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comparison dante.xml @ 22:1eabd42e00ef draft

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author petr-novak
date Fri, 03 Apr 2020 07:27:59 -0400
parents 3151a72a6671
children e2bbc79f0fac
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21:65a6fb89495d 22:1eabd42e00ef
1 <tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.0.0"> 1 <tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.0">
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">last</requirement>
5 <requirement type="package">numpy</requirement> 5 <requirement type="package">numpy</requirement>
6 <requirement type="package" version="1.0">rexdb</requirement> 6 <requirement type="package" version="1.0">rexdb</requirement>
24 python3 ${__tool_directory__}/dante.py --query \${INPUT_SEQUENCES} --domain_gff ${DomGff} 24 python3 ${__tool_directory__}/dante.py --query \${INPUT_SEQUENCES} --domain_gff ${DomGff}
25 --protein_database \${REXDB}/${db_type}_pdb 25 --protein_database \${REXDB}/${db_type}_pdb
26 --classification \${REXDB}/${db_type}_class 26 --classification \${REXDB}/${db_type}_class
27 --scoring_matrix ${scoring_matrix} 27 --scoring_matrix ${scoring_matrix}
28 28
29 &amp;&amp;
30 python3 ${__tool_directory__}/dante_gff_output_filtering.py --dom_gff ${DomGff}
31 --domains_prot_seq ${Domains_filtered} --domains_filtered ${DomGff_filtered}
32 --output_dir .
33 --selected_dom All --th_identity 0.35
34 --th_similarity 0.45 --th_length 0.8
35 --interruptions 3 --max_len_proportion 1.2
36 --element_type ''
29 37
30 #if str($input_type.input_type_selector) == "aln" 38 #if str($input_type.input_type_selector) == "aln"
31 &amp;&amp; 39 &amp;&amp;
32 python3 ${__tool_directory__}/coverage2gff.py -p sequences.profile -g ${DomGff} 40 python3 ${__tool_directory__}/coverage2gff.py -p sequences.profile -g ${DomGff}
33 #end if 41 #end if
98 <option value="Yes">Yes</option> 106 <option value="Yes">Yes</option>
99 </param> 107 </param>
100 </inputs> 108 </inputs>
101 109
102 <outputs> 110 <outputs>
103 <data format="gff3" name="DomGff" label="DANTE on ${on_string}" /> 111 <data format="gff3" name="DomGff" label="DANTE on ${on_string}, full output" />
112 <data format="gff3" name="DomGff_filtered" label="DANTE on ${on_string}, filtered output" />
113 <data format="fasta" name="Domains_filtered" label="DANTE on ${on_string}, protein domains, filtered output" />
104 <data format="gff3" name="DomGff2" label="DANTE on ${on_string}: 2nd pass"> 114 <data format="gff3" name="DomGff2" label="DANTE on ${on_string}: 2nd pass">
105 <filter>iterative == "Yes" </filter> 115 <filter>iterative == "Yes" </filter>
106 </data> 116 </data>
107 </outputs> 117 </outputs>
108 <tests> 118 <tests>
120 130
121 131
122 <help> 132 <help>
123 133
124 134
125 THIS IS A PRIMARY OUTPUT THAT SHOULD UNDERGO FURTHER QUALITY FILTERING TO GET RID OFF POTENTIAL FALSE POSITIVE DOMAINS 135
126 136
127 **WHAT IT DOES** 137 **WHAT IT DOES**
128 138
129 This tool uses external aligning programme `LAST`_ and RepeatExplorer database of TE protein domains(REXdb) (Viridiplantae and Metazoa) 139 This tool uses external aligning programme `LAST`_ and RepeatExplorer database of TE protein domains(REXdb) (Viridiplantae and Metazoa)
130 140