Mercurial > repos > iuc > mothur_cluster_split

diff cluster.split.xml @ 5:f14e393f1641 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 14:04:03 -0400
parents 063229a11154
children 9546bb7c1b61
line wrap: on
line diff
--- a/cluster.split.xml	Wed Feb 14 11:32:20 2018 -0500
+++ b/cluster.split.xml	Tue Mar 20 14:04:03 2018 -0400
@@ -177,6 +177,7 @@
         <param argument="cluster" type="boolean" falsevalue="false" truevalue="true" checked="true" label="perform clustering?"
             help="indicate whether you want to run the clustering or just split the distance matrix"/>
         <param argument="runsensspec" type="boolean" truevalue="true" falsevalue="false" checked="true" label="runsensspec" help="run the sens.spec command on the completed list file"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -229,6 +230,7 @@
                     <has_text text="0.03"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with cluster false -->
@@ -260,6 +262,7 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with classify method (mothur.names input file) -->
@@ -272,6 +275,7 @@
             <output name="otulist" md5="d6eba624ad79759c530b9bc3285a1361" ftype="mothur.list"/>
             <output name="rabund" md5="2a165e1e40644fccb8cc9f53d8915bc3" ftype="mothur.rabund"/>
             <output name="sabund" md5="7aad8a9ca0eade414d6eba1f8bef960f" ftype="mothur.sabund"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with classify method (mothur.count_table input file) -->
@@ -282,6 +286,7 @@
             <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
             <param name="method" value="average"/>
             <output name="otulist" md5="c5c28330434d3e773221f635d04d6af9" ftype="mothur.list"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with fasta -->
@@ -294,6 +299,7 @@
             <output name="otulist" md5="a1279248cf2bc1094e0046b2cff1b785" ftype="mothur.list"/>
             <output name="rabund" md5="65ec9f326cd92fc607679b9902ec8430" ftype="mothur.rabund"/>
             <output name="sabund" md5="854d3acd15f64299c5d9d9e18f2d51b4" ftype="mothur.sabund"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with vsearch executable (agc/dgc method) -->
@@ -305,6 +311,7 @@
             <output name="otulist" md5="0fbc5bf21331538dd50b6586c4005edc" ftype="mothur.list"/>
             <output name="rabund" md5="dcccca11d9fa7a186cd93e9d4592f832" ftype="mothur.rabund"/>
             <output name="sabund" md5="167815924b1b2b4d4e5e7468d41256cb" ftype="mothur.sabund"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with opticlust method -->
@@ -336,6 +343,7 @@
                     <has_text text="0.03"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>