diff sub.sample.xml @ 2:46d13e8c60ba draft

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

--- a/sub.sample.xml	Tue Sep 05 16:57:21 2017 -0400
+++ b/sub.sample.xml	Tue Mar 20 22:24:53 2018 -0400
@@ -7,64 +7,64 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$input.otu" input_otu.dat &&
-        ln -s "$count" count.dat &&
-        ln -s "$taxonomy" taxonomy.dat &&
-        #if $input.format == "fasta":
-            ln -s "$input.name_in" input_name_in.dat &&
-        #end if
-        #if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes":
-            ln -s "$input.use_group.group_in" input_use_group_group_in.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$input.otu' input_otu.dat &&
+ln -s '$count' count.dat &&
+ln -s '$taxonomy' taxonomy.dat &&
+#if $input.format == "fasta":
+    ln -s '$input.name_in' input_name_in.dat &&
+#end if
+#if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes":
+    ln -s '$input.use_group.group_in' input_use_group_group_in.dat &&
+#end if
 
-        echo 'sub.sample(
-            #if $input.format == "fasta":
-                fasta=input_otu.dat
-                #if $input.name_in:
-                    ,name=input_name_in.dat
-                #end if
-            #else
-                #if $input.format == "list":
-                    list=input_otu.dat
-                #elif $input.format == "sabund":
-                    sabund=input_otu.dat
-                #elif $input.format == "rabund":
-                    rabund=input_otu.dat
-                #elif $input.format == "shared":
-                    shared=input_otu.dat
-                    #if $input.groups:
-                        ,groups=${ str($input.groups).replace(",","-") }
-                    #end if
-                #end if
-                #if $input.label:
-                    ,label=${ str($input.label).replace(",","-") }
-                #end if
+echo 'sub.sample(
+    #if $input.format == "fasta":
+        fasta=input_otu.dat
+        #if $input.name_in:
+            ,name=input_name_in.dat
+        #end if
+    #else
+        #if $input.format == "list":
+            list=input_otu.dat
+        #elif $input.format == "sabund":
+            sabund=input_otu.dat
+        #elif $input.format == "rabund":
+            rabund=input_otu.dat
+        #elif $input.format == "shared":
+            shared=input_otu.dat
+            #if $input.groups:
+                ,groups=${ str($input.groups).replace(",","-") }
             #end if
-            #if $input.format == "fasta" or $input.format == "list":
-                #if $input.use_group.to_filter == "yes":
-                    ,group=input_use_group_group_in.dat
-                    #if $input.use_group.groups:
-                        ,groups=${ str($input.use_group.groups).replace(",","-") }
-                    #end if
-                    ,persample=$input.use_group.persample
-                #end if
+        #end if
+        #if $input.label:
+            ,label=${ str($input.label).replace(",","-") }
+        #end if
+    #end if
+    #if $input.format == "fasta" or $input.format == "list":
+        #if $input.use_group.to_filter == "yes":
+            ,group=input_use_group_group_in.dat
+            #if $input.use_group.groups:
+                ,groups=${ str($input.use_group.groups).replace(",","-") }
             #end if
-            #if $count:
-                ,count=count.dat
-            #end if
-            #if $taxonomy:
-                ,taxonomy=taxonomy.dat
-            #end if
-            #if $size:
-                ,size=$size
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+            ,persample=$input.use_group.persample
+        #end if
+    #end if
+    #if $count:
+        ,count=count.dat
+    #end if
+    #if $taxonomy:
+        ,taxonomy=taxonomy.dat
+    #end if
+    #if $size:
+        ,size=$size
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -144,6 +144,7 @@
         <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
         <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -186,6 +187,7 @@
                    </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with list and group file and label select-->
@@ -203,6 +205,7 @@
                    </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with fasta and taxonomy -->
@@ -219,6 +222,7 @@
                     <has_line_matching expression="^U[0-9]+\tBacteria.*$"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with fasta and group file and name file -->
@@ -243,6 +247,7 @@
                     <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with shared -->
@@ -260,6 +265,7 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with rabund -->
@@ -271,6 +277,7 @@
                     <has_text text="0.55"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with sabund -->
@@ -282,11 +289,11 @@
                     <has_text text="0.55"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -300,7 +307,6 @@
 .. _sabund: https://www.mothur.org/wiki/Sabund_file
 .. _sub.sample: https://www.mothur.org/wiki/Sub.sample
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>