# HG changeset patch
# User cpt
# Date 1704434201 0
# Node ID aacd746d1c8b10a93d608b6d0ee72fcc37653a78
# Parent  f7afd1480d0ff016007604d6aa7e73db8e6faaf3
planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc

diff -r f7afd1480d0f -r aacd746d1c8b cpt-macros.xml
--- a/cpt-macros.xml	Mon Jun 05 02:51:59 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,115 +0,0 @@
-<macros>
-    <xml name="gff_requirements">
-        <requirements>
-            <requirement type="package" version="2.7">python</requirement>
-            <requirement type="package" version="1.65">biopython</requirement>
-            <requirement type="package" version="2.12.1">requests</requirement>
-			<requirement type="package" version="1.2.2">cpt_gffparser</requirement>
-            <yield/>
-        </requirements>
-        <version_command>
-		<![CDATA[
-			cd '$__tool_directory__' && git rev-parse HEAD
-		]]>
-		</version_command>
-    </xml>
-    <xml name="citation/mijalisrasche">
-        <citation type="doi">10.1371/journal.pcbi.1008214</citation>
-        <citation type="bibtex">@unpublished{galaxyTools,
-		author = {E. Mijalis, H. Rasche},
-		title = {CPT Galaxy Tools},
-		year = {2013-2017},
-		note = {https://github.com/tamu-cpt/galaxy-tools/}
-		}
-		</citation>
-    </xml>
-    <xml name="citations">
-        <citations>
-            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
-            <citation type="bibtex">
-			@unpublished{galaxyTools,
-				author = {E. Mijalis, H. Rasche},
-				title = {CPT Galaxy Tools},
-				year = {2013-2017},
-				note = {https://github.com/tamu-cpt/galaxy-tools/}
-			}
-			</citation>
-            <yield/>
-        </citations>
-    </xml>
-    <xml name="citations-crr">
-        <citations>
-            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
-            <citation type="bibtex">
-			@unpublished{galaxyTools,
-				author = {C. Ross},
-				title = {CPT Galaxy Tools},
-				year = {2020-},
-				note = {https://github.com/tamu-cpt/galaxy-tools/}
-			}
-			</citation>
-            <yield/>
-        </citations>
-    </xml>
-    <xml name="citations-2020">
-        <citations>
-            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
-            <citation type="bibtex">
-			@unpublished{galaxyTools,
-				author = {E. Mijalis, H. Rasche},
-				title = {CPT Galaxy Tools},
-				year = {2013-2017},
-				note = {https://github.com/tamu-cpt/galaxy-tools/}
-			}
-			</citation>
-            <citation type="bibtex">
-			@unpublished{galaxyTools,
-				author = {A. Criscione},
-				title = {CPT Galaxy Tools},
-				year = {2019-2021},
-				note = {https://github.com/tamu-cpt/galaxy-tools/}
-			}
-                        </citation>
-            <yield/>
-        </citations>
-    </xml>
-    <xml name="citations-2020-AJC-solo">
-        <citations>
-            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
-            <citation type="bibtex">
-			@unpublished{galaxyTools,
-				author = {A. Criscione},
-				title = {CPT Galaxy Tools},
-				year = {2019-2021},
-				note = {https://github.com/tamu-cpt/galaxy-tools/}
-			}
-                        </citation>
-            <yield/>
-        </citations>
-    </xml>
-    <xml name="citations-clm">
-        <citations>
-            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
-            <citation type="bibtex">
-			@unpublished{galaxyTools,
-				author = {C. Maughmer},
-				title = {CPT Galaxy Tools},
-				year = {2017-2020},
-				note = {https://github.com/tamu-cpt/galaxy-tools/}
-			}
-			</citation>
-            <yield/>
-        </citations>
-    </xml>
-    <xml name="sl-citations-clm">
-        <citation type="bibtex">
-			@unpublished{galaxyTools,
-				author = {C. Maughmer},
-				title = {CPT Galaxy Tools},
-				year = {2017-2020},
-				note = {https://github.com/tamu-cpt/galaxy-tools/}
-			}
-			</citation>
-        <yield/>
-    </xml>
-</macros>
diff -r f7afd1480d0f -r aacd746d1c8b generate-putative-usp.xml
--- a/generate-putative-usp.xml	Mon Jun 05 02:51:59 2023 +0000
+++ b/generate-putative-usp.xml	Fri Jan 05 05:56:41 2024 +0000
@@ -2,7 +2,7 @@
     <description>constructs a putative list of potential u-spanin from an input genomic FASTA</description>
     <macros>
         <import>macros.xml</import>
-        <import>cpt-macros.xml</import>
+    
     </macros>
     <expand macro="requirements">
     </expand>
diff -r f7afd1480d0f -r aacd746d1c8b macros.xml
--- a/macros.xml	Mon Jun 05 02:51:59 2023 +0000
+++ b/macros.xml	Fri Jan 05 05:56:41 2024 +0000
@@ -1,16 +1,13 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package">progressivemauve</requirement>
-            <!--<requirement type="package" version="2.7">python</requirement>-->
-            <requirement type="package" version="0.6.4">bcbiogff</requirement>
+            <requirement type="package" version="3.9">python</requirement>
+            <requirement type="package" version="1.81">biopython</requirement>
+            <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
             <yield/>
         </requirements>
     </xml>
     <token name="@WRAPPER_VERSION@">2.4.0</token>
-    <xml name="citation/progressive_mauve">
-        <citation type="doi">10.1371/journal.pone.0011147</citation>
-    </xml>
     <xml name="citation/gepard">
         <citation type="doi">10.1093/bioinformatics/btm039</citation>
     </xml>
@@ -49,6 +46,105 @@
         <expand macro="gff3_input"/>
         <expand macro="genome_selector"/>
     </xml>
+    <xml name="citation/mijalisrasche">
+        <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+        <citation type="bibtex">@unpublished{galaxyTools,
+		author = {E. Mijalis, H. Rasche},
+		title = {CPT Galaxy Tools},
+		year = {2013-2017},
+		note = {https://github.com/tamu-cpt/galaxy-tools/}
+		}
+		</citation>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+            <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {E. Mijalis, H. Rasche},
+				title = {CPT Galaxy Tools},
+				year = {2013-2017},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+			</citation>
+            <yield/>
+        </citations>
+    </xml>
+    <xml name="citations-crr">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+            <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {C. Ross},
+				title = {CPT Galaxy Tools},
+				year = {2020-},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+			</citation>
+            <yield/>
+        </citations>
+    </xml>
+    <xml name="citations-2020">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+            <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {E. Mijalis, H. Rasche},
+				title = {CPT Galaxy Tools},
+				year = {2013-2017},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+			</citation>
+            <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {A. Criscione},
+				title = {CPT Galaxy Tools},
+				year = {2019-2021},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+                        </citation>
+            <yield/>
+        </citations>
+    </xml>
+    <xml name="citations-2020-AJC-solo">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+            <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {A. Criscione},
+				title = {CPT Galaxy Tools},
+				year = {2019-2021},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+                        </citation>
+            <yield/>
+        </citations>
+    </xml>
+    <xml name="citations-clm">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1008214</citation>
+            <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {C. Maughmer},
+				title = {CPT Galaxy Tools},
+				year = {2017-2020},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+			</citation>
+            <yield/>
+        </citations>
+    </xml>
+    <xml name="sl-citations-clm">
+        <citation type="bibtex">
+			@unpublished{galaxyTools,
+				author = {C. Maughmer},
+				title = {CPT Galaxy Tools},
+				year = {2017-2020},
+				note = {https://github.com/tamu-cpt/galaxy-tools/}
+			}
+			</citation>
+        <yield/>
+    </xml>
     <token name="@INPUT_GFF@">
 	    '$gff3_data'
 	</token>