diff list.seqs.xml @ 2:1dcdb5e6c780 draft

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

--- a/list.seqs.xml	Tue Sep 05 16:58:33 2017 -0400
+++ b/list.seqs.xml	Tue Mar 20 22:03:58 2018 -0400
@@ -7,33 +7,33 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$search.input" search.input.dat &&
+## create symlinks to input datasets
+ln -s '$search.input' search.input.dat &&
 
-        echo 'list.seqs(
-            #if $search.intype == "fasta":
-                fasta=search.input.dat
-            #elif $search.intype == "fastq":
-                fastq=search.input.dat
-            #elif $search.intype == "name":
-                name=search.input.dat
-            #else if $search.intype == "group":
-                group=search.input.dat
-            #elif $search.intype == "alignreport":
-                alignreport=search.input.dat
-            #elif $search.intype == "list":
-                list=search.input.dat
-            #elif $search.intype == "taxonomy":
-                taxonomy=search.input.dat
-            #elif $search.intype == "count":
-                count=search.input.dat
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'list.seqs(
+    #if $search.intype == "fasta":
+        fasta=search.input.dat
+    #elif $search.intype == "fastq":
+        fastq=search.input.dat
+    #elif $search.intype == "name":
+        name=search.input.dat
+    #else if $search.intype == "group":
+        group=search.input.dat
+    #elif $search.intype == "alignreport":
+        alignreport=search.input.dat
+    #elif $search.intype == "list":
+        list=search.input.dat
+    #elif $search.intype == "taxonomy":
+        taxonomy=search.input.dat
+    #elif $search.intype == "count":
+        count=search.input.dat
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="search">
@@ -72,27 +72,29 @@
                 <param name="input" type="data" format="mothur.count_table" label="count - Count Table"/>
             </when>
         </conditional>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="out_file" format="mothur.accnos" from_work_dir="search.input*.accnos" label="${tool.name} on ${on_string}: accnos"/>
+        <data name="accnos" format="mothur.accnos" from_work_dir="search.input*.accnos" label="${tool.name} on ${on_string}: accnos"/>
     </outputs>
     <tests>
         <test><!-- test with fasta -->
             <param name="intype" value="fasta"/>
             <param name="input" value="amazon.fasta"/>
-            <output name="out_file" md5="590f62ce757219c2e137a532fcd814d1" ftype="mothur.accnos"/>
+            <output name="accnos" md5="590f62ce757219c2e137a532fcd814d1" ftype="mothur.accnos"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with count file -->
             <param name="intype" value="count"/>
             <param name="input" value="amazon.count_table"/>
-            <output name="out_file" md5="360dfea2de2da4d55e75071b026c83b6" ftype="mothur.accnos"/>
+            <output name="accnos" md5="360dfea2de2da4d55e75071b026c83b6" ftype="mothur.accnos"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -108,7 +110,7 @@
 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
 
 v.1.20.0: Updated to mothur 1.33, added count and fastq option
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>