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update ppanggolin suite #7889

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Merged
pvanheus merged 1 commit into from
Apr 14, 2026
Merged

update ppanggolin suite #7889

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2 changes: 1 addition & 1 deletion tools/ppanggolin/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">2.3.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
<xml name="citation">
<citations>
<citation type="doi">10.1371/journal.pcbi.1007732</citation>
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4 changes: 2 additions & 2 deletions tools/ppanggolin/ppanggolin_msa.xml
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Expand Up @@ -74,7 +74,7 @@
<option value="dna">DNA</option>
</param>

<param argument="--phylo" name="do_phylo" type="boolean" checked="true" label="Writes a whole genome msa file for additional phylogenetic analysis (recommended)" truevalue="--phylo" falsevalue=""/>
<param argument="--phylo" name="do_phylo" type="boolean" checked="true" label="Writes a whole genome msa file (fasta format) for additional phylogenetic analysis (recommended)" truevalue="--phylo" falsevalue=""/>

<param argument="--single_copy" name="do_single_copy" type="boolean" checked="false" label="Report gene families that are considered 'single copy'" truevalue="--single_copy" falsevalue=""/>

Expand All @@ -84,7 +84,7 @@

<outputs>
<data name="archive_msa_partition_source" format="tar.gz" label="PPanGGOLiN msa on ${on_string}: archive msa ${choice_partition} ${choice_source}" />
<data name="partition_genome_alignment" format="maf" label="PPanGGOLiN msa on ${on_string}: ${choice_partition} genome alignment" >
<data name="partition_genome_alignment" format="fasta" label="PPanGGOLiN msa on ${on_string}: ${choice_partition} genome alignment" >
<filter>do_phylo is True</filter>
</data>
</outputs>
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