Mercurial > repos > iuc > gecko
comparison 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 |
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date | Sat, 05 Oct 2024 16:31:40 +0000 |
parents | 5efbd15675ca |
children |
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2:5efbd15675ca | 3:1de657a3198d |
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1 <tool id="gecko" name="Gecko" version="@TOOL_VERSION@" profile="20.01"> | 1 <tool id="gecko" name="Gecko" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1"> |
2 <description>Ungapped genome comparison</description> | 2 <description>Ungapped genome comparison</description> |
3 <macros> | 3 <macros> |
4 <token name="@TOOL_VERSION@">1.2</token> | 4 <token name="@TOOL_VERSION@">1.2</token> |
5 <token name="@VERSION_SUFFIX@">1</token> | |
5 </macros> | 6 </macros> |
6 <requirements> | 7 <requirements> |
7 <requirement type="package" version="@TOOL_VERSION@">gecko</requirement> | 8 <requirement type="package" version="@TOOL_VERSION@">gecko</requirement> |
8 </requirements> | 9 </requirements> |
9 <command><![CDATA[ | 10 <command><![CDATA[ |
12 #set $dbName=re.sub('/', '\\/', str($db.element_identifier)) | 13 #set $dbName=re.sub('/', '\\/', str($db.element_identifier)) |
13 cp $query query.fasta && | 14 cp $query query.fasta && |
14 cp $db db.fasta && | 15 cp $db db.fasta && |
15 workflow.sh query.fasta db.fasta $minlen $similarity $kmer 1 && | 16 workflow.sh query.fasta db.fasta $minlen $similarity $kmer 1 && |
16 rm -rf intermediateFiles && | 17 rm -rf intermediateFiles && |
17 #if str($options['selection_mode']) == "alignments": | 18 #if str($selection_mode) == "alignments": |
18 frags2align.sh results/query-db.frags query.fasta db.fasta results/query-db.txt && | 19 frags2align.sh results/query-db.frags query.fasta db.fasta results/query-db.txt && |
19 mv results/query-db.txt $alignments2 && | 20 mv results/query-db.txt $alignments2 && |
20 #end if | 21 #end if |
21 sed -i 's/query.fasta/$queryName/g' results/query-db.csv && | 22 sed -i 's/query.fasta/$queryName/g' results/query-db.csv && |
22 sed -i 's/db.fasta/$dbName/g' results/query-db.csv && | 23 sed -i 's/db.fasta/$dbName/g' results/query-db.csv && |
35 <option value="12">12</option> | 36 <option value="12">12</option> |
36 <option value="8">8</option> | 37 <option value="8">8</option> |
37 </param> | 38 </param> |
38 <param name="minlen" type="integer" value="40" min="8" label="Minimum length" help="The minimum length a fragment must achieve to be reported"/> | 39 <param name="minlen" type="integer" value="40" min="8" label="Minimum length" help="The minimum length a fragment must achieve to be reported"/> |
39 <param name="similarity" type="integer" value="60" min="1" max="99" label="Minimum similarity" help="Percentage of similarity threshold (calculated as the attained score divided by the maximum possible score)"/> | 40 <param name="similarity" type="integer" value="60" min="1" max="99" label="Minimum similarity" help="Percentage of similarity threshold (calculated as the attained score divided by the maximum possible score)"/> |
40 <conditional name="options"> | 41 <param label="Generate alignments file?" name="selection_mode" type="select"> |
41 <param label="Generate alignments file?" name="selection_mode" type="select"> | 42 <option selected="true" value="noalignments">Do not extract alignments (Only CSV file)</option> |
42 <option selected="true" value="noalignments">Do not extract alignments (Only CSV file)</option> | 43 <option value="alignments">Extract alignments (CSV and alignments file)</option> |
43 <option value="alignments">Extract alignments (CSV and alignments file)</option> | 44 </param> |
44 </param> | |
45 </conditional> | |
46 </inputs> | 45 </inputs> |
47 <outputs> | 46 <outputs> |
48 <data name="csv_output1" format="csv" label="${tool.name} on ${on_string}: CSV"/> | 47 <data name="csv_output1" format="csv" label="${tool.name} on ${on_string}: CSV"/> |
49 <data name="alignments2" format="txt" label="${tool.name} on ${on_string}: Alignments"> | 48 <data name="alignments2" format="txt" label="${tool.name} on ${on_string}: Alignments"> |
50 <filter> options['selection_mode'] == 'alignments'</filter> | 49 <filter> selection_mode == 'alignments'</filter> |
51 </data> | 50 </data> |
52 </outputs> | 51 </outputs> |
53 <tests> | 52 <tests> |
54 <!-- test run w defaults (no alignments) --> | 53 <!-- test run w defaults (no alignments) --> |
55 <test expect_num_outputs="1"> | 54 <test expect_num_outputs="1"> |