# HG changeset patch
# User jpayne
# Date 1765225595 0
# Node ID b32f43648fc3478eb5743253663716e622d52b51

planemo upload commit 23fc6f056e1ffffbf6af500e6fa87a14b9def8b6-dirty

diff -r 000000000000 -r b32f43648fc3 mashtree-gt.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mashtree-gt.xml	Mon Dec 08 20:26:35 2025 +0000
@@ -0,0 +1,57 @@
+<tool id="mashtree_cpu23mem86" name="Mashtree" version="1.4.6+galaxy0" python_template_version="3.5" profile="16.01">
+    <description>Create a tree using Mash distances</description>
+    <requirements>
+        <requirement type="package" version="1.4.6">mashtree</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #for $file in $input
+            ln -s ${file} ./${file.element_identifier}.fasta &&
+        #end for
+        mashtree --mindepth ${mindepth} 
+                 --genomesize ${genomesize} 
+                 --kmerlength ${kmerlength} 
+                 --sketch-size ${sketchsize} 
+                 --numcpus \${GALAXY_SLOTS:-4} 
+                 *.fasta
+                 --outmatrix ${matrix}
+                 --seed 223
+                 > ${mashtree}
+    ]]></command>
+    <inputs>
+        <param label="Genome assembliy collection in FASTA format" name="input" type="data_collection" format="fasta" collection_type="list" />
+        <param label="Minimum depth. Use 0 for smart depth" type="integer" name="mindepth" value="0" />
+        <param label="Estimated genome size in bp" type="integer" name="genomesize" value="5000000" />
+        <param label="Kmer length" type="integer" name="kmerlength" value="21" />
+        <param label="Sketch size" type="integer" name="sketchsize" value="10000" />
+    </inputs>
+    <outputs>
+        <data name="mashtree" format="newick" label="${tool.name} on ${on_string} tree" />
+        <data name="matrix" format="tabular" label="${tool.name} on ${on_string} distance matrix" hidden="true" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input">
+                <collection type="list">
+                    <element ftype="fasta" name="SRR13160357" value="SRR13160357.fasta" />
+                    <element ftype="fasta" name="SRR13160358" value="SRR13160358.fasta" />
+                    <element ftype="fasta" name="SRR13160359" value="SRR13160359.fasta" />
+                    <element ftype="fasta" name="SRR13160360" value="SRR13160360.fasta" />
+                    <element ftype="fasta" name="SRR13167188" value="SRR13167188.fasta" />
+                </collection>
+            </param>
+            <param name="mindepth" value="0" />
+            <param name="genomesize" value="2500000" />
+            <param name="kmerlength" value="23" />
+            <param name="sketchsize" value="10000" />
+            <output name="mashtree" file="tree.dnd" />
+            <output name="matrix" file="matrix.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Create a tree using Mash distances. The tree is created using the Mash distance matrix. The tree is created using the neighbor-joining algorithm. The tree is written in Newick format.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">Katz, L. S., Griswold, T., Morrison, S., Caravas, J., Zhang, S., den Bakker, H.C., Deng, X., and Carleton, H. A., (2019). Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software, 4(44), 1762</citation>
+        <citation type="doi">https://doi.org/10.21105/joss.01762</citation>
+    </citations>
+</tool>
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