--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_filter.xml	Thu Apr 25 13:51:33 2019 -0400
@@ -0,0 +1,122 @@
+<tool id="metaquantome_filter" name="metaQuantome: filter" version="@GVERSION@">
+    <description>for quality, redundancy, and sample coverage</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        metaquantome filter
+        --samps '$samps'
+        --mode '$mode_args.mode'
+        #if $mode_args.mode == 'f' or $mode_args.mode == 'ft'
+            --ontology='$mode_args.ontology_args.ontology'
+        #end if
+        --expand_file '$expand_file'
+        --min_peptides $min_peptides
+        #if $min_pep_nsamp != "":
+            --min_pep_nsamp $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 $min_child_nsamp
+        #else
+            --min_child_nsamp all
+        #end if
+        --qthreshold $qthreshold
+        --outfile='$outfile'
+    ]]></command>
+    <inputs>
+      <conditional name="mode_args">
+          <param argument="--mode" type="select" label="Mode">
+              <option value="f">Functional analysis</option>
+              <option value="t">Taxonomic analysis</option>
+              <option value="ft">Functional-taxonomic interaction analysis</option>
+          </param>
+          <when value="f">
+              <expand macro="ONTOLOGY_ARGS"/>
+          </when>
+          <when value="t">
+          </when>
+          <when value="ft">
+              <expand macro="ONTOLOGY_ARGS"/>
+          </when>
+      </conditional>
+      <expand macro="SAMPS"/>
+      <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. The default is all samples.
+          </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>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} filtered"/>
+    </outputs>
+    <tests>
+      <test>
+        <param name="expand_file" value="go_expanded.tab" ftype="tabular"/>
+        <param name="mode" value="f" />
+        <param name="ontology" value="go" />
+        <param name="samps" value="samples_basic.tab" ftype="tabular"/>
+        <param name="min_peptides" value="2" />
+        <param name="min_pep_nsamp" value="" />
+        <param name="min_children_non_leaf" value="2" />
+        <param name="min_child_nsamp" value="" />
+        <param name="qthreshold" value="0" />
+        <output name="outfile" file="go_filtered.tab" ftype="tabular"/>
+      </test>
+    </tests>
+    <help><![CDATA[
+metaQuantome filter
+===================
+
+The *filter* module is the second step in the metaQuantome analysis workflow. The
+purpose of the filter module is to filter expanded terms to those that are
+representative and well-supported by the data. Please see the manuscript for further
+details about filtering.
+
+
+Questions, Comments, Problems, Kudos
+--------------------------------------
+
+Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
+      ]]></help>
+    <expand macro="citations" />
+</tool>