Mercurial > repos > iuc > mothur_summary_single

changeset 8:88d39b1679df draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"
author iuc
date Thu, 05 Nov 2020 23:21:24 +0000
parents 72be09dfd803
children 782564664543
files macros.xml summary.single.xml
diffstat 2 files changed, 10 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Dec 02 06:22:46 2019 -0500
+++ b/macros.xml	Thu Nov 05 23:21:24 2020 +0000
@@ -15,7 +15,7 @@
             <exit_code range="1:" level="fatal"/>
         </stdio>
     </xml>
-    <token name="@SHELL_OPTIONS@">set -o pipefail;</token>
+    <token name="@SHELL_OPTIONS@">set -o pipefail; export TERM=vt100; </token>
 
 
     <!-- Input parameters -->
--- a/summary.single.xml	Mon Dec 02 06:22:46 2019 -0500
+++ b/summary.single.xml	Thu Nov 05 23:21:24 2020 +0000
@@ -1,4 +1,4 @@
-<tool profile="16.07" id="mothur_summary_single" name="Summary.single" version="@WRAPPER_VERSION@.0">
+<tool profile="16.07" id="mothur_summary_single" name="Summary.single" version="@WRAPPER_VERSION@.2">
     <description>Summary of calculator values for OTUs</description>
     <macros>
         <import>macros.xml</import>
@@ -50,7 +50,7 @@
 | mothur
 | tee mothur.out.log
 #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
-    && mv otu.*ave_std.summary otu.ave-std
+    && mv otu.*ave[_-]std.summary otu.ave-std
 #end if
     ]]></command>
     <inputs>
@@ -115,6 +115,13 @@
         </collection>
     </outputs>
     <tests>
+        <test><!-- test with shared and subsampling -->
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="use" value="yes"/>
+            <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
         <test><!-- test with shared and default params -->
             <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
             <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/>