--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PSM_Recombine.xml	Mon Jun 05 02:51:26 2023 +0000
@@ -0,0 +1,124 @@
+<tool id="edu.tamu.cpt.external.psm_recombine" name="PSM Prep and Table Generator:" version="21.0.0">
+  <description>: generates a raw PSM file for plotting and a tabular summary</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>cpt-macros.xml</import>
+  </macros>
+  <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>
+    <requirement type="package" version="3.7">python</requirement>
+    <requirement type="package" version="1.74">biopython</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 "TXT"
+
+--cpt_psm_object_id "${cpt_psm_object.id}" 
+
+&&
+
+mkdir tmp_001
+&&
+mkdir tmp_002
+
+&&
+
+perl -Mlib='$__tool_directory__/lib' '$__tool_directory__/cpt_psm_2_gentable.pl'
+--galaxy
+--outfile_supporting '$__new_file_path__'
+--file "${cpt_psm_object}"
+
+#if $evalue and $evalue is not "None":
+--evalue "${evalue}"
+#end if
+
+#if $dice and $dice is not "None":
+--dice "${dice}"
+#end if
+
+#if $mismatch and $mismatch is not "None":
+--mismatch "${mismatch}"
+#end if
+
+#if $gap_penalty and $gap_penalty is not "None":
+--gap_penalty "${gap_penalty}"
+#end if
+
+#if $match and $match is not "None":
+--match "${match}"
+#end if
+
+--diff_table "./tmpDiff.tsv"
+--diff_table_files_path "./tmp_001"
+--diff_table_format TSV_U
+--diff_table_id "000001"
+
+--blastclust "./tmpClust.tsv"
+--blastclust_files_path "./tmp_002"
+--blastclust_format TSV_U
+--blastclust_id "000002"
+
+&&
+
+'$__tool_directory__/PSM_Recombine.py'
+./tmpDiff.tsv
+#for $item in $repeat_file:
+"${item.file}"
+#end for
+> "${tableOut}" 
+]]>
+</command>
+  <inputs>
+    <repeat name="repeat_file" title="Genbank file(s) used to generate PSM">
+      <param name="file" optional="False" label="Gbk file" type="data" format="genbank"/>
+    </repeat>
+    <param value="0.0001" name="evalue" help="Evalue cutoff" optional="True" label="evalue" type="float"/>
+    <param value="50" name="dice" help="Dice cutoff" optional="True" label="dice" type="float"/>
+    <param value="-1" name="mismatch" help="Mismatch Score" optional="True" label="mismatch" type="float"/>
+    <param value="0.0" name="gap_penalty" help="Gap Penalty" optional="True" label="gap_penalty" type="float"/>
+    <param value="5" name="match" help="Match Score" optional="True" label="match" type="float"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="tableOut" label="PSM Tabular Results"/>
+    <data name="cpt_psm_object" label="Raw PSM Binary output" format="TXT"/>
+  </outputs>
+  <help><![CDATA[
+**What it does**
+
+This tool takes in 2 or more GenBank files, blasts, and prepares data
+structures for use in the companion tool, PSM Plotter, as well as a 
+tabular file read-out of the results. 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.
+
+IMPORTANT PARAMETERS
+--------------------
+
+-  ``mismatch``, ``gap_penalty``, ``match``
+
+   These parameters control the Needleman-Wunsch Multiple Sequence
+   Alignment library's scoring scheme. Mismatch scores are generally
+   negative and discourage unrelated proteins from being plotted in a
+   line together. Match scores encourage related proteins to line up.
+   Gap penalty is set at zero as we generally prefer gaps to mismatches
+   in this tool; phage genomes are small and gaps are "cheap" to use,
+   whereas mismatches can sometimes give an incorrect impression of
+   relatedness. That said, how your plots look is completely up to you
+   and we encourage experimentation!
+  ]]></help>
+  <expand macro="citations-2020"/>
+</tool>