Mercurial > repos > iuc > snap_training
comparison snap_training.xml @ 0:821bf8bc5623 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
| author | iuc |
|---|---|
| date | Fri, 20 Oct 2017 03:51:58 -0400 |
| parents | |
| children | 2a598c0aa042 |
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| -1:000000000000 | 0:821bf8bc5623 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="snap_training" name="Train SNAP" profile="16.04" version="@VERSION@"> | |
| 3 <description>ab-initio gene predictor</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"> | |
| 8 <requirement type="package" version="2.31.9">maker</requirement> | |
| 9 </expand> | |
| 10 <command><![CDATA[ | |
| 11 cp '${maker_gff}' input.gff3 && | |
| 12 echo "\##FASTA" >> input.gff3 && | |
| 13 cat '${genome}' >> input.gff3 && | |
| 14 maker2zff input.gff3 && | |
| 15 fathom -categorize ${gene_num} genome.ann genome.dna && | |
| 16 fathom -export ${gene_num} -plus uni.ann uni.dna && | |
| 17 forge export.ann export.dna && | |
| 18 hmm-assembler.pl snap_training . > '${output}' | |
| 19 ]]></command> | |
| 20 <inputs> | |
| 21 <param name="genome" type="data" format="fasta" label="Genome to annotate"/> | |
| 22 <param name="maker_gff" type="data" format="gff" label="Maker annotation to use for training"/> | |
| 23 <param name="gene_num" type="integer" value="1000" label="Number of gene model to use for training"/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format="snaphmm" name="output" label="${tool.name} on ${on_string}: SNAP trained model"/> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="genome" value="human.fa"/> | |
| 31 <param name="maker_gff" value="annot.gff3"/> | |
| 32 <output name="output" compare="sim_size" file="snap.hmm"/> | |
| 33 </test> | |
| 34 </tests> | |
| 35 <help><![CDATA[ | |
| 36 This tool allows to train SNAP (an ab-initio gene predictor) based on a previous prediction made with Maker. | |
| 37 ]]></help> | |
| 38 <expand macro="citations"/> | |
| 39 </tool> |