# HG changeset patch
# User iuc
# Date 1638007184 0
# Node ID bcd65de9725b6aa747e7674ae5164908764a1b2c
# Parent  48823c9635a4806a2e34f4217a558315776275d5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"

diff -r 48823c9635a4 -r bcd65de9725b macros.xml
--- a/macros.xml	Tue Oct 13 21:40:33 2020 +0000
+++ b/macros.xml	Sat Nov 27 09:59:44 2021 +0000
@@ -1,26 +1,24 @@
 <macros>
     <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">mumer4</xref>
+        </xrefs>
+    </xml>
     <xml name="citation">
         <citations>
-            <citation type="bibtex">
-                @misc{githubmummer,
-                author = {Art Delcher, Stefan Kurtz, Adam Phillippy, Steven Salzberg},
-                year = {2012},
-                title = {mummer4},
-                publisher = {GitHub},
-                journal = {GitHub repository},
-                url = {https://github.com/mummer4/mummer},
-            }</citation>
+            <citation type="doi">10.1371/journal.pcbi.1005944</citation>
         </citations>
     </xml>
     <xml name="gnuplot_requirement">
-        <requirement type="package" version="5.2.7">gnuplot</requirement>
+        <requirement type="package" version="5.4.1">gnuplot</requirement>
     </xml>
-    <token name="@MUMMER_VERSION@">4.0.0beta2</token>
-    <token name="@WRAPPER_VERSION@">+galaxy1</token>
+    <token name="@TOOL_VERSION@">4.0.0rc1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@PROFILE@">20.05</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@MUMMER_VERSION@">mummer4</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
             <yield />
         </requirements>
     </xml>
diff -r 48823c9635a4 -r bcd65de9725b mummer.xml
--- a/mummer.xml	Tue Oct 13 21:40:33 2020 +0000
+++ b/mummer.xml	Sat Nov 27 09:59:44 2021 +0000
@@ -1,8 +1,9 @@
-<tool id="mummer_mummer" name="Mummer" version="@MUMMER_VERSION@@WRAPPER_VERSION@">
+<tool id="mummer_mummer" name="Mummer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Align two or more sequences</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
         <expand macro="gnuplot_requirement"/>
     </expand>
@@ -114,7 +115,7 @@
         <test>
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
-            <param name="options" value="defaults" />
+            <param name="options|advanced" value="defaults" />
             <param name="plot" value="yes" />
             <output name="output" ftype="tabular" compare="diff" value="mummer.txt" />
             <output name="png_output" ftype="png" compare="sim_size" value="plot.png" />
diff -r 48823c9635a4 -r bcd65de9725b test-data/1delta.txt
--- a/test-data/1delta.txt	Tue Oct 13 21:40:33 2020 +0000
+++ b/test-data/1delta.txt	Sat Nov 27 09:59:44 2021 +0000
@@ -1,4 +1,4 @@
-reference.fa query.fa
+/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff -r 48823c9635a4 -r bcd65de9725b test-data/delta.txt
--- a/test-data/delta.txt	Tue Oct 13 21:40:33 2020 +0000
+++ b/test-data/delta.txt	Sat Nov 27 09:59:44 2021 +0000
@@ -1,4 +1,4 @@
-reference.fa query.fa
+/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff -r 48823c9635a4 -r bcd65de9725b test-data/gnuplot.txt
--- a/test-data/gnuplot.txt	Tue Oct 13 21:40:33 2020 +0000
+++ b/test-data/gnuplot.txt	Sat Nov 27 09:59:44 2021 +0000
@@ -11,7 +11,6 @@
 set format "%.0f"
 set mouse format "%.0f"
 set mouse mouseformat "[%.0f, %.0f]"
-if(GPVAL_VERSION < 5) { set mouse clipboardformat "[%.0f, %.0f]" }
 set xrange [1:6480]
 set yrange [1:5460]
 set style line 1  lt 2 lw 3 pt 6 ps 1
diff -r 48823c9635a4 -r bcd65de9725b test-data/mdelta.txt
--- a/test-data/mdelta.txt	Tue Oct 13 21:40:33 2020 +0000
+++ b/test-data/mdelta.txt	Sat Nov 27 09:59:44 2021 +0000
@@ -1,4 +1,4 @@
-reference.fa query.fa
+/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
 NUCMER
 >NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460
 74 223 43 194 19 19 0
diff -r 48823c9635a4 -r bcd65de9725b test-data/plot.png
Binary file test-data/plot.png has changed
diff -r 48823c9635a4 -r bcd65de9725b test-data/report.txt
--- a/test-data/report.txt	Tue Oct 13 21:40:33 2020 +0000
+++ b/test-data/report.txt	Sat Nov 27 09:59:44 2021 +0000
@@ -1,87 +1,87 @@
-
-
-
-
-
-
-
-
-
-
+/tmp/tmpm1aw7z9b/files/6/1/9/dataset_619c747c-cdb5-4d85-adda-e0ec5f7fa2fe.dat /tmp/tmpm1aw7z9b/files/f/e/c/dataset_fec4ecfe-55bb-4ff9-86e1-292952d00dd1.dat
+NUCMER
 
                                [REF]                [QRY]
-.A                          0(0.00%)             0(0.00%)
-.A                          0(0.00%)            3(23.08%)
-.C                          0(0.00%)             0(0.00%)
-.C                          0(0.00%)            5(38.46%)
-.G                          0(0.00%)             0(0.00%)
-.G                          1(7.69%)            2(15.38%)
-.T                          0(0.00%)             0(0.00%)
-.T                         2(15.38%)             0(0.00%)
-/Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/human_aqp3.fasta /Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/mouse_aqp3.fasta
+[Sequences]
+TotalSeqs                          1                    1
+AlignedSeqs              1(100.0000%)          1(100.0000%)
+UnalignedSeqs             0(0.0000%)           0(0.0000%)
+
+[Bases]
+TotalBases                      6480                 5460
+AlignedBases           670(10.3395%)        663(12.1429%)
+UnalignedBases        5810(89.6605%)       4797(87.8571%)
+
+[Alignments]
 1-to-1                             2                    2
-A.                          0(0.00%)             0(0.00%)
-A.                         3(23.08%)             0(0.00%)
-AC                          6(7.69%)             5(6.41%)
-AC                        1(100.00%)             0(0.00%)
-AG                          0(0.00%)             0(0.00%)
-AG                          2(2.56%)             5(6.41%)
-AT                          0(0.00%)             0(0.00%)
-AT                          2(2.56%)             2(2.56%)
-AlignedBases             670(10.34%)          663(12.14%)
-AlignedSeqs               1(100.00%)           1(100.00%)
-AvgIdentity                    86.48                86.48
-AvgIdentity                    86.48                86.48
-AvgLength                     335.00               331.50
-AvgLength                     335.00               331.50
+TotalLength                      670                  663
+AvgLength                   335.0000             331.5000
+AvgIdentity                  86.4791              86.4791
+
+M-to-M                             2                    2
+TotalLength                      670                  663
+AvgLength                   335.0000             331.5000
+AvgIdentity                  86.4791              86.4791
+
+[Feature Estimates]
 Breakpoints                        4                    4
-C.                          0(0.00%)             0(0.00%)
-C.                         5(38.46%)             0(0.00%)
-CA                          0(0.00%)           1(100.00%)
-CA                          5(6.41%)             6(7.69%)
-CG                          0(0.00%)             0(0.00%)
-CG                          6(7.69%)             6(7.69%)
-CT                          0(0.00%)             0(0.00%)
-CT                        28(35.90%)            9(11.54%)
-G.                          0(0.00%)             0(0.00%)
-G.                         2(15.38%)             1(7.69%)
-GA                          0(0.00%)             0(0.00%)
-GA                          5(6.41%)             2(2.56%)
-GC                          0(0.00%)             0(0.00%)
-GC                          6(7.69%)             6(7.69%)
-GT                          0(0.00%)             0(0.00%)
-GT                          5(6.41%)             2(2.56%)
-InsertionAvg                 1936.67              1599.00
-InsertionSum                    5810                 4797
-Insertions                         3                    3
+Relocations                        0                    0
+Translocations                     0                    0
 Inversions                         0                    0
-M-to-M                             2                    2
-NUCMER
-Relocations                        0                    0
-T.                          0(0.00%)             0(0.00%)
-T.                          0(0.00%)            2(15.38%)
-TA                          0(0.00%)             0(0.00%)
-TA                          2(2.56%)             2(2.56%)
-TC                          0(0.00%)             0(0.00%)
-TC                         9(11.54%)           28(35.90%)
-TG                          0(0.00%)             0(0.00%)
-TG                          2(2.56%)             5(6.41%)
+
+Insertions                         3                    3
+InsertionSum                    5810                 4797
+InsertionAvg               1936.6667            1599.0000
+
 TandemIns                          0                    0
-TandemInsAvg                    0.00                 0.00
 TandemInsSum                       0                    0
-TotalBases                      6480                 5460
-TotalGIndels                       0                    0
-TotalGSNPs                         1                    1
-TotalIndels                       13                   13
-TotalLength                      670                  663
-TotalLength                      670                  663
+TandemInsAvg                  0.0000               0.0000
+
+[SNPs]
 TotalSNPs                         78                   78
-TotalSeqs                          1                    1
-Translocations                     0                    0
-UnalignedBases          5810(89.66%)         4797(87.86%)
-UnalignedSeqs               0(0.00%)             0(0.00%)
-[Alignments]
-[Bases]
-[Feature Estimates]
-[SNPs]
-[Sequences]
+TG                        2(2.5641%)           5(6.4103%)
+TC                       9(11.5385%)         28(35.8974%)
+TA                        2(2.5641%)           2(2.5641%)
+GC                        6(7.6923%)           6(7.6923%)
+GA                        5(6.4103%)           2(2.5641%)
+GT                        5(6.4103%)           2(2.5641%)
+CT                      28(35.8974%)          9(11.5385%)
+CA                        5(6.4103%)           6(7.6923%)
+CG                        6(7.6923%)           6(7.6923%)
+AT                        2(2.5641%)           2(2.5641%)
+AG                        2(2.5641%)           5(6.4103%)
+AC                        6(7.6923%)           5(6.4103%)
+
+TotalGSNPs                         1                    1
+TA                        0(0.0000%)           0(0.0000%)
+TG                        0(0.0000%)           0(0.0000%)
+TC                        0(0.0000%)           0(0.0000%)
+AG                        0(0.0000%)           0(0.0000%)
+AC                       1(100.0000%)           0(0.0000%)
+AT                        0(0.0000%)           0(0.0000%)
+GC                        0(0.0000%)           0(0.0000%)
+GA                        0(0.0000%)           0(0.0000%)
+GT                        0(0.0000%)           0(0.0000%)
+CT                        0(0.0000%)           0(0.0000%)
+CG                        0(0.0000%)           0(0.0000%)
+CA                        0(0.0000%)          1(100.0000%)
+
+TotalIndels                       13                   13
+T.                        0(0.0000%)          2(15.3846%)
+G.                       2(15.3846%)           1(7.6923%)
+C.                       5(38.4615%)           0(0.0000%)
+A.                       3(23.0769%)           0(0.0000%)
+.G                        1(7.6923%)          2(15.3846%)
+.C                        0(0.0000%)          5(38.4615%)
+.A                        0(0.0000%)          3(23.0769%)
+.T                       2(15.3846%)           0(0.0000%)
+
+TotalGIndels                       0                    0
+T.                        0(0.0000%)           0(0.0000%)
+A.                        0(0.0000%)           0(0.0000%)
+G.                        0(0.0000%)           0(0.0000%)
+C.                        0(0.0000%)           0(0.0000%)
+.A                        0(0.0000%)           0(0.0000%)
+.C                        0(0.0000%)           0(0.0000%)
+.G                        0(0.0000%)           0(0.0000%)
+.T                        0(0.0000%)           0(0.0000%)