Mercurial > repos > iuc > mothur_screen_seqs

diff screen.seqs.xml @ 9:c1feef4d5e34 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
author iuc
date Tue, 08 Dec 2020 12:46:21 +0000
parents 6202ff80199f
children
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--- a/screen.seqs.xml	Thu Nov 05 23:12:15 2020 +0000
+++ b/screen.seqs.xml	Tue Dec 08 12:46:21 2020 +0000
@@ -1,4 +1,4 @@
-<tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.0">
+<tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.1">
     <description>Screen sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -48,7 +48,7 @@
         ,criteria=$criteria
     #end if
     #if $optimize:
-        ,optimize=$optimize
+        ,optimize=#echo str($optimize).replace(',','-') #
     #end if
     #if $qfile:
         ,qfile=qfile.dat
@@ -176,6 +176,24 @@
             <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
+        <test><!-- test for multiple optimize options minlenght, maxlength, maxhomop -->
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
+            <param name="criteria" value="50"/>
+            <param name="optimize" value="minlength,maxlength,maxhomop"/>
+            <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.minlength.maxlength.maxhomop.good.fasta" ftype="fasta"/>
+            <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.minlength.maxlength.maxhomop.bad.accnos" ftype="mothur.accnos"/>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test for multiple optimize options end, maxambig -->
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
+            <param name="criteria" value="50"/>
+            <param name="optimize" value="end,maxambig"/>
+            <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.end.maxambig.good.fasta" ftype="fasta"/>
+            <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.end.maxambig.bad.accnos" ftype="mothur.accnos"/>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
         <test><!-- test with count table -->
             <param name="fasta" value="amazon.fasta" ftype="mothur.align"/>
             <param name="count" value="amazon1.count_table"/>