diff lefse.xml @ 2:8c39f704d21a draft

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

--- a/lefse.xml	Tue Sep 05 16:56:54 2017 -0400
+++ b/lefse.xml	Tue Mar 20 21:58:54 2018 -0400
@@ -7,38 +7,41 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s '$otu' shared.dat &&
-        ln -s '$design' design.dat &&
+## create symlinks to input datasets
+ln -s '$otu' shared.dat &&
+ln -s '$design' design.dat &&
 
-        echo 'lefse(
-            shared=shared.dat,
-            design=design.dat,
-            #if $class:
-                class=$class,
-            #end if
-            #if $sclass:
-                subclass=$sclass,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            aalpha=$aalpha,
-            walpha=$walpha,
-            lda=$lda,
-            iters=$iters,
-            fboots=$fboots,
-            strict=$strict,
-            minc=$minc,
-            wilc=$wilc,
-            curv=$curv,
-            norm=$norm
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'lefse(
+    shared=shared.dat,
+    design=design.dat,
+    #if $class:
+        class=$class,
+    #end if
+    #if $sclass:
+        subclass=$sclass,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $sets:
+        sets=${ str($sets).replace(",","-") },
+    #end if
+    aalpha=$aalpha,
+    walpha=$walpha,
+    lda=$lda,
+    iters=$iters,
+    fboots=$fboots,
+    strict=$strict,
+    minc=$minc,
+    wilc=$wilc,
+    curv=$curv,
+    norm=$norm
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
@@ -46,6 +49,15 @@
         <param name="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
             <expand macro="labeloptions"/>
         </param>
+        <param name="sets" type="text" label="sets - Which of the sets in your design file you would like to analyze?" help="separate sets by dashes or commas, e.g. set1,set2 or set1-set2-set3"/>
+        <!-- TODO: update galaxy datatypes to set metadata for design files, then can switch to a select box
+        <param argument="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze."
+            help="The set names are separated by dashes. The defualt is all sets in designfile">
+            <options>
+                <filter type="data_meta" ref="design" key="sets"/>
+            </options>
+         </param>
+         -->
         <param name="class" type="text" optional="true" value="" label="class -indicate the which category you would like used for the Kruskal Wallis analysis" help="If none is provided first category is used"/>
         <param name="sclass" type="text" optional="true" value="" label="subclass - indicate the which category you would like used for the Kruskal Wallis analysis" help="If none is provided second category is used"/>
         <param name="aalpha" type="float" value="0.05" label="aalpha - alpha value for the Krukal Wallis Anova test" help=""/>
@@ -58,6 +70,7 @@
         <param name="wilc" type="boolean" truevalue="T" falsevalue="F" checked="true" label="wilc - indicate whether to perform the Wilcoxon test" help=""/>
         <param name="curv" type="boolean" truevalue="T" falsevalue="F" checked="false" label="curv - whether perform the wilcoxon testing the Curtis's approach (beta)" help=""/>
         <param name="norm" type="boolean" truevalue="T" falsevalue="F" checked="true" label="norm - multiply relative abundances by 1000000" help="Recommended when very low values are present"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -68,6 +81,7 @@
             <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
             <param name="design" value="mouse.design"/>
             <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with label and class select -->
@@ -76,6 +90,17 @@
             <param name="label" value="1"/>
             <param name="class" value="dpw"/>
             <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with sets -->
+            <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
+            <param name="design" value="mouse.design"/>
+            <param name="sets" value="8,142"/>
+            <param name="label" value="1"/>
+            <param name="class" value="dpw"/>
+            <output name="summary" md5="64ebfb48d8c3e0bcd993a7ea8aa60e62" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>