Mercurial > repos > iuc > metaeuk_easy_predict
comparison metaeuk_easy_predict.xml @ 2:be6bbdeafcb8 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit 3309bdde7b03c5c250a020b0aee221133d9ea79b"
| author | iuc |
|---|---|
| date | Thu, 21 Oct 2021 16:10:35 +0000 |
| parents | f91548912113 |
| children |
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| 1:f91548912113 | 2:be6bbdeafcb8 |
|---|---|
| 1 <tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy0"> | 1 <tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy0"> |
| 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> | |
| 4 <xref type="bio.tools">MetaEuk</xref> | |
| 5 </xrefs> | |
| 3 <macros> | 6 <macros> |
| 4 <token name="@TOOL_VERSION@">4.a0f584d</token> | 7 <token name="@TOOL_VERSION@">5.34c21f2</token> |
| 5 </macros> | 8 </macros> |
| 6 <requirements> | 9 <requirements> |
| 7 <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement> | 10 <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement> |
| 8 </requirements> | 11 </requirements> |
| 9 <command detect_errors="aggressive"><![CDATA[ | 12 <command detect_errors="aggressive"><![CDATA[ |
| 20 --metaeuk-tcov '${metaeuk_tcov}' | 23 --metaeuk-tcov '${metaeuk_tcov}' |
| 21 #if $adv.adv_options == "yes" | 24 #if $adv.adv_options == "yes" |
| 22 --max-intron '${adv.max_intron}' | 25 --max-intron '${adv.max_intron}' |
| 23 --min-intron '${adv.min_intron}' | 26 --min-intron '${adv.min_intron}' |
| 24 #end if | 27 #end if |
| 28 --write-frag-coords $write_frag_coords | |
| 25 && mv output.fasta.codon.fas '$output' | 29 && mv output.fasta.codon.fas '$output' |
| 30 && mv output.fasta.gff '$gff_output' | |
| 26 ]]></command> | 31 ]]></command> |
| 27 <inputs> | 32 <inputs> |
| 28 <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" /> |
| 29 <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" /> |
| 30 <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" /> |
| 41 <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" /> |
| 42 </when> | 47 </when> |
| 43 <when value="no"> | 48 <when value="no"> |
| 44 </when> | 49 </when> |
| 45 </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> | |
| 46 </inputs> | 55 </inputs> |
| 47 <outputs> | 56 <outputs> |
| 48 <data name="output" format="fasta" /> | 57 <data name="output" format="fasta" /> |
| 58 <data name="gff_output" format="gff" /> | |
| 49 </outputs> | 59 </outputs> |
| 50 | 60 |
| 51 <tests> | 61 <tests> |
| 52 <test> | 62 <test> |
| 53 <param name="contigs" ftype="fasta" value="contigs.fna" /> | 63 <param name="contigs" ftype="fasta" value="contigs.fna" /> |
| 54 <param name="query" ftype="fasta" value="proteins.faa" /> | 64 <param name="query" ftype="fasta" value="proteins.faa" /> |
| 55 <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" /> | |
| 56 </test> | 67 </test> |
| 57 <test> | 68 <test> |
| 58 <param name="contigs" ftype="fasta" value="contigs.fna" /> | 69 <param name="contigs" ftype="fasta" value="contigs.fna" /> |
| 59 <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" /> | |
| 60 <conditional name="adv"> | 72 <conditional name="adv"> |
| 61 <param name="adv_options" value="yes" /> | 73 <param name="adv_options" value="yes" /> |
| 62 <param name="max_intron" value="1000" /> | 74 <param name="max_intron" value="1000" /> |
| 63 </conditional> | 75 </conditional> |
| 64 <assert_command> | 76 <assert_command> |
| 65 <has_text text="--max-intron '1000'" /> | 77 <has_text text="--max-intron '1000'" /> |
| 66 </assert_command> | 78 </assert_command> |
| 67 <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" /> | |
| 68 </test> | 81 </test> |
| 69 </tests> | 82 </tests> |
| 70 <help><![CDATA[ | 83 <help><![CDATA[ |
| 71 | 84 |
| 72 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 |