dante: dante.xml annotate

annotate dante.xml @ 32:393fb45bd50f draft

planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty

author	petr-novak
date	Tue, 04 Feb 2025 09:48:33 +0000
parents	ae4cebdccf74
children	726b8447eb09

rev	line source
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	1 <tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="2.6.2">
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	2 <description> Tool for annotation of transposable elements based on the similarity to conserved protein domains database. </description>
77d9f2ecb28a Uploaded petr-novak parents: diff changeset	3 <requirements>
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	4 <requirement type="package">dante=0.2.5</requirement>
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	5 </requirements>
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	6 <stdio>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	7 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	8 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	9 </stdio>
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	10 <command><![CDATA[
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	11 #if str($input_type.input_type_selector) == "aln"
23 e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	12 parse_aln.py -a $(input_sequences) -f sequences.fasta -p sequences.profile
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	13 &&
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	14 INPUT_SEQUENCES="sequences.fasta"
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	15 #else
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	16 INPUT_SEQUENCES=$(input_sequences)
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	17 #end if
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	18 &&
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	19 grep -c "^>" \${INPUT_SEQUENCES}
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	20 &&
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	21 NUMBER_OF_SEQUENCES=`grep -c "^>" \${INPUT_SEQUENCES}`
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	22 &&
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	23 if [ \${NUMBER_OF_SEQUENCES} -gt 10000 ]; then
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	24 SHORT_READS="--short_reads";
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	25 else
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	26 SHORT_READS="";
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	27 fi
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	28
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	29 &&
23 e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	30 dante --query \${INPUT_SEQUENCES} --domain_gff ${DomGff}
e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	31 --database $database
e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	32 --scoring_matrix ${scoring_matrix}
24 df99812ded92 "planemo upload commit a0a9b02c60a91942a271b8b35648c0b152fe1ebd-dirty" petr-novak parents: 23 diff changeset	33 --cpu \${GALAXY_SLOTS:-1}
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	34 \${SHORT_READS}
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	35
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	36 &&
23 e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	37 dante_gff_output_filtering.py --dom_gff ${DomGff}
22 1eabd42e00ef Uploaded petr-novak parents: 15 diff changeset	38 --domains_prot_seq ${Domains_filtered} --domains_filtered ${DomGff_filtered}
1eabd42e00ef Uploaded petr-novak parents: 15 diff changeset	39 --output_dir .
1eabd42e00ef Uploaded petr-novak parents: 15 diff changeset	40 --selected_dom All --th_identity 0.35
1eabd42e00ef Uploaded petr-novak parents: 15 diff changeset	41 --th_similarity 0.45 --th_length 0.8
1eabd42e00ef Uploaded petr-novak parents: 15 diff changeset	42 --interruptions 3 --max_len_proportion 1.2
1eabd42e00ef Uploaded petr-novak parents: 15 diff changeset	43 --element_type ''
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	44
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	45 #if str($input_type.input_type_selector) == "aln"
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	46 &&
23 e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	47 coverage2gff.py -p sequences.profile -g ${DomGff}
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	48 #end if
10 d0431a839606 Uploaded petr-novak parents: 6 diff changeset	49
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	50 #if str($iterative) == "Yes"
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	51 &&
23 e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	52 dante_gff_output_filtering.py --dom_gff ${DomGff}
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	53 --domains_prot_seq domains_filtered.fasta --domains_filtered domains_filtered.gff
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	54 --output_dir .
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	55 --selected_dom All --th_identity 0.35
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	56 --th_similarity 0.45 --th_length 0.9
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	57 --interruptions 1 --max_len_proportion 1.1
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	58 --element_type ''
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	59 &&
10 d0431a839606 Uploaded petr-novak parents: 6 diff changeset	60
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	61
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	62
23 e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	63 fasta2database.py domains_filtered.fasta domains_filtered.db
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	64 domains_filtered.class
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	65 &&
10 d0431a839606 Uploaded petr-novak parents: 6 diff changeset	66
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	67 lastdb -p domains_filtered.db domains_filtered.db
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	68 &&
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	69
23 e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	70 dante.py --query \${INPUT_SEQUENCES} --domain_gff ${DomGff2}
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	71 --protein_database domains_filtered.db
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	72 --classification domains_filtered.class
23 e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	73 --scoring_matrix BL80
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	74
10 d0431a839606 Uploaded petr-novak parents: 6 diff changeset	75
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	76 #if str($input_type.input_type_selector) == "aln"
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	77 &&
23 e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	78 coverage2gff.py -p sequences.profile -g ${DomGff2}
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	79 #end if
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	80 #end if
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	81 ]]>
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	82 </command>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	83 <inputs>
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	84
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	85 <conditional name="input_type">
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	86 <param name="input_type_selector" type="select" label="Choose the type of sequence data">
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	87 <option value="fasta" selected="true">Fasta</option>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	88 <option value="aln">Aln file</option>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	89 </param>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	90 <when value="fasta">
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	91 <param name="input_sequences" type="data" format="fasta" label="Sequences in fasta format"/>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	92 </when>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	93 <when value="aln">
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	94 <param name="input_sequences" type="data" format="txt" label="Sequences in ALN format (extracted from RepeatExplorer)"/>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	95 </when>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	96 </conditional>
23 e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	97 <param name="database" type="select" label="Select REXdb database">
30 f0663cdbae66 planemo upload commit 29868d121127a8bb509a42fb917b09f669ad4a09-dirty petr-novak parents: 28 diff changeset	98 <option value="Viridiplantae_v4.0" selected="true">Viridiplantae_v4.0</option>
23 e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	99 <option value="Viridiplantae_v3.0" selected="true">Viridiplantae_v3.0</option>
e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	100 <option value="Metazoa_v3.1" selected="true">Metazoa_v3.1</option>
e2bbc79f0fac "planemo upload commit baf4ca09569b1b709c37f2df712e778da05edaf9-dirty" petr-novak parents: 22 diff changeset	101 <option value="Viridiplantae_v2.2" selected="true">Viridiplantae_v2.2</option>
30 f0663cdbae66 planemo upload commit 29868d121127a8bb509a42fb917b09f669ad4a09-dirty petr-novak parents: 28 diff changeset	102 <option value="Metazoa_v3.0" selected="true">Metazoa_v3.0</option>
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	103 </param>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	104 <param name="scoring_matrix" type="select" label="Select scoring matrix">
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	105 <option value="BL80" selected="true" >BLOSUM80</option>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	106 <option value="BL62">BLOSUM62</option>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	107 <option value="MIQS">MIQS</option>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	108 </param>
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	109
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	110 <param name="iterative" type="select" label="Run iterative search" truevalue="true" valsevalue="false"
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	111 help="Second iteration run search against database of proteins extracted from query. Second iteration can yield some extra hits in some cases.">
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	112 <option value="No" selected="true">No</option>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	113 <option value="Yes">Yes</option>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	114 </param>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	115 </inputs>
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	116
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	117 <outputs>
22 1eabd42e00ef Uploaded petr-novak parents: 15 diff changeset	118 <data format="gff3" name="DomGff" label="DANTE on ${on_string}, full output" />
1eabd42e00ef Uploaded petr-novak parents: 15 diff changeset	119 <data format="gff3" name="DomGff_filtered" label="DANTE on ${on_string}, filtered output" />
1eabd42e00ef Uploaded petr-novak parents: 15 diff changeset	120 <data format="fasta" name="Domains_filtered" label="DANTE on ${on_string}, protein domains, filtered output" />
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	121 <data format="gff3" name="DomGff2" label="DANTE on ${on_string}: 2nd pass">
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	122 <filter>iterative == "Yes" </filter>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	123 </data>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	124 </outputs>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	125 <tests>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	126 <test>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	127 <param name="input_type" value="fasta"/>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	128 <param name="input_sequences" value="GEPY_test_long_1.fa"/>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	129 <param name="db_type" value="Viridiplantae_v3.0"/>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	130 <param name="scoring_matrix" value="BL80"/>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	131 <param name="iterative" value="No"/>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	132 <output name="DomGff" value="GEPY_test_long_1_output_unfiltered.gff3"/>
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	133 </test>
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	134
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	135
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	136 </tests>
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	137
77d9f2ecb28a Uploaded petr-novak parents: diff changeset	138
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	139 <help>
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	140
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	141
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	142
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	143
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	144 WHAT IT DOES
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	145
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	146 This tool uses external aligning programme `LAST`_ and RepeatExplorer database of TE protein domains(REXdb) (Viridiplantae and Metazoa)
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	147
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	148 .. _LAST: http://last.cbrc.jp/
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	149
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	150 Lastal runs similarity search to find hits between query DNA sequence and our database of protein domains from all Viridiplantae repetitive elements. Hits with overlapping positions in the sequence (even through other hits) forms a cluster which represents one potential protein domain. Strand orientation is taken into consideration when forming the clusters which means each cluster is built from forward or reverse stranded hits exclusively. The clusters are subsequently processed separately; within one cluster positions are scanned base-by-base and classification strings are assigned for each of them based on the database sequences which were mapped on that place. These asigned classification strings consist of a domain type as well as class and lineage of the repetitive element where the database protein comes from. Different classification levels are separated by "\|" character. Every hit is scored according to the scoring matrix used for DNA-protein alignment (BLOSUM80). For single position only the hits reaching certain percentage (80% by default) of the overall best score within the whole cluster are reported. One cluster of overlapping hits represents one domain region and is recorded as one line in the resulting GFF3 file. Regarding the classition strings assigned to one region (cluster) there are three situations that can occur:
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	151
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	152 1. There is a single classification string assigned to each position as well as classifications along all the positions in the region are mutually uniform, in this case domain's final classification is equivalent to this unique classification.
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	153 2. There are multiple classification strings assigned to one cluster, i.e. one domain, which leads to classification to the common (less specific) level of all the strings
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	154 3. There is a conflict at the domain type level, domains are reported with slash (e.g. RT/INT) and the classification is in this case ambiguous
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	155
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	156 There are 2 outputs produced by this tool:
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	157
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	158 1. GFF3 file of all proteins domains built from all hits found by LAST. Domains are reported per line as regions (start - end) on the original DNA sequence including the seq ID, alignment score and strand orientation. The last "Attributes" column contains several semicolon-separated information related to annotation, repetitive classification, alignment and its quality. This file can undergo further filtering using Protein Domain Filter tool
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	159
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	160 - Attributes reported always:
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	161
3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	162 Name
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	163 type of domain; if ambiguous reported with slash
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	164
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	165 Final_classification
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	166 definite classification based on all partial classifications of Region_hits_classifications attribute or
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	167 "Ambiguous_domain" when there is an ambiguous domain type
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	168
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	169 Region_Hits_Classifications
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	170 all hits classifications (comma separated) from a certain domain region that reach the set score threshold; in case of multiple annotations the square brackets indicate the number of bases having this particular classification
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	171
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	172 - Attributes only reported in case of unambiguous domain type (all the attributes including quality information are related to the Best_Hit of the region):
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	173
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	174 Best_hit
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	175 classification and position of the best alignment with the highest score within the cluster; in the square brackets is the percentage of the whole cluster range that this best hit covers
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	176
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	177 Best_Hit_DB_Pos
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	178 showing which part of the original datatabase domain corresponding to the Best Hit was aligned on query DNA (e.g. Best_Hit_DB_Pos=17:75of79 means the Best Hit reported in GFF represents region from 17th to 75th of total 79 aminoacids in the original domain from the database)
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	179
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	180 DB_Seq
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	181 database protein sequence of the best hit mapped to the query DNA
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	182
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	183 Query_Seq
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	184 alignment sequence of the query DNA for the best hit
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	185
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	186 Identity
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	187 ratio of identical amino acids in alignment sequence to the length of alignment
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	188
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	189 Similarity
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	190 ratio of alignment positions with positive score (according to the scoring matrix) to the length of alignment
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	191
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	192 Relat_Length
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	193 ratio of gapless length of the aligned protein sequence to the whole length of the database protein
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	194
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	195 Relat_Interruptions
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	196 number of the interruptions (frameshifts + stop codons) in aligned translated query sequence per each starting 100 AA
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	197
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	198 Hit_to_DB_Length
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	199 proportion of alignment length to the original length of the protein domain from database
32 393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	200
393fb45bd50f planemo upload commit ca3e700d61477ca5de353babb7f5f1db469d937b-dirty petr-novak parents: 31 diff changeset	201
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	202
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	203 !NOTE: Tool can in average process 0.5 Gbps of the DNA sequence per day. This is only a rough estimate and it is highly dependent on input data (repetive elements occurence) as well as computing resources. Maximum running time of the tool is 7 days.
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	204
15 3151a72a6671 Uploaded petr-novak parents: 10 diff changeset	205 </help>
0 77d9f2ecb28a Uploaded petr-novak parents: diff changeset	206 </tool>
77d9f2ecb28a Uploaded petr-novak parents: diff changeset	207

Mercurial > repos > petr-novak > dante

annotate dante.xml @ 32:393fb45bd50f draft