--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pepquery2_show_sets.xml	Sun Nov 06 16:24:53 2022 +0000
@@ -0,0 +1,86 @@
+<tool id="pepquery2_show_sets" name="PepQuery2 Show Sets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
+    <description>PepQueryDB datasets, Parameters, PTMs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+echo "PepQuery2 Show Sets $sets"
+#if 'PepQueryDB_datasets' in $sets
+  && pepquery -b show_full | sed 's/.*\(NO[.]\)/\1/' | grep '^[N1-9]' | sed 's/[ ][ ]*\$//' | sed 's/[ ][ ]*/\t/g'  > '$pepquerydb'
+#end if
+#if 'parameter_sets' in $sets
+  && pepquery -p show | grep -v INFO | sed 's/^.\[m//' > $parameters
+#end if
+#if 'printPTM' in $sets
+  && pepquery -printPTM | grep -v INFO | sed 's/^.\[m//' > $ptm_list
+#end if
+    ]]></command>
+    <inputs>
+        <param name="sets" type="select" multiple="true" optional="false" label="PepQuery Set">
+            <option value="PepQueryDB_datasets" selected="true">PepQueryDB Datasets</option>
+            <option value="parameter_sets">PepQuery Predefined Parameter Sets</option>
+            <option value="printPTM">PepQuery Modifications</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="pepquerydb" format="tabular" label="PepQueryDB datasets">
+           <filter>'PepQueryDB_datasets' in sets</filter>
+           <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="NO.,dataset_name,short_name,parameter_set,species,data_type,n_spectra,n_ms_file,data_link" />
+            </actions>
+        </data>
+        <data name="parameters" format="txt" label="PepQuery Predefined Parameter Sets">
+           <filter>'parameter_sets' in sets</filter>
+        </data>
+        <data name="ptm_list" format="tabular" label="PepQuery Modifications">
+           <filter>'printPTM' in sets</filter>
+           <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="mod_id,mod_name,mod_mass,mod_type,mod_category,unimod_accession" />
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <output name="pepquerydb">
+                <assert_contents>
+                    <has_text text="CPTAC_PDA_Discovery_Study_Proteome_PDC000270" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**Show available: PepQueryDB Datasets, Parameter Sets, and PTMs** *(Post Translational Modifications)*
+    
+@PEPQUERY_DOCUMANTATION_URL@
+
+**PepQueryDB Datasets**
+
+    - Shows a table of all the indexed MS/MS datasets available in PepQueryDB.
+    - *java -jar pepquery-2.0.2.jar -b show_full*
+    - These datasets can be used for the **-b** option in **PepQuery**.
+    - The parameter_set value can be used in the **-p** option in **PepQuery**.
+    - Columns: NO. dataset_name short_name parameter_set species data_type n_spectra n_ms_file data_link
+
+
+**PepQuery Predefined Parameter Sets**
+
+    - Shows the predefined Parameter Set Names with the option settings
+    - *java -jar pepquery-2.0.2.jar -p show*
+    - The parameterset names can be used for the **-p** option in **PepQuery**.
+
+
+**PepQuery Modifications**
+
+    - Shows a table of the PTMs available
+    - *java -jar pepquery-2.0.2.jar -printPTM*
+    - The mod_id numbers can be used in the **-fixMOD** and **-varMOD** options in **PepQuery**.
+    - Columns: mod_id mod_name mod_mass mod_type mod_category unimod_accession
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>