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

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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
comparison
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2:5efbd15675ca 3:1de657a3198d
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">