--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaquantome_expand.xml	Tue Dec 04 17:17:41 2018 -0500
@@ -0,0 +1,76 @@
+<tool id="metaquantome_expand" name="MetaQuantome Expand" version="@VERSION@.0">
+    <description>annotated functional or taxonomy terms to include all terms</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p data && #slurp
+        @MAKE_SAMPS_TSV@
+        metaquantome expand
+        @COMMON_PARAMS@
+        @DB_DIR@
+        #if $input.input_type == 'nopep':
+            --nopep --nopep_file='$input.nopep_file' 
+        #else:
+            --int_file='$input.int_file' 
+            --pep_colname_int='$input.pep_colname_int'
+        #end if
+       --outfile='$outfile'
+    ]]></command>
+    <inputs>
+        <expand macro="data_dir"/>
+        <expand macro="common_params"/>
+        <conditional name="input">
+            <param name="input_type" type="select" label="Select input data">
+                <option value="int">tabular intensity file with peptide column</option>
+                <option value="nopep">file without a peptide column</option>
+            </param>
+            <when value="int">
+                <param argument="--int_file" type="data" format="tabular" label="intensity data"
+                    help=""/>
+                <param argument="--pep_colname_int" type="text" value="" label="Peptide column name" 
+                    help="The column name within the intensity file that corresponds to the peptide sequences">
+                    <validator type="empty_field"/>
+                </param>
+            </when>
+            <when value="nopep">
+                <param argument="--nopep_file" type="data" format="tabular" label="intensity data"
+                    help=""/>
+            </when>
+        </conditional>
+        <expand macro="output_samples_choice"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/>
+        <expand macro="output_samples"/>
+    </outputs>
+    <tests>
+        <test>
+            <!-- expand('f', sinfo=TTEST_SINFO, int_file=int, pep_colname_int='peptide', pep_colname_func='peptide',
+                         pep_colname_tax='peptide', data_dir=GO_TEST_DIR, outfile=expanded, func_file=func,
+                         func_colname='go', ontology='go') -->
+             <param name="int_file" value="int_ttest.tab" ftype="tabular"/>
+             <param name="pep_colname_int" value="peptide" />
+             <param name="func_file" value="multiple_func.tab" />
+             <param name="pep_colname_func" value="peptide" />
+             <param name="func_colname" value="go"/>
+             <param name="mode" value="f" />
+             <param name="ontology" value="go" />
+             <param name="samps_src" value="build" />
+             <repeat name="samps">
+                 <param name="group_name" value="s1"/>
+                 <param name="col_names" value="int1,int2,int3"/>
+             </repeat>
+             <repeat name="samps">
+                 <param name="group_name" value="s2"/>
+                 <param name="col_names" value="int4,int5,int6"/>
+             </repeat>
+             <output name="outfile" file="go_expanded.tab" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        help
+    ]]></help>
+    <expand macro="citations" />
+</tool>