Mercurial > repos > petr-novak > dante

comparison dante_gff_to_dna.xml @ 30:f0663cdbae66 draft default tip

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planemo upload commit 29868d121127a8bb509a42fb917b09f669ad4a09-dirty
author petr-novak
date Tue, 05 Nov 2024 15:14:35 +0000
parents 8f2bd3cae2de
children
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29:8f2bd3cae2de 30:f0663cdbae66
1 <tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="1.1.8"> 1 <tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="2.5.1">
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">dante=0.1.8</requirement> 4 <requirement type="package">dante=0.2.5</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 TEMP_DIR_LINEAGES=\$(mktemp -d) &amp;&amp; 7 TEMP_DIR_LINEAGES=\$(mktemp -d) &amp;&amp;
8 dante_gff_to_dna.py --domains_gff ${domains_gff} --input_dna ${input_dna} --out_dir \$TEMP_DIR_LINEAGES 8 dante_gff_to_dna.py --domains_gff ${domains_gff} --input_dna ${input_dna} --out_dir \$TEMP_DIR_LINEAGES
9 9
20 </command> 20 </command>
21 <inputs> 21 <inputs>
22 <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" />
23 <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)" />
24 <param name="database" type="select" label="Select REXdb database"> 24 <param name="database" type="select" label="Select REXdb database">
25 <option value="Viridiplantae_v4.0" selected="true">Viridiplantae_v4.0</option>
25 <option value="Viridiplantae_v3.0" selected="true">Viridiplantae_v3.0</option> 26 <option value="Viridiplantae_v3.0" selected="true">Viridiplantae_v3.0</option>
26 <option value="Metazoa_v3.1" selected="true">Metazoa_v3.1</option> 27 <option value="Metazoa_v3.1" selected="true">Metazoa_v3.1</option>
27 <option value="Viridiplantae_v2.2" selected="true">Viridiplantae_v2.2</option> 28 <option value="Viridiplantae_v2.2" selected="true">Viridiplantae_v2.2</option>
28 <option value="Metazoa_v3.0" selected="true">Metazoa_v3.1</option> 29 <option value="Metazoa_v3.0" selected="true">Metazoa_v3.0</option>
29 </param> 30 </param>
30 31
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"/> 32 <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"/>
32 </inputs> 33 </inputs>
33 <outputs> 34 <outputs>