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comparison dante.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 1eabd42e00ef
children df99812ded92
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22:1eabd42e00ef 23:e2bbc79f0fac
1 <tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.0"> 1 <tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.4">
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">last</requirement> 4 <requirement type="package">dante=0.1.4</requirement>
5 <requirement type="package">numpy</requirement>
6 <requirement type="package" version="1.0">rexdb</requirement>
7 <requirement type="set_environment">REXDB</requirement>
8 </requirements> 5 </requirements>
9 <stdio> 6 <stdio>
10 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> 7 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
11 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> 8 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
12 </stdio> 9 </stdio>
13 <command> 10 <command>
14 #if str($input_type.input_type_selector) == "aln" 11 #if str($input_type.input_type_selector) == "aln"
15 python3 ${__tool_directory__}/parse_aln.py -a $(input_sequences) -f sequences.fasta -p sequences.profile 12 parse_aln.py -a $(input_sequences) -f sequences.fasta -p sequences.profile
16 &amp;&amp; 13 &amp;&amp;
17 INPUT_SEQUENCES="sequences.fasta" 14 INPUT_SEQUENCES="sequences.fasta"
18 #else 15 #else
19 INPUT_SEQUENCES=$(input_sequences) 16 INPUT_SEQUENCES=$(input_sequences)
20 #end if 17 #end if
21 &amp;&amp; 18 &amp;&amp;
22 19
23 20
24 python3 ${__tool_directory__}/dante.py --query \${INPUT_SEQUENCES} --domain_gff ${DomGff} 21 dante --query \${INPUT_SEQUENCES} --domain_gff ${DomGff}
25 --protein_database \${REXDB}/${db_type}_pdb 22 --database $database
26 --classification \${REXDB}/${db_type}_class 23 --scoring_matrix ${scoring_matrix}
27 --scoring_matrix ${scoring_matrix}
28 24
29 &amp;&amp; 25 &amp;&amp;
30 python3 ${__tool_directory__}/dante_gff_output_filtering.py --dom_gff ${DomGff} 26 dante_gff_output_filtering.py --dom_gff ${DomGff}
31 --domains_prot_seq ${Domains_filtered} --domains_filtered ${DomGff_filtered} 27 --domains_prot_seq ${Domains_filtered} --domains_filtered ${DomGff_filtered}
32 --output_dir . 28 --output_dir .
33 --selected_dom All --th_identity 0.35 29 --selected_dom All --th_identity 0.35
34 --th_similarity 0.45 --th_length 0.8 30 --th_similarity 0.45 --th_length 0.8
35 --interruptions 3 --max_len_proportion 1.2 31 --interruptions 3 --max_len_proportion 1.2
36 --element_type '' 32 --element_type ''
37 33
38 #if str($input_type.input_type_selector) == "aln" 34 #if str($input_type.input_type_selector) == "aln"
39 &amp;&amp; 35 &amp;&amp;
40 python3 ${__tool_directory__}/coverage2gff.py -p sequences.profile -g ${DomGff} 36 coverage2gff.py -p sequences.profile -g ${DomGff}
41 #end if 37 #end if
42 38
43 #if str($iterative) == "Yes" 39 #if str($iterative) == "Yes"
44 &amp;&amp; 40 &amp;&amp;
45 python3 ${__tool_directory__}/dante_gff_output_filtering.py --dom_gff ${DomGff} 41 dante_gff_output_filtering.py --dom_gff ${DomGff}
46 --domains_prot_seq domains_filtered.fasta --domains_filtered domains_filtered.gff 42 --domains_prot_seq domains_filtered.fasta --domains_filtered domains_filtered.gff
47 --output_dir . 43 --output_dir .
48 --selected_dom All --th_identity 0.35 44 --selected_dom All --th_identity 0.35
49 --th_similarity 0.45 --th_length 0.9 45 --th_similarity 0.45 --th_length 0.9
50 --interruptions 1 --max_len_proportion 1.1 46 --interruptions 1 --max_len_proportion 1.1
51 --element_type '' 47 --element_type ''
52 &amp;&amp; 48 &amp;&amp;
53 49
54 50
55 51
56 python3 ${__tool_directory__}/fasta2database.py domains_filtered.fasta domains_filtered.db 52 fasta2database.py domains_filtered.fasta domains_filtered.db
57 domains_filtered.class 53 domains_filtered.class
58 &amp;&amp; 54 &amp;&amp;
59 55
60 lastdb -p domains_filtered.db domains_filtered.db 56 lastdb -p domains_filtered.db domains_filtered.db
61 &amp;&amp; 57 &amp;&amp;
62 58
63 python3 ${__tool_directory__}/dante.py --query \${INPUT_SEQUENCES} --domain_gff ${DomGff2} 59 dante.py --query \${INPUT_SEQUENCES} --domain_gff ${DomGff2}
64 --protein_database domains_filtered.db 60 --protein_database domains_filtered.db
65 --classification domains_filtered.class 61 --classification domains_filtered.class
66 --scoring_matrix BL80 62 --scoring_matrix BL80
67 63
68 64
69 #if str($input_type.input_type_selector) == "aln" 65 #if str($input_type.input_type_selector) == "aln"
70 &amp;&amp; 66 &amp;&amp;
71 python3 ${__tool_directory__}/coverage2gff.py -p sequences.profile -g ${DomGff2} 67 coverage2gff.py -p sequences.profile -g ${DomGff2}
72 #end if 68 #end if
73 #end if 69 #end if
74 70
75 </command> 71 </command>
76 <inputs> 72 <inputs>
85 </when> 81 </when>
86 <when value="aln"> 82 <when value="aln">
87 <param name="input_sequences" type="data" format="txt" label="Sequences in ALN format (extracted from RepeatExplorer)"/> 83 <param name="input_sequences" type="data" format="txt" label="Sequences in ALN format (extracted from RepeatExplorer)"/>
88 </when> 84 </when>
89 </conditional> 85 </conditional>
90 <param name="db_type" type="select" label="Select taxon and protein domain database version (REXdb)" help=""> 86 <param name="database" type="select" label="Select REXdb database">
91 <options from_file="rexdb_versions.loc"> 87 <option value="Viridiplantae_v3.0" selected="true">Viridiplantae_v3.0</option>
92 <column name="name" index="0"/> 88 <option value="Metazoa_v3.1" selected="true">Metazoa_v3.1</option>
93 <column name="value" index="1"/> 89 <option value="Viridiplantae_v2.2" selected="true">Viridiplantae_v2.2</option>
94 </options> 90 <option value="Metazoa_v3.0" selected="true">Metazoa_v3.1</option>
95 </param> 91 </param>
96
97 <param name="scoring_matrix" type="select" label="Select scoring matrix"> 92 <param name="scoring_matrix" type="select" label="Select scoring matrix">
98 <option value="BL80" selected="true" >BLOSUM80</option> 93 <option value="BL80" selected="true" >BLOSUM80</option>
99 <option value="BL62">BLOSUM62</option> 94 <option value="BL62">BLOSUM62</option>
100 <option value="MIQS">MIQS</option> 95 <option value="MIQS">MIQS</option>
101 </param> 96 </param>