--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_psm_0_prep.xml	Mon Jun 05 02:50:07 2023 +0000
@@ -0,0 +1,62 @@
+<tool id="PSM.Prep" name="PSM Prep" version="1.94.2">
+  <description>prepares data for the PSM Plotter</description>
+  <version_command>perl cpt_psm_0_prep.pl --version</version_command>
+  <stdio>
+    <exit_code range="1:" level="fatal"/>
+  </stdio>
+  <requirements>
+    <requirement type="package" version="5.22.1">perl</requirement>
+    <requirement type="package">perl-bioperl</requirement>
+    <requirement type="package">perl-moose</requirement>
+    <requirement type="package">perl-ipc-run</requirement>
+    <requirement type="package">perl-getopt-long-descriptive</requirement>
+  </requirements>
+  <command detect_errors="aggressive"><![CDATA[
+perl -Mlib='$__tool_directory__/lib' '$__tool_directory__/cpt_psm_0_prep.pl'
+--galaxy
+--outfile_supporting '$__new_file_path__'
+#for $item in $repeat_file:
+--file "${item.file}"
+#end for
+
+--cpt_psm_object "${cpt_psm_object}"
+
+--cpt_psm_object_files_path "${cpt_psm_object.files_path}"
+
+--cpt_psm_object_format "${cpt_psm_object_format}"
+
+--cpt_psm_object_id "${cpt_psm_object.id}"
+
+]]></command>
+  <inputs>
+    <repeat name="repeat_file" title="File">
+      <param name="file" help="Input file" optional="False" label="file" type="data"/>
+    </repeat>
+    <param name="cpt_psm_object_format" help="Output PSM Object" optional="False" label="Format of cpt_psm_object" type="select">
+      <option value="TXT" selected="True">TXT</option>
+      <option value="CONF">CONF</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="cpt_psm_object" format="TXT">
+      <change_format>
+        <when input="cpt_psm_object_format" value="TXT" format="txt"/>
+        <when input="cpt_psm_object_format" value="CONF" format="txt"/>
+      </change_format>
+    </data>
+  </outputs>
+  <help>NAME
+====
+
+PSM Prep
+
+DESCRIPTION
+===========
+
+This tool takes in 2 or more GenBank files, blasts, and prepares data
+structures for use in the companion tool: PSM Plotter. Select as many
+(multi)-gbk files as you *might* want to plot. Once this tool is done,
+you can select any subset of those to plot then.
+</help>
+  <tests/>
+</tool>