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Changeset 3:4fc0cb2ac8ae (2021-11-27)

Previous changeset 2:ebe3b0f84de9 (2020-10-13) Next changeset 4:fb43e8887350 (2024-03-18)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"

modified:
macros.xml
mummerplot.xml
test-data/1delta.txt
test-data/delta.txt
test-data/gnuplot.txt
test-data/mdelta.txt
test-data/plot.png
test-data/report.txt

diff -r ebe3b0f84de9 -r 4fc0cb2ac8ae macros.xml
--- a/macros.xml Tue Oct 13 21:40:53 2020 +0000
+++ b/macros.xml Sat Nov 27 09:58:54 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 ebe3b0f84de9 -r 4fc0cb2ac8ae mummerplot.xml
--- a/mummerplot.xml Tue Oct 13 21:40:53 2020 +0000
+++ b/mummerplot.xml Sat Nov 27 09:58:54 2021 +0000

@@ -1,8 +1,9 @@
-<tool id="mummer_mummerplot" name="Mummerplot" version="@MUMMER_VERSION@@WRAPPER_VERSION@">
+<tool id="mummer_mummerplot" name="Mummerplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Generate 2-D dotplot of aligned sequences</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
         <expand macro="gnuplot_requirement"/>
     </expand>
@@ -75,7 +76,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="delta" ftype="txt" value="nucmer.txt" />
+            <param name="delta" value="nucmer.txt" ftype="tabular" />
             <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
             <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
             <param name="seq_input" value="no" />

diff -r ebe3b0f84de9 -r 4fc0cb2ac8ae test-data/1delta.txt
--- a/test-data/1delta.txt Tue Oct 13 21:40:53 2020 +0000
+++ b/test-data/1delta.txt Sat Nov 27 09:58:54 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 ebe3b0f84de9 -r 4fc0cb2ac8ae test-data/delta.txt
--- a/test-data/delta.txt Tue Oct 13 21:40:53 2020 +0000
+++ b/test-data/delta.txt Sat Nov 27 09:58:54 2021 +0000

diff -r ebe3b0f84de9 -r 4fc0cb2ac8ae test-data/gnuplot.txt
--- a/test-data/gnuplot.txt Tue Oct 13 21:40:53 2020 +0000
+++ b/test-data/gnuplot.txt Sat Nov 27 09:58:54 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 ebe3b0f84de9 -r 4fc0cb2ac8ae test-data/mdelta.txt
--- a/test-data/mdelta.txt Tue Oct 13 21:40:53 2020 +0000
+++ b/test-data/mdelta.txt Sat Nov 27 09:58:54 2021 +0000

diff -r ebe3b0f84de9 -r 4fc0cb2ac8ae test-data/plot.png

Binary file test-data/plot.png has changed

diff -r ebe3b0f84de9 -r 4fc0cb2ac8ae test-data/report.txt
--- a/test-data/report.txt Tue Oct 13 21:40:53 2020 +0000
+++ b/test-data/report.txt Sat Nov 27 09:58:54 2021 +0000

[

b'@@ -1,87 +1,87 @@\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n+/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\n+NUCMER\n \n [REF] [QRY]\n-.A 0(0.00%) 0(0.00%)\n-.A 0(0.00%) 3(23.08%)\n-.C 0(0.00%) 0(0.00%)\n-.C 0(0.00%) 5(38.46%)\n-.G 0(0.00%) 0(0.00%)\n-.G 1(7.69%) 2(15.38%)\n-.T 0(0.00%) 0(0.00%)\n-.T 2(15.38%) 0(0.00%)\n-/Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/human_aqp3.fasta /Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/mouse_aqp3.fasta\n+[Sequences]\n+TotalSeqs 1 1\n+AlignedSeqs 1(100.0000%) 1(100.0000%)\n+UnalignedSeqs 0(0.0000%) 0(0.0000%)\n+\n+[Bases]\n+TotalBases 6480 5460\n+AlignedBases 670(10.3395%) 663(12.1429%)\n+UnalignedBases 5810(89.6605%) 4797(87.8571%)\n+\n+[Alignments]\n 1-to-1 2 2\n-A. 0(0.00%) 0(0.00%)\n-A. 3(23.08%) 0(0.00%)\n-AC 6(7.69%) 5(6.41%)\n-AC 1(100.00%) 0(0.00%)\n-AG 0(0.00%) 0(0.00%)\n-AG 2(2.56%) 5(6.41%)\n-AT 0(0.00%) 0(0.00%)\n-AT 2(2.56%) 2(2.56%)\n-AlignedBases 670(10.34%) 663(12.14%)\n-AlignedSeqs 1(100.00%) 1(100.00%)\n-AvgIdentity 86.48 86.48\n-AvgIdentity 86.48 86.48\n-AvgLength 335.00 331.50\n-AvgLength 335.00 331.50\n+TotalLength 670 663\n+AvgLength 335.0000 331.5000\n+AvgIdentity 86.4791 86.4791\n+\n+M-to-M 2 2\n+TotalLength 670 663\n+AvgLength 335.0000 331.5000\n+AvgIdentity 86.4791 86.4791\n+\n+[Feature Estimates]\n Breakpoints 4 4\n-C. 0(0.00%) 0(0.00%)\n-C. 5(38.46%) 0(0.00%)\n-CA 0(0.00%) 1(100.00%)\n-CA 5(6.41%) 6(7.69%)\n-CG 0(0.00%) 0(0.00%)\n-CG 6(7.69%) 6(7.69%)\n-CT 0(0.00%) 0(0.00%)\n-CT 28(35.90%) 9(11.54%)\n-G. 0(0.00%) 0(0.00%)\n-G. 2(15.38%) 1(7.69%)\n-GA 0(0.00%) 0(0.00%)\n-GA 5(6.41%) 2(2.56%)\n-GC 0(0.00%) 0(0.00%)\n-GC 6(7.69%) 6(7.69%)\n-GT 0(0.00%) 0(0.00%)\n-GT 5(6.41%) 2(2.56%)\n-InsertionAvg 1936.67 1599.00\n-InsertionSum 5810 4797\n-Insertions 3 3\n+Relocations 0 0\n+Translocations 0 0\n Inversions 0 0\n-M-to-M '..b' 0(0.00%)\n-TA 2(2.56%) 2(2.56%)\n-TC 0(0.00%) 0(0.00%)\n-TC 9(11.54%) 28(35.90%)\n-TG 0(0.00%) 0(0.00%)\n-TG 2(2.56%) 5(6.41%)\n+\n+Insertions 3 3\n+InsertionSum 5810 4797\n+InsertionAvg 1936.6667 1599.0000\n+\n TandemIns 0 0\n-TandemInsAvg 0.00 0.00\n TandemInsSum 0 0\n-TotalBases 6480 5460\n-TotalGIndels 0 0\n-TotalGSNPs 1 1\n-TotalIndels 13 13\n-TotalLength 670 663\n-TotalLength 670 663\n+TandemInsAvg 0.0000 0.0000\n+\n+[SNPs]\n TotalSNPs 78 78\n-TotalSeqs 1 1\n-Translocations 0 0\n-UnalignedBases 5810(89.66%) 4797(87.86%)\n-UnalignedSeqs 0(0.00%) 0(0.00%)\n-[Alignments]\n-[Bases]\n-[Feature Estimates]\n-[SNPs]\n-[Sequences]\n+TG 2(2.5641%) 5(6.4103%)\n+TC 9(11.5385%) 28(35.8974%)\n+TA 2(2.5641%) 2(2.5641%)\n+GC 6(7.6923%) 6(7.6923%)\n+GA 5(6.4103%) 2(2.5641%)\n+GT 5(6.4103%) 2(2.5641%)\n+CT 28(35.8974%) 9(11.5385%)\n+CA 5(6.4103%) 6(7.6923%)\n+CG 6(7.6923%) 6(7.6923%)\n+AT 2(2.5641%) 2(2.5641%)\n+AG 2(2.5641%) 5(6.4103%)\n+AC 6(7.6923%) 5(6.4103%)\n+\n+TotalGSNPs 1 1\n+TA 0(0.0000%) 0(0.0000%)\n+TG 0(0.0000%) 0(0.0000%)\n+TC 0(0.0000%) 0(0.0000%)\n+AG 0(0.0000%) 0(0.0000%)\n+AC 1(100.0000%) 0(0.0000%)\n+AT 0(0.0000%) 0(0.0000%)\n+GC 0(0.0000%) 0(0.0000%)\n+GA 0(0.0000%) 0(0.0000%)\n+GT 0(0.0000%) 0(0.0000%)\n+CT 0(0.0000%) 0(0.0000%)\n+CG 0(0.0000%) 0(0.0000%)\n+CA 0(0.0000%) 1(100.0000%)\n+\n+TotalIndels 13 13\n+T. 0(0.0000%) 2(15.3846%)\n+G. 2(15.3846%) 1(7.6923%)\n+C. 5(38.4615%) 0(0.0000%)\n+A. 3(23.0769%) 0(0.0000%)\n+.G 1(7.6923%) 2(15.3846%)\n+.C 0(0.0000%) 5(38.4615%)\n+.A 0(0.0000%) 3(23.0769%)\n+.T 2(15.3846%) 0(0.0000%)\n+\n+TotalGIndels 0 0\n+T. 0(0.0000%) 0(0.0000%)\n+A. 0(0.0000%) 0(0.0000%)\n+G. 0(0.0000%) 0(0.0000%)\n+C. 0(0.0000%) 0(0.0000%)\n+.A 0(0.0000%) 0(0.0000%)\n+.C 0(0.0000%) 0(0.0000%)\n+.G 0(0.0000%) 0(0.0000%)\n+.T 0(0.0000%) 0(0.0000%)\n'