# HG changeset patch
# User jpayne
# Date 1716296654 14400
# Node ID f2c1f3fa6e37c4bed40e166c3ece575c36d04f60
# Parent  903a73fe724edf9ea10bd7d301b0cd3e8ecd7fc8
planemo upload for repository https://toolrepo.galaxytrakr.org/view/jpayne/mashtree_gt/000000000000

diff -r 903a73fe724e -r f2c1f3fa6e37 mashtree-gt.xml
--- a/mashtree-gt.xml	Tue May 21 05:09:17 2024 -0400
+++ b/mashtree-gt.xml	Tue May 21 09:04:14 2024 -0400
@@ -13,8 +13,9 @@
                  --sketch-size ${sketchsize} 
                  --numcpus \${GALAXY_SLOTS:-4} 
                  *.fasta
-                 --outmatrix ${mashtree}
+                 --outmatrix ${matrix}
                  --seed 223
+                 > ${mashtree}
     ]]></command>
     <inputs>
         <param label="Genome assembliy collection in FASTA format" name="input" type="data_collection" format="fasta" collection_type="list" />
@@ -24,7 +25,8 @@
         <param label="Sketch size" type="integer" name="sketchsize" value="10000" />
     </inputs>
     <outputs>
-        <data name="mashtree" format="newick" />
+        <data name="mashtree" format="newick" label="${tool.name} on ${on_string} tree" />
+        <data name="matrix" format="tabular" label="${tool.name} on ${on_string} distance matrix" hidden="true" />
     </outputs>
     <tests>
         <test>
@@ -42,6 +44,7 @@
             <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[
diff -r 903a73fe724e -r f2c1f3fa6e37 test-data/matrix.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix.tsv	Tue May 21 09:04:14 2024 -0400
@@ -0,0 +1,6 @@
+.	SRR13160360	SRR13160357	SRR13160359	SRR13160358	SRR13167188
+SRR13160360	0	0.00171808	0.00165962	0.00177675	0.00179146
+SRR13160357	0.00171808	0	0.0021562	0.000172763	0.00223928
+SRR13160359	0.00165962	0.0021562	0	0.00223675	0.000459344
+SRR13160358	0.00177675	0.000172763	0.00223675	0	0.00229491
+SRR13167188	0.00179146	0.00223928	0.000459344	0.00229491	0
diff -r 903a73fe724e -r f2c1f3fa6e37 test-data/tree.dnd
--- a/test-data/tree.dnd	Tue May 21 05:09:17 2024 -0400
+++ b/test-data/tree.dnd	Tue May 21 09:04:14 2024 -0400
@@ -1,6 +1,1 @@
-.	SRR13160360	SRR13167188	SRR13160358	SRR13160357	SRR13160359
-SRR13160360	0	0.00179146	0.00177675	0.00171808	0.00165962
-SRR13167188	0.00179146	0	0.00229491	0.00223928	0.000459344
-SRR13160358	0.00177675	0.00229491	0	0.000172763	0.00223675
-SRR13160357	0.00171808	0.00223928	0.000172763	0	0.0021562
-SRR13160359	0.00165962	0.000459344	0.00223675	0.0021562	0
+(SRR13160359:0.00018,(SRR13160360:0.00062,(SRR13160358:0.00012,SRR13160357:0.00005):0.00104):0.00088,SRR13167188:0.00028);