Mercurial > repos > iuc > dram_annotate
comparison dram_annotate.xml @ 1:4058af4457c0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
author | iuc |
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date | Tue, 11 Jul 2023 23:46:40 +0000 |
parents | cf3f6929b52c |
children | 0515750e7b10 |
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0:cf3f6929b52c | 1:4058af4457c0 |
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1 <tool id="dram_annotate" name="DRAM annotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | 1 <tool id="dram_annotate" name="DRAM annotate" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
2 <description>metagenome-assembled-genomes (MAGs)</description> | 2 <description>metagenome-assembled-genomes (MAGs)</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
39 $use_uniref | 39 $use_uniref |
40 $use_vogdb | 40 $use_vogdb |
41 $low_mem_mode | 41 $low_mem_mode |
42 $skip_trnascan | 42 $skip_trnascan |
43 --threads \${GALAXY_SLOTS:-10} | 43 --threads \${GALAXY_SLOTS:-10} |
44 && test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced' | 44 && (test -f 'output_dir/genes.faa' && mv 'output_dir/genes.faa' '$output_genes_faa' || echo 'No genes.faa output produced') |
45 && test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced' | 45 && (test -f 'output_dir/genes.fna' && mv 'output_dir/genes.fna' '$output_genes_fna' || echo 'No genes.fna output produced') |
46 && test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced' | 46 && (test -f 'output_dir/genes.gff' && mv 'output_dir/genes.gff' '$output_genes_gff' || echo 'No genes.gff output produced') |
47 && test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced' | 47 && (test -f 'output_dir/scaffolds.fna' && mv 'output_dir/scaffolds.fna' '$output_scaffolds_fna' || echo 'No scaffolds.fna output produced') |
48 && test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced' | 48 && (test -f 'output_dir/rrnas.tsv' && mv 'output_dir/rrnas.tsv' '$output_rrnas' || echo 'No rrnas.tsv output produced') |
49 && test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced' | 49 && (test -f 'output_dir/trnas.tsv' && mv 'output_dir/trnas.tsv' '$output_trnas' || echo 'No trnas.tsv output produced') |
50 && test -f 'output_dir/genbank/$output_gbk_file_name' && mv 'output_dir/genbank/$output_gbk_file_name' '$output_genbank' || echo 'No genbank output produced' | 50 && (test -f 'output_dir/genbank/$output_gbk_file_name' && mv 'output_dir/genbank/$output_gbk_file_name' '$output_genbank' || echo 'No genbank output produced') |
51 && test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced' | 51 && (test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced') |
52 ]]></command> | 52 ]]></command> |
53 <inputs> | 53 <inputs> |
54 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file"/> | 54 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file"/> |
55 <param argument="--min_contig_size" type="integer" value="2500" min="0" label="Minimum contig size to be used for gene prediction"/> | 55 <param argument="--min_contig_size" type="integer" value="2500" min="0" label="Minimum contig size to be used for gene prediction"/> |
56 <param argument="--prodigal_mode" type="select" label="Select mode of prodigal to use for gene calling" help="Single mode requires genomes which are high quality with low contamination and long contigs (average length >3 Kbp)"> | 56 <param argument="--prodigal_mode" type="select" label="Select mode of prodigal to use for gene calling" help="Single mode requires genomes which are high quality with low contamination and long contigs (average length >3 Kbp)"> |