annotate gecko.xml @ 3:1de657a3198d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit b55cfca7f53d2eaa3f4c7c4ce09436371b088000
author iuc
date Sat, 05 Oct 2024 16:31:40 +0000
parents 5efbd15675ca
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
1de657a3198d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit b55cfca7f53d2eaa3f4c7c4ce09436371b088000
iuc
parents: 2
diff changeset
1 <tool id="gecko" name="Gecko" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
0
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
2 <description>Ungapped genome comparison</description>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
3 <macros>
2
5efbd15675ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit 52b2b430b2d0ac983f426da298d966074a24f5cd"
iuc
parents: 1
diff changeset
4 <token name="@TOOL_VERSION@">1.2</token>
3
1de657a3198d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit b55cfca7f53d2eaa3f4c7c4ce09436371b088000
iuc
parents: 2
diff changeset
5 <token name="@VERSION_SUFFIX@">1</token>
0
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
6 </macros>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
7 <requirements>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">gecko</requirement>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
9 </requirements>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
10 <command><![CDATA[
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
11 #import re
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
12 #set $queryName=re.sub('/', '\\/', str($query.element_identifier))
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
13 #set $dbName=re.sub('/', '\\/', str($db.element_identifier))
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
14 cp $query query.fasta &&
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
15 cp $db db.fasta &&
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
16 workflow.sh query.fasta db.fasta $minlen $similarity $kmer 1 &&
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
17 rm -rf intermediateFiles &&
3
1de657a3198d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit b55cfca7f53d2eaa3f4c7c4ce09436371b088000
iuc
parents: 2
diff changeset
18 #if str($selection_mode) == "alignments":
0
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
19 frags2align.sh results/query-db.frags query.fasta db.fasta results/query-db.txt &&
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
20 mv results/query-db.txt $alignments2 &&
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
21 #end if
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
22 sed -i 's/query.fasta/$queryName/g' results/query-db.csv &&
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
23 sed -i 's/db.fasta/$dbName/g' results/query-db.csv &&
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
24 mv results/query-db.csv $csv_output1 &&
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
25 rm -rf results
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
26 ]]></command>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
27 <inputs>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
28 <param name="query" type="data" format="fasta" label="Query sequence" help="Query sequence file in fasta format"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
29 <param name="db" type="data" format="fasta" label="Reference sequence" help="Reference sequence file in fasta format"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
30 <param name="kmer" type="select" label="K-mer seed size" help="Use 32 for larger sequences (above 5mbps) and 16 or smaller otherwise">
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
31 <option value="32" selected="true">32</option>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
32 <option value="28">28</option>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
33 <option value="24">24</option>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
34 <option value="20">20</option>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
35 <option value="16">16</option>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
36 <option value="12">12</option>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
37 <option value="8">8</option>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
38 </param>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
39 <param name="minlen" type="integer" value="40" min="8" label="Minimum length" help="The minimum length a fragment must achieve to be reported"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
40 <param name="similarity" type="integer" value="60" min="1" max="99" label="Minimum similarity" help="Percentage of similarity threshold (calculated as the attained score divided by the maximum possible score)"/>
3
1de657a3198d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit b55cfca7f53d2eaa3f4c7c4ce09436371b088000
iuc
parents: 2
diff changeset
41 <param label="Generate alignments file?" name="selection_mode" type="select">
1de657a3198d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit b55cfca7f53d2eaa3f4c7c4ce09436371b088000
iuc
parents: 2
diff changeset
42 <option selected="true" value="noalignments">Do not extract alignments (Only CSV file)</option>
1de657a3198d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit b55cfca7f53d2eaa3f4c7c4ce09436371b088000
iuc
parents: 2
diff changeset
43 <option value="alignments">Extract alignments (CSV and alignments file)</option>
1de657a3198d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit b55cfca7f53d2eaa3f4c7c4ce09436371b088000
iuc
parents: 2
diff changeset
44 </param>
0
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
45 </inputs>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
46 <outputs>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
47 <data name="csv_output1" format="csv" label="${tool.name} on ${on_string}: CSV"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
48 <data name="alignments2" format="txt" label="${tool.name} on ${on_string}: Alignments">
3
1de657a3198d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit b55cfca7f53d2eaa3f4c7c4ce09436371b088000
iuc
parents: 2
diff changeset
49 <filter> selection_mode == 'alignments'</filter>
0
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
50 </data>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
51 </outputs>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
52 <tests>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
53 <!-- test run w defaults (no alignments) -->
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
54 <test expect_num_outputs="1">
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
55 <param name="query" value="hyopneumoniae_16S.fasta"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
56 <param name="db" value="flocculare_16S.fasta"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
57 <param name="kmer" value="8"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
58 <param name="minlen" value="20"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
59 <param name="similarity" value="50"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
60 <param name="selection_mode" value="noalignments"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
61 <output name="csv_output1" ftype="csv">
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
62 <assert_contents>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
63 <has_n_lines n="20"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
64 </assert_contents>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
65 </output>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
66 </test>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
67 <!-- test run w non defaults (alignment included) -->
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
68 <test expect_num_outputs="2">
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
69 <param name="query" value="hyopneumoniae_16S.fasta"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
70 <param name="db" value="flocculare_16S.fasta"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
71 <param name="kmer" value="8"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
72 <param name="minlen" value="20"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
73 <param name="similarity" value="50"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
74 <param name="selection_mode" value="alignments"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
75 <output name="csv_output1" ftype="csv">
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
76 <assert_contents>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
77 <has_n_lines n="20"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
78 </assert_contents>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
79 </output>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
80 <output name="alignments2" ftype="txt">
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
81 <assert_contents>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
82 <has_n_lines n="96"/>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
83 </assert_contents>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
84 </output>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
85 </test>
1
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
86 <test expect_num_outputs="2">
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
87 <param name="query" value="mycoplasma-232.fasta"/>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
88 <param name="db" value="mycoplasma-7422.fasta"/>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
89 <param name="kmer" value="16"/>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
90 <param name="minlen" value="50"/>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
91 <param name="similarity" value="60"/>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
92 <param name="selection_mode" value="alignments"/>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
93 <output name="csv_output1" ftype="csv">
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
94 <assert_contents>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
95 <has_n_lines n="640"/>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
96 </assert_contents>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
97 </output>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
98 <output name="alignments2" ftype="txt">
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
99 <assert_contents>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
100 <has_n_lines n="54138"/>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
101 </assert_contents>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
102 </output>
8acaa11e3b6b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit d5a38da952de32b218895725c80b5bdac54c7dbf"
iuc
parents: 0
diff changeset
103 </test>
0
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
104 </tests>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
105 <help>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
106 *GECKO*
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
107
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
108 A pairwise genome comparison software for the detection of High-scoring Segment Pairs.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
109
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
110 GECKO (GEnome Comparison with K-mers Out-of-core) is a fast, modular application designed to identify collections of High-scoring Segment Pairs in a pairwise genome comparisons. By employing novel filtering and data storing strategies, it is able to compare chromosome-sized sequences in less time.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
111
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
112 *How to use*
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
113
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
114 To use GECKO, upload two .fasta datasets and select these as "Query sequence" and as "Reference sequence". Once so, choose the parameters that best suite your comparison:
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
115
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
116 **Input parameters**
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
117
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
118 - Query sequence: The sequence that will be compared against the reference. Use only FASTA format.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
119 - Reference sequence: The reference sequence where to look for matches from the query. Note that the reverse strand is computed for the reference and also matched. Use only FASTA format.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
120 - Length: This parameter is the minimum length in nucleotides for an HSP (similarity fragment) to be conserved. Any HSP below this length will be filtered out of the comparison. It is recommended to use around 40 bp for small organisms (e.g. bacterial mycoplasma or E. Coli) and around 100 bp or more for larger organisms (e.g. human chromosomes).
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
121 - Similarity: This parameter is analogous to the minimum length, however, instead of length, the similarity is used as threshold. The similarity is calculated as the score attained by an HSP divided by the maximum possible score. Use values above 50-60 to filter noise.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
122 - Word length: This parameter is the seed size used to find HSPs. A smaller seed size will increase sensitivity and decrease performance, whereas a larger seed size will decrease sensitivity and increase performance. Recommended values are 12 or 16 for smaller organisms (bacteria) and 32 for larger organisms (chromosomes). These values must be multiples of 4.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
123 - Alignment extraction: Select "Yes" if you want to generate a file containing the alingments in a format similar to BLAST.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
124
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
125 **Output data sets**
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
126
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
127 Two files are produced when running GECKO:
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
128
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
129 - query-reference.csv: A CSV file that includes metadata about the sequence compared and each HSP detected. See section "Interpreting the CSV" below for more information. This file can be used to visualize the comparison in the interactive sequence visualizer GECKO-MGV (use online here or download and install here).
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
130 - query-reference.txt: This file contains the alignments in a BLAST-like format (only generated if alignment extraction is selected).
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
131
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
132 The CSV file can be interpreted as follows. Each column represents:
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
133
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
134 `Type,xStart,yStart,xEnd,yEnd,strand(f/r),block,length,score,ident,similarity,%ident,SeqX,SeqY`
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
135
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
136
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
137 - Type: currently, this field is reserved for Frag.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
138 - xStart: starting coordinates of the alignment in the query sequence.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
139 - yStart: starting coordinates of the alignment in the reference sequence.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
140 - xEnd: ending coordinates of the alignment in the query sequence.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
141 - yEnd: ending coordinates of the alignment in the reference sequence.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
142 - strand: a character f or r encoding whether the alignment is in the forward or reverse strand.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
143 - block: currently reserved.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
144 - length: the length in nucleotides of the alignment.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
145 - score: the raw score of the alignment calculated with +4 and -4 per match and mismatch.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
146 - ident: the number of identities found in the alignment (i.e. matches).
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
147 - similarity: the similarity percentage calculated as the achieved raw score divided by the maximum possible score.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
148 - %ident: the number of identities divided by the length of the alignment.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
149 - SeqX: the ID corresponding to the sequence in the query file to which the xStart and xEnd coordinates correspond (0=> first sequence, 1=> second sequence, etc).
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
150 - SeqY: same as above but for the reference file.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
151
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
152 Note that fragments in the reverse strand (marked with the r field) have their yStart and yEnd coordinates switched, i.e. yEnd is smaller than yStart.
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
153 </help>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
154 <citations>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
155 <citation type="doi">10.1186/s12859-015-0679-9</citation>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
156 </citations>
09459f6ffe08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit f0c70444d9781900f0af1638792818543c65acfc"
iuc
parents:
diff changeset
157 </tool>