Mercurial > repos > petr-novak > dante

comparison dante.xml @ 24:df99812ded92 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit a0a9b02c60a91942a271b8b35648c0b152fe1ebd-dirty"
author petr-novak
date Fri, 27 Jan 2023 08:15:31 +0000
parents e2bbc79f0fac
children 74babe57d739
comparison
equal deleted inserted replaced
23:e2bbc79f0fac 24:df99812ded92
1 <tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.4"> 1 <tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.5">
2 <description> Tool for annotation of transposable elements based on the similarity to conserved protein domains database. </description> 2 <description> Tool for annotation of transposable elements based on the similarity to conserved protein domains database. </description>
3 <requirements> 3 <requirements>
4 <requirement type="package">dante=0.1.4</requirement> 4 <requirement type="package">dante=0.1.5</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> 7 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
8 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> 8 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
9 </stdio> 9 </stdio>
15 #else 15 #else
16 INPUT_SEQUENCES=$(input_sequences) 16 INPUT_SEQUENCES=$(input_sequences)
17 #end if 17 #end if
18 &amp;&amp; 18 &amp;&amp;
19 19
20
21 dante --query \${INPUT_SEQUENCES} --domain_gff ${DomGff} 20 dante --query \${INPUT_SEQUENCES} --domain_gff ${DomGff}
22 --database $database 21 --database $database
23 --scoring_matrix ${scoring_matrix} 22 --scoring_matrix ${scoring_matrix}
24 23 --cpu \${GALAXY_SLOTS:-1}
25 &amp;&amp;
26 dante_gff_output_filtering.py --dom_gff ${DomGff} 24 dante_gff_output_filtering.py --dom_gff ${DomGff}
27 --domains_prot_seq ${Domains_filtered} --domains_filtered ${DomGff_filtered} 25 --domains_prot_seq ${Domains_filtered} --domains_filtered ${DomGff_filtered}
28 --output_dir . 26 --output_dir .
29 --selected_dom All --th_identity 0.35 27 --selected_dom All --th_identity 0.35
30 --th_similarity 0.45 --th_length 0.8 28 --th_similarity 0.45 --th_length 0.8