Mercurial > repos > iuc > snap_training
changeset 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 |
| files | macros.xml snap_training.xml test-data/annot.gff3 test-data/annot_aa.fasta test-data/annot_tx.fasta test-data/human.fa test-data/snap.hmm test-data/snap_annot.gff |
| diffstat | 8 files changed, 1987 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Oct 20 03:51:58 2017 -0400 @@ -0,0 +1,17 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">snap</requirement> + <yield /> + </requirements> + </xml> + + <token name="@VERSION@">2013_11_29</token> + + <xml name="citations"> + <citations> + </citations> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snap_training.xml Fri Oct 20 03:51:58 2017 -0400 @@ -0,0 +1,39 @@ +<?xml version="1.0"?> +<tool id="snap_training" name="Train SNAP" profile="16.04" version="@VERSION@"> + <description>ab-initio gene predictor</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="2.31.9">maker</requirement> + </expand> + <command><![CDATA[ + cp '${maker_gff}' input.gff3 && + echo "\##FASTA" >> input.gff3 && + cat '${genome}' >> input.gff3 && + maker2zff input.gff3 && + fathom -categorize ${gene_num} genome.ann genome.dna && + fathom -export ${gene_num} -plus uni.ann uni.dna && + forge export.ann export.dna && + hmm-assembler.pl snap_training . > '${output}' + ]]></command> + <inputs> + <param name="genome" type="data" format="fasta" label="Genome to annotate"/> + <param name="maker_gff" type="data" format="gff" label="Maker annotation to use for training"/> + <param name="gene_num" type="integer" value="1000" label="Number of gene model to use for training"/> + </inputs> + <outputs> + <data format="snaphmm" name="output" label="${tool.name} on ${on_string}: SNAP trained model"/> + </outputs> + <tests> + <test> + <param name="genome" value="human.fa"/> + <param name="maker_gff" value="annot.gff3"/> + <output name="output" compare="sim_size" file="snap.hmm"/> + </test> + </tests> + <help><![CDATA[ + This tool allows to train SNAP (an ab-initio gene predictor) based on a previous prediction made with Maker. + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot.gff3 Fri Oct 20 03:51:58 2017 -0400 @@ -0,0 +1,41 @@ +##gff-version 3 +HS08198 maker gene 352 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0 +HS08198 maker mRNA 352 1848 2869 + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192 +HS08198 maker exon 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 421 582 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 812 894 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1053 1123 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1208 1315 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1587 1688 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1772 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 421 444 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 445 582 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 812 894 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1053 1123 . + 1 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1208 1315 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1587 1688 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1772 1848 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +### +HS04636 maker gene 1813 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0 +HS04636 maker mRNA 1813 6903 8728 + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572 +HS04636 maker exon 1813 1934 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 2055 2198 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 2852 2995 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 3426 3607 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4340 4423 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4543 4789 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5072 5358 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5860 6007 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 6494 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker five_prime_UTR 1813 1861 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 1862 1934 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2055 2198 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2852 2995 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 3426 3607 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4340 4423 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4543 4789 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 5072 5358 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 5860 6007 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 6494 6903 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +###
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_aa.fasta Fri Oct 20 03:51:58 2017 -0400 @@ -0,0 +1,19 @@ +>HS04636-snap.1 +MSYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFKGFWNV +VNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRA +LPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPDPQGSNMMFAFF +AQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGK +MKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLMMY +ATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQH +LSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQK +YNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQAS +IDQSRQMKYQSFNEYRKRFMLKPYESFEELTGEKEMSAELEALYGDIDAV +ELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFG +GEVGFQIINTASIQSLICNNVKGCPFTSFSVPDPELIKTVTINASSSRSG +LDDINPTVLLKERSTEL* +>HS08198-snap.1 +MNPSCHPAAATMLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPK +ANFDAQQEQGHRAEATTLHVAPQGTAMAPVVPPPRPPRDGICWQVRQLYG +DTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARS +LPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQFHVLDGECTAG +ASMAAW*
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_tx.fasta Fri Oct 20 03:51:58 2017 -0400 @@ -0,0 +1,42 @@ +>HS04636-snap.1 +atgagttataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccg +gaatttttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacata +cttacccacttcaagggattttggaacgttgtgaataacattcccttccttcgaaatgca +attatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaat +gctgactatggctacaaaagctgggaagccttctctaacctctcctattatactagagcc +cttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt +cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccc +cagggctcaaacatgatgtttgcattctttgcccagcacttcacgcatcagtttttcaag +acagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaat +catatttacggtgaaactctggctagacagcgtaaactgcgccttttcaaggatggaaaa +atgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatactcaggca +gagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtc +tttggtctggtgcctggtctgatgatgtatgccacaatctggctgcgggaacacaacaga +gtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagaca +agcaggctaatactgataggagagactattaagattgtgattgaagattatgtgcaacac +ttgagtggctatcacttcaaactgaaatttgacccagaactacttttcaacaaacaattc +cagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctg +cctgacacctttcaaattcatgaccagaaatacaactatcaacagtttatctacaacaac +tctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgct +ggcagggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttcc +attgaccagagcaggcagatgaaataccagtcttttaatgagtaccgcaaacgctttatg +ctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttg +gaagcactctatggtgacatcgatgctgtggagctgtatcctgcccttctggtagaaaag +cctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctccttg +aaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggt +ggagaagtgggttttcaaatcatcaacactgcctcaattcagtctctcatctgcaataac +gtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtc +accatcaatgcaagttcttcccgctccggactagatgatatcaatcccacagtactacta +aaagaacgttcgactgaactgtag +>HS08198-snap.1 +atgaacccctcctgccaccctgctgccgccaccatgctgccccctgggactgcgaccctc +ttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccacgccggccc +gcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggc +caccgggccgaggccaccacactgcatgtggctccccagggcacagccatggctcctgtg +gtgcctcctccccgcccccccagggatgggatctgctggcaggtgcgccagctctatgga +gacacaggggtcctcggccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcac +gtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcgggcgggg +cagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtggg +tttgagcagcgggtccaggaggcccacctgactgaggaccagatcttctacttccccaag +tacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggg +gcaagcatggcggcgtggtga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human.fa Fri Oct 20 03:51:58 2017 -0400 @@ -0,0 +1,200 @@ +>HS04636 +gagctcacattaactatttacagggtaactgcttaggaccagtattatgaggagaattta +cctttcccgcctctctttccaagaaacaaggagggggtgaaggtacggagaacagtattt +cttctgttgaaagcaacttagctacaaagataaattacagctatgtacactgaaggtagc +tatttcattccacaaaataagagttttttaaaaagctatgtatgtatgtgctgcatatag +agcagatatacagcctattaagcgtcgtcactaaaacataaaacatgtcagcctttctta +accttactcgccccagtctgtcccgacgtgacttcctcgaccctctaaagacgtacagac +cagacacggcggcggcggcgggagaggggattccctgcgcccccggacctcagggccgct +cagattcctggagaggaagccaagtgtccttctgccctcccccggtatcccatccaaggc +gatcagtccagaactggctctcggaagcgctcgggcaaagactgcgaagaagaaaagaca +tctggcggaaacctgtgcgcctggggcggtggaactcggggaggagagggagggatcaga +caggagagtggggactaccccctctgctcccaaattggggcagcttcctgggtttccgat +tttctcatttccgtgggtaaaaaaccctgcccccaccgggcttacgcaatttttttaagg +ggagaggagggaaaaaatttgtgggggggtacgaaaaggcggaaagaaacagtcattcac +atgggcttggttttcagtcttataaaaaggaaggttctctcggttagcgaccaattgtca 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