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comparison dante_gff_to_dna.xml @ 19:b34483adf8f0 draft

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author petr-novak
date Tue, 24 Sep 2019 08:00:54 -0400
parents 039c45c01b47
children 31449f1183d8
comparison
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18:039c45c01b47 19:b34483adf8f0
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) &amp;&amp; 8 TEMP_DIR_LINEAGES=\$(mktemp -d) &amp;&amp;
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 &amp;&amp; 17 &amp;&amp;
17 18
18 cat \$TEMP_DIR_LINEAGES/domains_counts.txt \$TEMP_DIR_LINEAGES/*fasta > $out_fasta &amp;&amp; 19 cat \$TEMP_DIR_LINEAGES/domains_counts.txt \$TEMP_DIR_LINEAGES/*fasta > $out_fasta &amp;&amp;
19 rm -rf \$TEMP_DIR_LINEAGES 20 rm -rf \$TEMP_DIR_LINEAGES
20 </command> 21 </command>