Mercurial > repos > cpt > cpt_gff_rebase

diff macros.xml @ 2:d0b52c1d6b25 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:52:31 +0000
parents 4f4b413056f6
children
line wrap: on
line diff
--- a/macros.xml	Mon Jun 05 02:44:12 2023 +0000
+++ b/macros.xml	Fri Jan 05 05:52:31 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@unpublished{galaxyTools,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+			@unpublished{galaxyTools,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+			@unpublished{galaxyTools,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>