1000" /> 74 <param name="max_intron" value="1000" />
66 </conditional> 75 </conditional>
67 <assert_command> 76 <assert_command>
68 <has_text text="--max-intron '1000'" /> 77 <has_text text="--max-intron '1000'" />
69 </assert_command> 78 </assert_command>
70 <output name="output" ftype="fasta" value="output.fasta" /> 79 <output name="output" ftype="fasta" value="output_w_frag_coords.fasta" />
80 <output name="gff_output" ftype="gff" value="output.gff" />
71 </test> 81 </test>
72 </tests> 82 </tests>
73 <help><![CDATA[ 83 <help><![CDATA[
74 84
75 MetaEuk_ is a modular toolkit designed for large-scale gene discovery and 85 MetaEuk_ is a modular toolkit designed for large-scale gene discovery and