Mercurial > repos > iuc > mothur_clearcut

changeset 8:f7fabe2362b8 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 23:08:51 +0000
parents 7ad44d831a1f
children a735e855f28f
files clearcut.xml macros.xml
diffstat 2 files changed, 2 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/clearcut.xml	Mon Dec 02 05:44:42 2019 -0500
+++ b/clearcut.xml	Thu Nov 05 23:08:51 2020 +0000
@@ -118,13 +118,12 @@
 
 The clearcut_ command runs clearcut
 
-The clearcut command allows mothur users to run the clearcut_program_ from within mothur. The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. For more information about clearcut please refer to http://bioinformatics.hungry.com/clearcut/
+The clearcut command allows mothur users to run the clearcut program from within mothur. The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. 
 
 Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ).
 
 Clearcut is capable of taking either a distance matrix or a multiple sequence alignment (MSA) as input.  If necessary, Clearcut will compute corrected distances based on a configurable distance correction model (Jukes-Cantor or Kimura).  Clearcut outputs a phylogenetic tree in Newick format and an optional corrected distance matrix.
 
-.. _clearcut_program: http://bioinformatics.hungry.com/clearcut/
 .. _clearcut: https://www.mothur.org/wiki/Clearcut
 
 v.1.20.0: Trivial upgrade to Mothur 1.33
--- a/macros.xml	Mon Dec 02 05:44:42 2019 -0500
+++ b/macros.xml	Thu Nov 05 23:08:51 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 -->