diff remove.dists.xml @ 2:0df1987fb914 draft

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

--- a/remove.dists.xml	Tue Sep 05 17:03:44 2017 -0400
+++ b/remove.dists.xml	Tue Mar 20 22:20:36 2018 -0400
@@ -7,23 +7,23 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$accnos" accnos.dat &&
-        ln -s "$input.dist" input_dist.dat &&
+## create symlinks to input datasets
+ln -s '$accnos' accnos.dat &&
+ln -s '$input.dist' input_dist.dat &&
 
-        echo 'remove.dists(
-            accnos=accnos.dat,
-            #if $input.source == "phylip":
-                phylip=input_dist.dat
-            #else
-                column=input_dist.dat
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'remove.dists(
+    accnos=accnos.dat,
+    #if $input.source == "phylip":
+        phylip=input_dist.dat
+    #else
+        column=input_dist.dat
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -32,13 +32,14 @@
                 <option value="phylip">Phylip Distance Matrix</option>
             </param>
             <when value="column">
-                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
+                <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
             </when>
             <when value="phylip">
-                <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+                <param name="dist" argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
             </when>
         </conditional>
-        <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
+        <param argument="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -49,12 +50,18 @@
             <param name="source" value="phylip"/>
             <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
             <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
-            <output name="pick_dist" md5="ec444ddb897d21864a245e8645fcda33" ftype="mothur.square.dist"/>
+            <output name="pick_dist" ftype="mothur.square.dist">
+                <assert_contents>
+                    <expand macro="test-dist-format"/>
+                    <has_text text="U68589"/>
+                    <has_line_matching expression="^90$"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -64,7 +71,6 @@
 
 .. _remove.dists: https://www.mothur.org/wiki/Remove.dists
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>