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comparison dante_gff_output_filtering.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="domains_filter" name="Protein Domains Filter" version="1.0.1"> 1 <tool id="domains_filter" name="Protein Domains Filter" version="1.1.4">
2 <description> Tool for filtering of gff3 output from DANTE. Filtering can be performed based domain type and alignment quality. </description> 2 <description> Tool for filtering of gff3 output from DANTE. Filtering can be performed based domain type and alignment quality. </description>
3 <stdio> 3 <requirements>
4 <requirement type="package">dante=0.1.4</requirement>
5 </requirements>
6 <stdio>
7 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
8 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> 9 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
5 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> 10 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
6 </stdio> 11 </stdio>
7 <command> 12 <command>
8 python3 ${__tool_directory__}/dante_gff_output_filtering.py --dom_gff ${DomGff} --domains_prot_seq ${dom_prot_seq} --domains_filtered ${dom_filtered} --selected_dom ${selected_domain} --th_identity ${th_identity} --th_similarity ${th_similarity} --th_length ${th_length} --interruptions ${interruptions} --max_len_proportion ${th_len_ratio} --element_type '${element_type}' 13 dante_gff_output_filtering.py --dom_gff ${DomGff} --domains_prot_seq ${dom_prot_seq} --domains_filtered ${dom_filtered} --selected_dom ${selected_domain} --th_identity ${th_identity} --th_similarity ${th_similarity} --th_length ${th_length} --interruptions ${interruptions} --max_len_proportion ${th_len_ratio} --element_type '${element_type}'
9 14
10 </command> 15 </command>
11 <inputs> 16 <inputs>
12 <param format="gff" type="data" name="DomGff" label="Choose primary GFF3 file of all domains from Protein Domains Finder" /> 17 <param format="gff" type="data" name="DomGff" label="Choose primary GFF3 file of all domains from Protein Domains Finder" />
13 <param name="th_identity" type="float" value="0.35" min="0" max="1" label="Minimum identity" help="Protein sequence indentity threshold between input and mapped protein from db [0-1]" /> 18 <param name="th_identity" type="float" value="0.35" min="0" max="1" label="Minimum identity" help="Protein sequence indentity threshold between input and mapped protein from db [0-1]" />
14 <param name="th_similarity" type="float" value="0.45" min="0" max="1" label="Minimum similarity" help="Protein sequence similarity threshold between input and mapped protein from db [0-1]" /> 19 <param name="th_similarity" type="float" value="0.45" min="0" max="1" label="Minimum similarity" help="Protein sequence similarity threshold between input and mapped protein from db [0-1]" />
15 <param name="th_length" type="float" value="0.8" min="0" max="1" label="Minimum alignment length" help="Proportion of the hit length without gaps to the length of the database sequence [0-1]" /> 20 <param name="th_length" type="float" value="0.8" min="0" max="1" label="Minimum alignment length" help="Proportion of the hit length without gaps to the length of the database sequence [0-1]" />
16 <param name="interruptions" type="integer" value="3" label="Interruptions [frameshifts + stop codons]" help="Tolerance threshold per every starting 100 amino acids of alignment sequence" /> 21 <param name="interruptions" type="integer" value="3" label="Interruptions [frameshifts + stop codons]" help="Tolerance threshold per every starting 100 amino acids of alignment sequence" />
17 <param name="th_len_ratio" type="float" value="1.2" label="Maximal length proportion" help="Maximal proportion of alignment length to the original length of protein domain from database (including indels)" /> 22 <param name="th_len_ratio" type="float" value="1.2" label="Maximal length proportion" help="Maximal proportion of alignment length to the original length of protein domain from database (including indels)" />
18 <param name="selected_domain" type="select" label="Select protein domain type" > 23 <param name="selected_domain" type="select" label="Select protein domain type" >
19 <options from_file="select_domain.loc" > 24 <option value="All" selected="true">All</option>
20 <column name="name" index="0"/> 25 <option value="GAG">GAG</option>
21 <column name="value" index="0"/> 26 <option value="INT">INT</option>
22 </options> 27 <option value="PROT">PROT</option>
28 <option value="RH">RH</option>
29 <option value="RT">RT</option>
30 <option value="aRH">aRH</option>
31 <option value="CHDCR">CHDCR</option>
32 <option value="CHDII">CHDII</option>
33 <option value="TPase">TPase</option>
34 <option value="YR">YR</option>
35 <option value="HEL1">HEL1</option>
36 <option value="HEL2">HEL2</option>
37 <option value="ENDO">ENDO</option>
23 </param> 38 </param>
24 <param name="element_type" type="text" value="" label="Filter based on classification" help="You can use preset options or enter an arbitrary string to filter a certain repetitive element type of any level. It must be a continuous substring in a proper format of Final_Classification attribute of GFF3 file. Classification levels are separated by | character. Filtering is case sensitive"> 39 <param name="element_type" type="text" value="" label="Filter based on classification" help="You can use preset options or enter an arbitrary string to filter a certain repetitive element type of any level. It must be a continuous substring in a proper format of Final_Classification attribute of GFF3 file. Classification levels are separated by | character. Filtering is case sensitive">
25 <option value="Ty1/copia">Ty1/copia</option> 40 <option value="Ty1/copia">Ty1/copia</option>
26 <option value="Ty3/gypsy">Ty3/gypsy</option> 41 <option value="Ty3/gypsy">Ty3/gypsy</option>
27 <option value="Class_I|">Class_I|</option> 42 <option value="Class_I|">Class_I|</option>