diff phyloseq_filter.xml @ 1:9fbb104e16d9 draft

update

--- a/phyloseq_filter.xml	Wed Sep 05 22:21:43 2018 -0400
+++ b/phyloseq_filter.xml	Mon Nov 12 22:42:14 2018 -0500
@@ -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" >
-                <assert_contents>
+            <output name="outputbiom" file="out.biom" lines_diff="2" ftype="biom1"/>
+                <!-- <assert_contents>
                     <has_text text="Biological Observation Matrix"/>
                 </assert_contents>
-            </output>
+            </output> -->
         </test>
         <test>  <!-- Test #2: Test TABULAR format inputs -->
             <conditional name="file_source">
@@ -94,22 +94,20 @@
 
     <help>
 **What it does**
-Filter BIOM file using R package called phyloseq_.
+Filter out low abundance OTUs and/or data corresponding to the least represented taxonomic grouping using R package called R_package_called_phyloseq_, and specifically according to the pre-processing step outlined in the Phyloseq_Ordination_Plot_Tutorial_.
 
-.. _phyloseq: https://joey711.github.io/phyloseq/plot_ordination-examples.html
+.. _R_package_called_phyloseq: https://joey711.github.io/phyloseq/index.html
+.. _Phyloseq_Ordination_Plot_Tutorial: https://joey711.github.io/phyloseq/plot_ordination-examples.html
 
 -----
 
 **Input**
 
-- **Choose an input file type** - BIOM File or TABULAR file
-- **OTU TABLE** - this is a OTU matrix
-- **Taxonomy TABLE** - this is a TAX matrix
-- **Metadata TABLE** - this is a metadata file of the experiment design
-- **Select a taxonomic rank for the analysis** - select a taxonomy for filtering
-- **Specify value of Y (where 1.0=100%)** - Filter out OTUs from the analysis that do not appear more than X times in more than Y% of the samples
-- **Specify value of X** - Remove OTUs that do not appear more than X times (e.g., 5 times)
-- **Number of the most abundant taxonomic rank units to keep in the filtered BIOM file** - taxonomic rank units (e.g. Phyla, Class etc) to keep
+- **Choose an input file type** - either 1 BIOM file or 3 TABULAR files (i.e. OTU, Taxonomy and Metadata tables)
+- **Select a taxonomic rank for the analysis** - if filtering out low abundance taxa, this is the level of the taxonomy that you want to filter on (e.g. phyla, species)
+- **Number of the most abundant taxonomic rank units to keep in the filtered BIOM file** - the number of the most abundant taxonomic rank units specified above to keep (e.g. remove all the most abundant 5 phyla or species)
+- **Specify value of X** - if filtering out low abundance OTUs, use this to specify a value of X (where OTUs are removed that do not appear more than X times in more than Y% of the samples)
+- **Specify value of Y (where 1.0=100%)** - if filtering out low abundance OTUs use this to specify a value of Y (where OTUs are removed that do not appear more than X times in more than Y% of the samples)
 
 -----