# HG changeset patch
# User iuc
# Date 1524488034 14400
# Node ID f93cee78b339eef55c00a3c479988b67f027a415
# Parent  b26cced02072b09110323afc79767268a075bcf3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb

diff -r b26cced02072 -r f93cee78b339 filter.seqs.xml
--- a/filter.seqs.xml	Fri Apr 06 03:22:18 2018 -0400
+++ b/filter.seqs.xml	Mon Apr 23 08:53:54 2018 -0400
@@ -8,6 +8,7 @@
     <expand macro="version_command"/>
     <command><![CDATA[
 @SHELL_OPTIONS@
+#import re
 
 ## create symlinks to input datasets
 ln -s '$fasta' fasta.dat &&
@@ -33,9 +34,11 @@
 | tee mothur.out.log &&
 
 ## rename collection files for more transparent element naming
-mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta
+#set $identifier=re.sub('[^\w\-\s\.]', '_', str($fasta.element_identifier))
+mv fasta.filter.fasta '${identifier}.filter.fasta'
 #for i in $inputs:
-    && mv fasta${inputs.index($i)}.filter.fasta "${i.fasta.element_identifier}".filter.fasta
+    #set $identifier=re.sub('[^\w\-\s]', '_', str($i.fasta.element_identifier))
+    && mv fasta${inputs.index($i)}.filter.fasta '${identifier}.filter.fasta'
 #end for
     ]]></command>
     <inputs>
diff -r b26cced02072 -r f93cee78b339 test-data/make_group_collection.groups
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/make_group_collection.groups	Mon Apr 23 08:53:54 2018 -0400
@@ -0,0 +1,20 @@
+M00967_43_000000000-A3JHG_1_1101_19936_3208	test_group
+M00967_43_000000000-A3JHG_1_1101_15923_3823	test_group
+M00967_43_000000000-A3JHG_1_1101_14010_4122	test_group
+M00967_43_000000000-A3JHG_1_1101_13293_4703	test_group
+M00967_43_000000000-A3JHG_1_1101_24357_4866	test_group
+M00967_43_000000000-A3JHG_1_1101_23552_5194	test_group
+M00967_43_000000000-A3JHG_1_1101_7326_5417	test_group
+M00967_43_000000000-A3JHG_1_1101_11148_6457	test_group
+M00967_43_000000000-A3JHG_1_1101_7079_6722	test_group
+M00967_43_000000000-A3JHG_1_1101_8607_6805	test_group
+M00967_43_000000000-A3JHG_1_1101_19936_3208	test_group2
+M00967_43_000000000-A3JHG_1_1101_15923_3823	test_group2
+M00967_43_000000000-A3JHG_1_1101_14010_4122	test_group2
+M00967_43_000000000-A3JHG_1_1101_13293_4703	test_group2
+M00967_43_000000000-A3JHG_1_1101_24357_4866	test_group2
+M00967_43_000000000-A3JHG_1_1101_23552_5194	test_group2
+M00967_43_000000000-A3JHG_1_1101_7326_5417	test_group2
+M00967_43_000000000-A3JHG_1_1101_11148_6457	test_group2
+M00967_43_000000000-A3JHG_1_1101_7079_6722	test_group2
+M00967_43_000000000-A3JHG_1_1101_8607_6805	test_group2