| Previous changeset 2:60698466facd (2020-10-13) Next changeset 4:5561a1193611 (2024-03-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a" |
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modified:
dnadiff.xml macros.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 |
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| diff -r 60698466facd -r c9685bc0407c dnadiff.xml --- a/dnadiff.xml Tue Oct 13 21:39:50 2020 +0000 +++ b/dnadiff.xml Sat Nov 27 09:58:09 2021 +0000 |
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| @@ -1,8 +1,9 @@ -<tool id="mummer_dnadiff" name="DNAdiff" version="@MUMMER_VERSION@@WRAPPER_VERSION@"> +<tool id="mummer_dnadiff" name="DNAdiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Evaluate similarities/differences between two sequences</description> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ @@ -26,13 +27,13 @@ <data name="delta" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta"> <filter> report_only == 'no'</filter> </data> - <data name="1delta" format="tabular" from_work_dir="out.1delta" label="${tool.name} on ${on_string}: 1delta" > + <data name="delta1" format="tabular" from_work_dir="out.1delta" label="${tool.name} on ${on_string}: 1delta" > <filter> report_only == 'no' </filter> </data> <data name="mdelta" format="tabular" from_work_dir="out.mdelta" label="${tool.name} on ${on_string}: mdelta" > <filter> report_only == 'no' </filter> </data> - <data name="1coords" format="tabular" from_work_dir="out.1coords" label="${tool.name} on ${on_string}: 1coords" > + <data name="coords1" format="tabular" from_work_dir="out.1coords" label="${tool.name} on ${on_string}: 1coords" > <filter> report_only == 'no' </filter> <actions> <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" /> @@ -67,13 +68,12 @@ <test> <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" /> <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta"/> - <param name="input_type" value="sequence" /> <param name="report_only" value="no" /> <output name="report" ftype="txt" compare="diff" sort="true" lines_diff="2" value="report.txt"/> <output name="delta" ftype="tabular" compare="diff" lines_diff="2" value="delta.txt"/> - <output name="1delta" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/> + <output name="delta1" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/> <output name="mdelta" ftype="tabular" compare="diff" lines_diff="2" value="mdelta.txt"/> - <output name="1coords" ftype="tabular" compare="diff" value="1coords.txt"/> + <output name="coords1" ftype="tabular" compare="diff" value="1coords.txt"/> <output name="mcoords" ftype="tabular" compare="diff" value="mcoords.txt"/> <output name="snps" ftype="tabular" compare="diff" value="snps.txt"/> <output name="rdiff" ftype="tabular" compare="diff" value="rdiff.txt"/> |
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| diff -r 60698466facd -r c9685bc0407c macros.xml --- a/macros.xml Tue Oct 13 21:39:50 2020 +0000 +++ b/macros.xml Sat Nov 27 09:58:09 2021 +0000 |
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| @@ -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> |
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| diff -r 60698466facd -r c9685bc0407c test-data/1delta.txt --- a/test-data/1delta.txt Tue Oct 13 21:39:50 2020 +0000 +++ b/test-data/1delta.txt Sat Nov 27 09:58:09 2021 +0000 |
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| @@ -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 |
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| diff -r 60698466facd -r c9685bc0407c test-data/delta.txt --- a/test-data/delta.txt Tue Oct 13 21:39:50 2020 +0000 +++ b/test-data/delta.txt Sat Nov 27 09:58:09 2021 +0000 |
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| @@ -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 |
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| diff -r 60698466facd -r c9685bc0407c test-data/gnuplot.txt --- a/test-data/gnuplot.txt Tue Oct 13 21:39:50 2020 +0000 +++ b/test-data/gnuplot.txt Sat Nov 27 09:58:09 2021 +0000 |
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| @@ -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 |
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| diff -r 60698466facd -r c9685bc0407c test-data/mdelta.txt --- a/test-data/mdelta.txt Tue Oct 13 21:39:50 2020 +0000 +++ b/test-data/mdelta.txt Sat Nov 27 09:58:09 2021 +0000 |
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| @@ -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 |
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| diff -r 60698466facd -r c9685bc0407c test-data/plot.png |
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| Binary file test-data/plot.png has changed |
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| diff -r 60698466facd -r c9685bc0407c test-data/report.txt --- a/test-data/report.txt Tue Oct 13 21:39:50 2020 +0000 +++ b/test-data/report.txt Sat Nov 27 09:58:09 2021 +0000 |
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| 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' |
