diff phyloseq_filter.xml @ 2:54897b7e0551 draft default tip

Updated tool

--- a/phyloseq_filter.xml	Mon Nov 12 22:42:14 2018 -0500
+++ b/phyloseq_filter.xml	Thu Nov 22 08:13:52 2018 -0500
@@ -54,8 +54,8 @@
             <option value="Species">Species</option>
         </param>
         <param name="keep" size="10" type="integer" value="5" label="Number of the most abundant taxonomic rank units to keep in the filtered BIOM file" help="e.g. Phyla, Class and etc. as specified above. Select a value > 1."/>
-        <param name="cutoff" size="10" type="integer" value="5" label="Filter out OTUs. Remove OTUs from the analysis that do not appear more than X times in more than Y% of the samples. Specify value of X" help="Remove OTUs that do not appear more than X times (e.g., 5 times)"/>
-        <param name="nsample" size="10" type="float" value="0.5" label="Specify value of Y (where 1.0 = 100%)"/>
+        <param name="cutoff" size="10" type="integer" value="1" label="Filter out OTUs. Remove OTUs from the analysis that do not appear more than X times in more than Y% of the samples. Specify value of X" help="Remove OTUs that do not appear more than X times (e.g., 5 times)"/>
+        <param name="nsample" size="10" type="float" value="0.0" label="Specify value of Y (where 1.0 = 100%)"/>
     </inputs>
 
     <outputs>
@@ -70,11 +70,11 @@
                 <param name="input" value="GP.biom" ftype="biom1"/>
             </conditional>
             <output name="htmlfile" ftype="html" file="biom_out.html" />
-            <output name="outputbiom" file="out.biom" lines_diff="2" ftype="biom1"/>
-                <!-- <assert_contents>
+            <output name="outputbiom" >
+                <assert_contents>
                     <has_text text="Biological Observation Matrix"/>
                 </assert_contents>
-            </output> -->
+            </output>
         </test>
         <test>  <!-- Test #2: Test TABULAR format inputs -->
             <conditional name="file_source">