--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotation_collector.xml	Mon Jun 29 03:39:57 2015 -0400
@@ -0,0 +1,54 @@
+<tool id="annotation_collector" name="Collect Annotation counts" version="0.9.0">
+    <description> from matched fasta files</description>
+    <command interpreter="python">
+        annotation_collector.py
+        $out_file
+        $input1 $label1
+        #for $q in $queries
+            ${q.input2} ${q.label2}
+        #end for
+        $title
+    </command>
+    <inputs>
+        <param label="Annotation Title" name="title" type="text" />
+        <param label="fasta file to annotate" name="input1" type="data" format="fasta"/>
+        <param label="category label" name="label1" type="text" />
+        <repeat name="queries" title="Additional fasta file and label">
+            <param label="Select" name="input2" type="data" format="fasta"/>
+            <param label="Label" name="label2" type="text" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data format="tabular" label="Annotations" metadata_source="input1" name="out_file" />
+    </outputs>
+    <tests>
+        <test>
+           <param name="title" value="Test Title"/>
+           <param name="input1" value="input1.fa" ftype="fasta"/>
+           <param name="label1" value="label1" />
+           <param name="queries_0|input2" value="input2.fa" ftype="fasta"/>
+           <param name="queries_0|label2" value="label2" />
+           <output name="out_file" file="output.tab" ftype="tabular" />
+        </test>
+    </tests>
+    <help>
+
+.. class:: warningmark
+
+**WARNING:** Be careful not to agregate datasets of different kinds (e.g., datasets must be matched fasta files). This tool does not check if the datasets being annotated are in the same format. 
+
+-----
+
+**What it does**
+
+Generates Annotation Table from fasta files
+
+Collect Annotation counts from matched fasta files.
+Counts number of lines in fasta files and outputs a
+tabular file with Label in the first column, number of fasta
+sequences in second column. Percent of counts is in the third
+column with the number of fasta entries in the first file
+set to 100%, and the remaining lines expressed as fractions.
+
+   </help>
+</tool>