--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/psm_validation.xml	Thu Oct 15 07:45:17 2020 +0000
@@ -0,0 +1,56 @@
+    <tool id="psmvalidator" name="PSM-Fragment Validator" version="@VERSION@">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <description>Validate PSMs against Ion Fragmentation</description>
+    <expand macro="pkg_requirement" />
+    <command detect_errors="exit_code">
+        <![CDATA[
+        python '$__tool_directory__/application.py' 
+            -d '$mz_db_name'
+            -p '$peptide_sequences'
+            #if $neutral_loss_ions:
+                -n
+            #end if
+            #if $internal_ions:
+                -i
+            #end if
+            -b $b_ion_run
+            -y $y_ion_run
+            -e $epsilon
+            #if $b_ion_run < 0:
+                --test
+            #end if
+        ]]>
+    </command>
+    <inputs>
+        <param name="mz_db_name" type="data" format="mz.sqlite" label="MZSQLite DB" />
+        <param name="peptide_sequences" type="data" format="tabular" label="Peptide Sequence List" />
+        <param name="b_ion_run" type="integer" value="2" label="Consecutive B-Ions" />
+        <param name="y_ion_run" type="integer" value="2" label="Consecutive Y-Ions" />
+        <param name="neutral_loss_ions" type="boolean" checked="True" label="Use Neutral Loss" />
+        <param name="internal_ions" type="boolean" checked="True" label="Use Internals" />
+        <param name="epsilon" type="float" value="0.5" label="Epsilon" />
+    </inputs>
+    <outputs>
+        <data name="html_output" format="html" from_work_dir="index.html" label="PSM Ion Fragementation Report" />
+        <data name="text_output" format="tabular" from_work_dir="results.tab" label="Tabular Results" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="mz_db_name" value="test.db" />
+            <param name="peptide_sequences" value="test-peptides.txt" />
+            <param name="b_ion_run" value="-99" />
+            <param name="y_ion_run" value="-99" />
+            <param name="neutral_loss_ions" value="True" />
+            <param name="internal_ions" value="True" />
+            <param name="epsilon" value="0.5" />
+            <output name="html_output">
+                <assert_contents>
+                    <has_text text="success" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <expand macro="help-text" />
+</tool>