--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_filter.xml	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,81 @@
+<tool id="metaquantome_filter" name="MetaQuantome Filter" version="@VERSION@.0">
+    <description>for quality, redundancy, and sample coverage</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @MAKE_SAMPS_TSV@
+        metaquantome filter
+        @COMMON_PARAMS@
+        --expand_file '$expand_file'
+        --min_peptides $min_peptides 
+        #if $min_pep_nsamp:
+            --min_pep_nsamp max($min_peptides,$min_pep_nsamp)
+        #else
+            --min_pep_nsamp all
+        #end if
+        --min_children_non_leaf $min_children_non_leaf
+        #if $min_child_nsamp:
+            --min_child_nsamp max($min_peptides,$min_child_nsamp)
+        #else
+            --min_child_nsamp all
+        #end if
+        --qthreshold $qthreshold
+        --outfile='$output'
+    ]]></command>
+    <inputs>
+        <expand macro="common_params"/>
+        <param argument="--expand_file" type="data" format="tabular" label="metaquantome expand file"
+                    help=""/>
+        <param argument="--min_peptides" type="integer" value="0" min="0" label="min_peptides">
+            <help>
+                Used for filtering to well-supported annotations. The
+                number of peptides providing evidence for a term is
+                the number of peptides directly annotated with that
+                term plus the number of peptides annotated with any of
+                its descendants. Terms with a number of peptides
+                greater than or equal to min_peptides are retained.
+                The default is 0.
+            </help>
+        </param>
+        <param argument="--min_pep_nsamp" type="integer" value="" min="0" optional="true" label="min_pep_nsamp">
+            <help>
+                Number of samples per group that must meet or exceed
+                min_peptides. Default is 'all'.
+            </help>
+        </param>
+        <param argument="--min_children_non_leaf" type="integer" value="0" min="0" label="min_children_non_leaf">
+            <help>
+                Used for filtering to informative annotations. A term
+                is retained if it has a number of children greater
+                than or equal to min_children_non_leaf. The default is 0.
+            </help>
+        </param>
+        <param argument="--min_child_nsamp" type="integer" value="" min="0" optional="true" label="min_child_nsamp">
+            <help>
+                Number of samples per group that must meet or exceed
+                min_children_nsamp. Default is 'all'.
+            </help>
+        </param>
+        <param argument="--qthreshold" type="integer" value="3" min="0" label="qthreshold">
+            <help>
+                Minimum number of intensities in each sample group.
+                Any functional/taxonomic term with lower number of
+                per-group intensities will be filtered out. The
+                default is 3, because this is the minimum number for
+                t-tests.
+            </help>
+        </param>
+
+        <expand macro="output_samples_choice"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} filtered"/>
+        <expand macro="output_samples"/>
+    </outputs>
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+    <expand macro="citations" />
+</tool>