diff split.abund.xml @ 2:407a5352f0ec draft

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

--- a/split.abund.xml	Tue Sep 05 17:01:32 2017 -0400
+++ b/split.abund.xml	Tue Mar 20 22:01:54 2018 -0400
@@ -7,41 +7,41 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$search.input" search_input.dat &&
-        #if $split.dosplit == "yes":
-            ln -s "$split.group" split_group.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$search.input' search_input.dat &&
+#if $split.dosplit == "yes":
+    ln -s '$split.group' split_group.dat &&
+#end if
 
-        echo 'split.abund(
-            fasta=fasta.dat,
-            #if $search.type == "list":
-                list=search_input.dat,
-                #if $search.label:
-                    label=${ str($search.label).replace(",","-") },
-                #end if
-            #elif $search.type == "name":
-                name=search_input.dat,
-            #else
-                count=search_input.dat,
-            #end if
-            #if $split.dosplit == "yes":
-                #if $split.group:
-                    group=split_group.dat,
-                #end if
-                #if $split.groups:
-                    groups=${ str($split.groups).replace(",","-") },
-                #end if
-            #end if
-            accnos=$accnos,
-            cutoff=$cutoff
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'split.abund(
+    fasta=fasta.dat,
+    #if $search.type == "list":
+        list=search_input.dat,
+        #if $search.label:
+            label=${ str($search.label).replace(",","-") },
+        #end if
+    #elif $search.type == "name":
+        name=search_input.dat,
+    #else
+        count=search_input.dat,
+    #end if
+    #if $split.dosplit == "yes":
+        #if $split.group:
+            group=split_group.dat,
+        #end if
+        #if $split.groups:
+            groups=${ str($split.groups).replace(",","-") },
+        #end if
+    #end if
+    accnos=$accnos,
+    cutoff=$cutoff
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
@@ -83,6 +83,7 @@
             <when value="no"/>
         </conditional>
         <param name="accnos" type="boolean" truevalue="true" falsevalue="false" checked="false" label="accnos - Produce rare and abundant Accession outputs"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -170,6 +171,7 @@
             <output name="rare_count" md5="dc7be856861ef53faa73a5312b0661c3" ftype="mothur.count_table"/>
             <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
             <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with name file and accnos output -->
@@ -184,6 +186,7 @@
             <output name="rare_names" md5="12527477b2c1891c9278f417a5ece45d" ftype="mothur.names"/>
             <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
             <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with name file and accnos output with groups-->
@@ -219,6 +222,7 @@
             <output_collection name="rare_groups_coll" count="2">
                 <element name="pasture" md5="5907bd7fe874a29fcc57930ecb0f65d1" ftype="mothur.groups"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with list -->
@@ -254,6 +258,7 @@
             <output_collection name="rare_groups_coll" count="72">
                 <element name="0.05.pasture" md5="ddcf8bc26a0815fd366deceec64133ee" ftype="mothur.groups"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with list and label and group select-->
@@ -290,11 +295,11 @@
             <output_collection name="rare_groups_coll" count="4">
                 <element name="0.05.forest" md5="53a2f24a4d69f92661b94bc4b813ce69" ftype="mothur.groups"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -305,7 +310,7 @@
 .. _list: https://www.mothur.org/wiki/List_file
 .. _name: https://www.mothur.org/wiki/Name_file
 .. _split.abund: https://www.mothur.org/wiki/Split.abund
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>