Mercurial > repos > petr-novak > dante

comparison dante_gff_to_dna.xml @ 23:e2bbc79f0fac draft

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"planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty"
author petr-novak
date Wed, 25 Jan 2023 13:06:55 +0000
parents 65a6fb89495d
children df99812ded92
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22:1eabd42e00ef 23:e2bbc79f0fac
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="1.1.4">
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">dante=0.1.4</requirement>
5 <requirement type="package" version="1.0">rexdb</requirement>
6 <requirement type="set_environment">REXDB</requirement>
7 </requirements> 5 </requirements>
8 <command> 6 <command>
9 TEMP_DIR_LINEAGES=\$(mktemp -d) &amp;&amp; 7 TEMP_DIR_LINEAGES=\$(mktemp -d) &amp;&amp;
10 python3 ${__tool_directory__}/dante_gff_to_dna.py --domains_gff ${domains_gff} --input_dna ${input_dna} --out_dir \$TEMP_DIR_LINEAGES 8 /mnt/raid/users/petr/workspace/dante/dante_gff_to_dna.py --domains_gff ${domains_gff} --input_dna ${input_dna} --out_dir \$TEMP_DIR_LINEAGES
11 9
12 #if $extend_edges: 10 #if $extend_edges:
13 --extended True 11 --extended True
14 #else: 12 #else:
15 --extended False 13 --extended False
16 #end if 14 #end if
17 --classification \${REXDB}/${db_type}_class 15 --database ${database}
18 &amp;&amp; 16 &amp;&amp;
19 17
20 cat \$TEMP_DIR_LINEAGES/*fasta > $out_fasta &amp;&amp; 18 cat \$TEMP_DIR_LINEAGES/*fasta > $out_fasta &amp;&amp;
21 rm -rf \$TEMP_DIR_LINEAGES 19 rm -rf \$TEMP_DIR_LINEAGES
22 </command> 20 </command>
23 <inputs> 21 <inputs>
24 <param format="fasta" type="data" name="input_dna" label="Input DNA" help="Choose input DNA sequence(s) to extract the domains from" /> 22 <param format="fasta" type="data" name="input_dna" label="Input DNA" help="Choose input DNA sequence(s) to extract the domains from" />
25 <param format="gff" type="data" name="domains_gff" label="Protein domains GFF" help="Choose filtered protein domains GFF3 (DANTE's output)" /> 23 <param format="gff" type="data" name="domains_gff" label="Protein domains GFF" help="Choose filtered protein domains GFF3 (DANTE's output)" />
26 <param name="db_type" type="select" label="Select taxon and protein domain database version (REXdb)" help=""> 24 <param name="database" type="select" label="Select REXdb database">
27 <options from_file="rexdb_versions.loc"> 25 <option value="Viridiplantae_v3.0" selected="true">Viridiplantae_v3.0</option>
28 <column name="name" index="0"/> 26 <option value="Metazoa_v3.1" selected="true">Metazoa_v3.1</option>
29 <column name="value" index="1"/> 27 <option value="Viridiplantae_v2.2" selected="true">Viridiplantae_v2.2</option>
30 </options> 28 <option value="Metazoa_v3.0" selected="true">Metazoa_v3.1</option>
31 </param> 29 </param>
32 30
33 <param name="extend_edges" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Extend sequence edges" help="Extend extracted sequence edges to the full length of database domains sequences"/> 31 <param name="extend_edges" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Extend sequence edges" help="Extend extracted sequence edges to the full length of database domains sequences"/>
34 </inputs> 32 </inputs>
35 <outputs> 33 <outputs>
36 <data format="fasta" name="out_fasta" label="Concatenated fasta domains NT sequences from ${input_dna.hid}" /> 34 <data format="fasta" name="out_fasta" label="Concatenated fasta domains NT sequences from ${input_dna.hid}" />