--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_genome_editor/genome_editor.xml	Fri Jun 17 12:48:06 2022 +0000
@@ -0,0 +1,169 @@
+<?xml version="1.0"?>
+<tool id="edu.tamu.cpt.gff3.genome_editor" name="Genome Editor" version="2.1">
+  <description>allows you to re-arrange a genome</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>cpt-macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command><![CDATA[
+@GENOME_SELECTOR_PRE@
+python $__tool_directory__/genome_editor.py
+
+@GENOME_SELECTOR@
+@INPUT_GFF@
+"$new_id"
+
+--out_fasta "$out_fasta"
+--out_gff3 "$out_gff3"
+--out_simpleChain "$out_chain"
+--customSeqs "$custom_seqs"
+--changes
+#for $idx, $change in enumerate($changes):
+	#if $change.input_type.input_type_select == "region":
+		${change.input_type.start},${change.input_type.end},${change.input_type.revcom}
+	#else
+		custom${idx}
+	#end if
+#end for
+]]></command>
+	<configfiles>
+		<configfile name="custom_seqs">
+		<![CDATA[
+#for $idx, $change in enumerate($changes):
+	#if $change.input_type.input_type_select == "custom":
+>custom${idx}
+${change.input_type.seq}
+	#end if
+#end for
+		]]>
+		</configfile>
+	</configfiles>
+  <inputs>
+      <expand macro="input/gff3+fasta" />
+      <param label="New ID" name="new_id" type="text" help="New ID for the sequence to uniquely identify it from the previous build of the sequence. E.g. append Miro could become Miro.2 or Miro.v2 ">
+		  <validator type="expression" message="You must specify a new ID"><![CDATA[value and len(value) > 0]]></validator>
+	  </param>
+      <repeat name="changes" title="Sequence Component Selections">
+		<conditional name="input_type">
+			<param name="input_type_select" type="select" label="Data Source">
+				<option value="region" selected="True">Region from FASTA file</option>
+				<option value="custom">Custom Additional Sequence</option>
+			</param>
+			<when value="region">
+				<param label="Start" name="start" type="integer" min="1" value="1" help="Inclusive range, 1-indexed genome. (I.e. specifying 1-2000 will include base number 1)"/>
+				<param label="End" name="end" type="integer" min="1" value="1" help="Inclusive range. (I.e. specifying 1-2000 will include base number 2000)"/>
+				<param label="Reverse + Complement" name="revcom" type="boolean" truevalue="-" falsevalue="+" />
+			</when>
+			<when value="custom">
+				<param label="Custom Sequence" name="seq" type="text" help="Enter the sequence, e.g. 'ACTG'. No FASTA definition line."/>
+			</when>
+		</conditional>
+      </repeat>
+  </inputs>
+  <outputs>
+	<data format="gff3" name="out_gff3" label="${new_id} Features"/>
+    <data format="fasta" name="out_fasta" label="${new_id}"/>
+    <data format="tabular" name="out_chain" label="${new_id} Change Table"/>
+  </outputs>
+  <tests>
+      <test>
+			<param name="reference_genome_source" value="history" />
+			<param name="genome_fasta" value="genome_editor.simple.fa" />
+			<param name="gff3_data" value="genome_editor.simple.gff3" />
+			<param name="new_id" value="test2" />
+			<repeat name="changes">
+				<conditional name="input_type">
+					<param name="input_type_select" value="region" />
+					<param name="start" value="1"/>
+					<param name="end" value="4"/>
+					<param name="revcom" value="+"/>
+				</conditional>
+			</repeat>
+			<repeat name="changes">
+				<conditional name="input_type">
+					<param name="input_type_select" value="custom" />
+					<param name="seq" value="cccggg"/>
+				</conditional>
+			</repeat>
+			<repeat name="changes">
+				<conditional name="input_type">
+					<param name="input_type_select" value="region" />
+					<param name="start" value="5"/>
+					<param name="end" value="8"/>
+					<param name="revcom" value="-"/>
+				</conditional>
+			</repeat>
+			<output name="out_gff3" file="genome_editor.simple.out.gff3" />
+			<output name="out_fasta" file="genome_editor.simple.out.fa" />
+			<output name="out_chain" file="genome_editor.simple.out.chain" />
+      </test>
+      <test>
+
+			<param name="reference_genome_source" value="history" />
+			<param name="genome_fasta" value="miro.fa" />
+			<param name="gff3_data" value="miro.2.gff3" />
+			<param name="new_id" value="Miro.v2" />
+			<repeat name="changes">
+				<conditional name="input_type">
+					<param name="input_type_select" value="region" />
+					<param name="start" value="1"/>
+					<param name="end" value="950"/>
+					<param name="revcom" value="+"/>
+				</conditional>
+			</repeat>
+			<repeat name="changes">
+				<conditional name="input_type">
+					<param name="input_type_select" value="custom" />
+					<param name="seq" value="aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa"/>
+				</conditional>
+			</repeat>
+			<repeat name="changes">
+				<conditional name="input_type">
+					<param name="input_type_select" value="region" />
+					<param name="start" value="3170"/>
+					<param name="end" value="3450"/>
+					<param name="revcom" value="+"/>
+				</conditional>
+			</repeat>
+			<output name="out_gff3" file="genome_editor.mirov2.gff3" />
+			<output name="out_fasta" file="genome_editor.mirov2.fa" />
+			<output name="out_chain" file="genome_editor.mirov2.chain" />
+      </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Allows for re-arranging a FASTA genomic sequence, and remaps the associated features 
+from a gff3 file with the new coordinates. Segments of the genome are moved around 
+and stitched back together according to user-specified positions. 
+
+**Example FASTA input** (spaces added for clarity)::
+	>Miro
+	TTA GTA ATG GCT AAA
+
+With user-specified *sequence component selections*:
+
+- start: 1, end: 10, strand: +
+- start: 6, end: 10, strand: +
+
+the first ten bases will be listed, followed by a duplication of bases 6-10. 
+Bases 11-15 are not part of the sequence component selection parameters and 
+are therefore not in the output:: 
+
+	>Miro.v2
+	TTA GTA ATG GAA TGG
+
+Alternatively, with user-specified *sequence component selections*::
+
+- start: 1, end: 10, strand: +
+- start: 6, end: 10, strand: -
+
+the last section with be reverse-complemented and give the following output::
+
+	>Miro.v2
+	TTA GTA ATG GCC ATT
+
+]]></help>
+  <expand macro="citations" />
+</tool>