--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blastp_to_gff3.xml	Mon Jun 05 02:39:51 2023 +0000
@@ -0,0 +1,74 @@
+<tool id="edu.tamu.cpt.blastp_to_gff3" name="BlastP Results to GFF3" version="19.1.0.0">
+  <description>converts blast xml results to a JBrowse-compatible file</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>cpt-macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="aggressive"><![CDATA[
+'$__tool_directory__/blast_to_gff3.py'
+'$input_type.blast_input'
+#if $input_type.input_type_selector == "xml":
+  --blastxml
+  '$input_type.include_seq'
+#elif $input_type.input_type_selector == "tsv":
+  --blasttab
+#end if
+> $output]]></command>
+  <inputs>
+    <conditional name="input_type">
+      <param name="input_type_selector" type="select" label="Choose BlastP File Format">
+        <option value="xml" selected="true">BlastXML</option>
+        <option value="tsv">Blast 25 Column Table"</option>
+      </param>
+      <when value="xml">
+        <param name="blast_input" type="data" format="xml" label="BlastXML Input"/>
+        <param name="include_seq" type="boolean" label="Include protein alignment in Blast view in Apollo/JBrowse" truevalue="--include_seq" falsevalue=""/>
+      </when>
+      <when value="tsv">
+        <param name="blast_input" type="data" format="tabular" label="Blast 25 Column Table"/>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="gff3" name="output"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_type_selector" value="xml"/>
+      <param name="blast_input" value="BlastpXmlToGff_In.blastxml" ftype="xml"/>
+      <param name="include_seq" value="false"/>
+      <output name="output" file="BlastpXmlToGff_Out.gff3" ftype="gff3"/>
+    </test>
+    <test>
+      <param name="input_type_selector" value="xml"/>
+      <param name="blast_input" value="BlastpXmlToGff_In.blastxml" ftype="xml"/>
+      <param name="include_seq" value="true"/>
+      <output name="output" file="BlastpXmlToGff_OutWithSeq.gff3" ftype="gff3"/>
+    </test>
+    <test>
+      <param name="input_type_selector" value="tsv"/>
+      <param name="blast_input" value="BlastpTabToGff_In.tabular" ftype="tabular"/>
+      <param name="include_seq" value="false"/>
+      <output name="output" ftype="gff3">
+        <assert_contents>
+          <has_line line="##gff-version 3"/>
+          <has_n_lines n="122"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Convert BlastP XML or tabular results into GFF3 format for visualization within JBrowse, please be sure to select the correct input option for your data. 
+This is critical for displaying the position of high-scoring pairs of the Target aligned against the Query. If you need to convert BlastN results, please use the "BlastN Results to GFF3" tool.
+
+**Options::**
+
+By selecting **Include protein alignment…**, the actual sequence alignment will be displayed 
+in the pop-up BLAST view in Apollo/JBrowse. This option currently only works when using XML input.
+
+]]></help>
+  <expand macro="citations"/>
+</tool>