diff seq.error.xml @ 2:a5418319c97a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

--- a/seq.error.xml	Tue Sep 05 17:12:13 2017 -0400
+++ b/seq.error.xml	Tue Mar 20 22:06:03 2018 -0400
@@ -7,45 +7,45 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta_in" fasta_in.dat &&
-        ln -s "$name_in" name_in.dat &&
-        ln -s "$count" count.dat &&
-        ln -s "$alignment.template" alignment.template.dat &&
-        #if $qual.use == "yes":
-            ln -s "$qual.qfile_in" qfile_in.dat &&
-            ln -s "$qual.alignreport_in" alignreport_in.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$fasta_in' fasta_in.dat &&
+ln -s '$name_in' name_in.dat &&
+ln -s '$count' count.dat &&
+ln -s '$alignment.template' alignment.template.dat &&
+#if $qual.use == "yes":
+    ln -s '$qual.qfile_in' qfile_in.dat &&
+    ln -s '$qual.alignreport_in' alignreport_in.dat &&
+#end if
 
-        echo 'seq.error(
-            fasta=fasta_in.dat,
-            reference=alignment.template.dat,
-            #if $name_in:
-                name=name_in.dat,
-            #end if
-            #if $qual.use == "yes":
-                qfile=qfile_in.dat,
-                report=alignreport_in.dat,
-            #end if
-            #if $threshold:
-                threshold=$threshold,
-            #end if
-            ignorechimeras=$ignorechimeras,
-            #if $count:
-                count=count.dat,
-            #end if
-            #if $fasta_in.is_of_type('mothur.align')
-                aligned=T,
-            #else
-                aligned=F,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'seq.error(
+    fasta=fasta_in.dat,
+    reference=alignment.template.dat,
+    #if $name_in:
+        name=name_in.dat,
+    #end if
+    #if $qual.use == "yes":
+        qfile=qfile_in.dat,
+        report=alignreport_in.dat,
+    #end if
+    #if $threshold:
+        threshold=$threshold,
+    #end if
+    ignorechimeras=$ignorechimeras,
+    #if $count:
+        count=count.dat,
+    #end if
+    #if $fasta_in.is_of_type('mothur.align')
+        aligned=T,
+    #else
+        aligned=F,
+    #end if
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta_in" type="data" format="mothur.align,fasta" label="fasta - Candidate Sequences" help="sequences must be aligned"/>
@@ -78,6 +78,7 @@
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count table"/>
         <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/>
         <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -129,6 +130,7 @@
             <output name="seq_forward_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
             <output name="seq_reverse_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
             <output name="summary_out" md5="04abbbd6aa82f084e4a3bd51c4ce98e6"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!--test with qual file and all outputs -->
@@ -150,11 +152,11 @@
             <output name="seq_forward_out" md5="dbcbbefdc83c2a7c045e3930850cdbd9"/>
             <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/>
             <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -166,7 +168,6 @@
 .. _template_alignment: https://www.mothur.org/wiki/Alignment_database
 .. _seq.error: https://www.mothur.org/wiki/Seq.error
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>