Mercurial > repos > petr-novak > dante
comparison dante_gff_to_dna.xml @ 19:b34483adf8f0 draft
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author | petr-novak |
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date | Tue, 24 Sep 2019 08:00:54 -0400 |
parents | 039c45c01b47 |
children | 31449f1183d8 |
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18:039c45c01b47 | 19:b34483adf8f0 |
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1 <tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="1.0.0"> | 1 <tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="1.0.0"> |
2 <description> Tool to extract nucleotide sequences of protein domains found by DANTE </description> | 2 <description> Tool to extract nucleotide sequences of protein domains found by DANTE </description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package">biopython</requirement> | 4 <requirement type="package">biopython</requirement> |
5 <requirement type="set_environment">REXDB</requirement> | |
5 </requirements> | 6 </requirements> |
6 <command> | 7 <command> |
7 TEMP_DIR_LINEAGES=\$(mktemp -d) && | 8 TEMP_DIR_LINEAGES=\$(mktemp -d) && |
8 python3 ${__tool_directory__}/dante_gff_to_dna.py --domains_gff ${domains_gff} --input_dna ${input_dna} --out_dir \$TEMP_DIR_LINEAGES | 9 python3 ${__tool_directory__}/dante_gff_to_dna.py --domains_gff ${domains_gff} --input_dna ${input_dna} --out_dir \$TEMP_DIR_LINEAGES |
9 | 10 |
10 #if $extend_edges: | 11 #if $extend_edges: |
11 --extended True | 12 --extended True |
12 #else: | 13 #else: |
13 --extended False | 14 --extended False |
14 #end if | 15 #end if |
15 --classification ${__tool_data_path__ }/protein_domains/${db_type}_class | 16 --classification \${REXDB}/${db_type}_class |
16 && | 17 && |
17 | 18 |
18 cat \$TEMP_DIR_LINEAGES/domains_counts.txt \$TEMP_DIR_LINEAGES/*fasta > $out_fasta && | 19 cat \$TEMP_DIR_LINEAGES/domains_counts.txt \$TEMP_DIR_LINEAGES/*fasta > $out_fasta && |
19 rm -rf \$TEMP_DIR_LINEAGES | 20 rm -rf \$TEMP_DIR_LINEAGES |
20 </command> | 21 </command> |