diff heatmap.sim.xml @ 2:6c7e2e05f606 draft

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

--- a/heatmap.sim.xml	Tue Sep 05 17:16:13 2017 -0400
+++ b/heatmap.sim.xml	Tue Mar 20 22:14:21 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 "$count" count.dat &&
-        #if $input.source == 'shared':
-            ln -s "$input.otu" input_otu.dat &&
-        #else
-            ln -s "$input.dist" input_dist.dat &&
-            #if $input.source == 'column':
-                ln -s "$input.name" input_name.dat &&
-            #end if
-        #end if
+## create symlinks to input datasets
+ln -s '$count' count.dat &&
+#if $input.source == 'shared':
+    ln -s '$input.otu' input_otu.dat &&
+#else
+    ln -s '$input.dist' input_dist.dat &&
+    #if $input.source == 'column':
+        ln -s '$input.name' input_name.dat &&
+    #end if
+#end if
 
-        echo 'heatmap.sim(
-            #if $input.source == "shared":
-                shared=input_otu.dat,
-                #if $input.label:
-                    label=${ str($input.label).replace(",","-") },
-                #end if
-                #if $input.groups:
-                    groups=${ str($input.groups).replace(",","-") },
-                #end if
-                #if $input.calc:
-                    calc=${ str($input.calc).replace(",","-") },
-                #end if
-            #elif $input.source == "column":
-                column=input_dist.dat,
-                name=input_name.dat,
-            #elif $input.source == "phylip":
-                phylip=input_dist.dat,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            fontsize=$fontsize
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'heatmap.sim(
+    #if $input.source == "shared":
+        shared=input_otu.dat,
+        #if $input.label:
+            label=${ str($input.label).replace(",","-") },
+        #end if
+        #if $input.groups:
+            groups=${ str($input.groups).replace(",","-") },
+        #end if
+        #if $input.calc:
+            calc=${ str($input.calc).replace(",","-") },
+        #end if
+    #elif $input.source == "column":
+        column=input_dist.dat,
+        name=input_name.dat,
+    #elif $input.source == "phylip":
+        phylip=input_dist.dat,
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    fontsize=$fontsize
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -87,6 +87,7 @@
         </conditional>
         <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table" help="generated by count.seqs"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -109,14 +110,21 @@
                     <has_text text="U68640"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
             <param name="source" value="shared"/>
             <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
             <output_collection name="heatmaps" count="72">
-                <element name="0.55.jest.heatmap" md5="c48bac26a84f657ead8dd43af0401317"/>
+                <element name="0.55.jest.heatmap">
+                    <assert_contents>
+                        <has_text text="svg xmlns:svg="/>
+                        <has_text text="Heatmap at distance 0.55"/>
+                    </assert_contents>
+                </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
@@ -126,13 +134,18 @@
             <param name="calc" value="jclass,jest,sorclass,sorest,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc"/>
             <param name="groups" value="forest,pasture"/>
             <output_collection name="heatmaps" count="30">
-                <element name="0.03.braycurtis.heatmap" md5="6a3f261e1012edaf620f78b62eff5c88"/>
+                <element name="0.03.braycurtis.heatmap">
+                    <assert_contents>
+                        <has_text text="svg xmlns:svg="/>
+                        <has_text text="Heatmap at distance 0.03"/>
+                    </assert_contents>
+                </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -147,7 +160,7 @@
 .. _heatmap.sim: https://www.mothur.org/wiki/Heatmap.sim
 
 v.1.24.0: Updated to Mothur 1.33, added count parameter
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>