--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastg2protlib-peptides.xml	Fri Aug 07 06:17:31 2020 -0400
@@ -0,0 +1,59 @@
+<tool id="fastg2protlib-peptides" name="FASTG2Protlib-Peptides" version="@VERSION@">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <description>Generate FASTA from FASTG</description>
+    <expand macro="pkg_requirement" />
+    <command detect_errors="exit_code">
+        <![CDATA[
+        python '$__tool_directory__/application.py' 
+        -m $min_peptide_length
+        -p $min_protein_length  
+        -c $cleavage 
+        -d 'results.db' 
+        -l $show_plots
+        '$fastg_file'
+        ]]>
+    </command>
+    <inputs>
+        <param name="fastg_file" type="data" format="fastg" label="FASTG file" />
+        <param name="cleavage" type="select" label="Peptide Cleavage">
+            <option value="trypsin" selected="true">Trypsin</option>
+            <expand macro="cleavages" />
+        </param>
+        <param name="min_protein_length" type="integer" value="55" label="Minimum Protein Length in Amino Acids" />
+        <param name="min_peptide_length" type="integer" value="8" label="Minimum Peptide Length in Amino Acids" />
+        <param name="show_plots" type="boolean" checked="true" label="Create Diagnostic Plots" />
+    </inputs>
+    <outputs>
+        <data name="peptide_fasta" format="txt" from_work_dir="peptide.fasta" label="${on_string} Peptides from FASTG" />
+        <data name="results_db" format="sqlite" from_work_dir="results.db" label="${on_string} Results DB" />
+        <data name="aa_count_plot" format="png" from_work_dir="aa_count_chart.png" label="${on_string} AA Count Plot">
+            <filter>show_plots == True</filter>
+        </data>
+        <data name="fastg_length_plot" format="png" from_work_dir="fastg_seq_lengths.png" label="${on_string} FASTG Sequence Length Plot">
+            <filter>show_plots == True</filter>
+        </data>
+        <data name="protein_length_plot" format="png" from_work_dir="protein_seq_lengths.png" label="${on_string} Protein Sequence Length Plot">
+            <filter>show_plots == True</filter>
+        </data>
+        <data name="gc_pct_plot" format="png" from_work_dir="gc_pct.png" label="${on_string} GC Percent Plot">
+            <filter>show_plots == True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fastg_file" value="two.fastg" />
+            <param name="cleavage" value="trypsin" />
+            <param name="min_protein_length" value="20" />
+            <param name="min_peptide_length" value="8" />
+            <param name="show_plots" value="false" />
+            <output name="peptide_fasta">
+                <assert_contents>
+                    <has_text text="IFLPFSTHSR" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <expand macro="help-text" />
+</tool>