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comparison dram_annotate.xml @ 1:4058af4457c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
author iuc
date Tue, 11 Jul 2023 23:46:40 +0000
parents cf3f6929b52c
children 0515750e7b10
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0:cf3f6929b52c 1:4058af4457c0
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)">