Mercurial > repos > iuc > gecko
diff 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 |
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--- a/gecko.xml Mon Jan 04 21:01:55 2021 +0000 +++ b/gecko.xml Sat Oct 05 16:31:40 2024 +0000 @@ -1,7 +1,8 @@ -<tool id="gecko" name="Gecko" version="@TOOL_VERSION@" profile="20.01"> +<tool id="gecko" name="Gecko" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1"> <description>Ungapped genome comparison</description> <macros> <token name="@TOOL_VERSION@">1.2</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">gecko</requirement> @@ -14,7 +15,7 @@ cp $db db.fasta && workflow.sh query.fasta db.fasta $minlen $similarity $kmer 1 && rm -rf intermediateFiles && - #if str($options['selection_mode']) == "alignments": + #if str($selection_mode) == "alignments": frags2align.sh results/query-db.frags query.fasta db.fasta results/query-db.txt && mv results/query-db.txt $alignments2 && #end if @@ -37,17 +38,15 @@ </param> <param name="minlen" type="integer" value="40" min="8" label="Minimum length" help="The minimum length a fragment must achieve to be reported"/> <param name="similarity" type="integer" value="60" min="1" max="99" label="Minimum similarity" help="Percentage of similarity threshold (calculated as the attained score divided by the maximum possible score)"/> - <conditional name="options"> - <param label="Generate alignments file?" name="selection_mode" type="select"> - <option selected="true" value="noalignments">Do not extract alignments (Only CSV file)</option> - <option value="alignments">Extract alignments (CSV and alignments file)</option> - </param> - </conditional> + <param label="Generate alignments file?" name="selection_mode" type="select"> + <option selected="true" value="noalignments">Do not extract alignments (Only CSV file)</option> + <option value="alignments">Extract alignments (CSV and alignments file)</option> + </param> </inputs> <outputs> <data name="csv_output1" format="csv" label="${tool.name} on ${on_string}: CSV"/> <data name="alignments2" format="txt" label="${tool.name} on ${on_string}: Alignments"> - <filter> options['selection_mode'] == 'alignments'</filter> + <filter> selection_mode == 'alignments'</filter> </data> </outputs> <tests>