Mercurial > repos > iuc > mummer_dnadiff
changeset 3:c9685bc0407c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
| author | iuc |
|---|---|
| date | Sat, 27 Nov 2021 09:58:09 +0000 |
| parents | 60698466facd |
| children | 5561a1193611 |
| files | 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 |
| diffstat | 8 files changed, 99 insertions(+), 102 deletions(-) [+] |
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--- a/dnadiff.xml Tue Oct 13 21:39:50 2020 +0000 +++ b/dnadiff.xml Sat Nov 27 09:58:09 2021 +0000 @@ -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"/>
--- a/macros.xml Tue Oct 13 21:39:50 2020 +0000 +++ b/macros.xml Sat Nov 27 09:58:09 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>
--- 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 @@ -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
--- 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 @@ -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
--- 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 @@ -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
--- 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 @@ -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
--- 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 @@ -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%)