| Previous changeset 1:adea31d84cb9 (2020-10-02) Next changeset 3:a6d1f83c46b4 (2021-01-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 732d2f1bd7944e0ad8f6660eb10b33acc635ff3d" |
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modified:
chromeister.xml |
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removed:
test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.csv test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.events.txt test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.filt.png test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.scr.txt |
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| diff -r adea31d84cb9 -r 7e2fe094981e chromeister.xml --- a/chromeister.xml Fri Oct 02 18:23:26 2020 +0000 +++ b/chromeister.xml Mon Dec 14 14:10:04 2020 +0000 |
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| @@ -1,7 +1,7 @@ <tool id="chromeister" name="Chromeister" version="@TOOL_VERSION@"> <description>ultra-fast pairwise genome comparisons</description> <macros> - <token name="@TOOL_VERSION@">1.2</token> + <token name="@TOOL_VERSION@">1.3.c</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">chromeister</requirement> @@ -29,6 +29,15 @@ #end if '$queryName'-'$dbName'.mat $dimension > '$output_score' && + + detect_events.py '$queryName'-'$dbName'.mat.raw.txt + #if str($pngevents) == "pngevents": + png && + mv '$queryName'-'$dbName'.mat.events.png '$output_events_png' + #end if + + && + mv '$queryName'-'$dbName'.mat '$output' && mv '$queryName'-'$dbName'.mat.filt.png '$output_imagen' && mv '$queryName'-'$dbName'.mat.events.txt '$output_events' && @@ -44,14 +53,19 @@ </param> <param name="diffuse" type="integer" value="4" min="1" max="4" label="Diffuse value" help="Level of the heuristic subsampling employed. Change to 1 or 2 if no similarity is found"/> <param name="grid" type="boolean" truevalue="grid" falsevalue="" checked="true" label="Add grid to plot for multi-fasta data sets" help="Do not use grid if your multi-fasta contains more than a hundred sequences (approximately)"/> + <param name="pngevents" type="boolean" truevalue="pngevents" falsevalue="" checked="true" label="Generate image of detected events" help="If enabled, a png image will be generated showing the detected blocks and classified by color"/> </inputs> <outputs> <data name="output" format="txt" label="${tool.name} on ${on_string}: Comparison matrix"/> <data name="output_imagen" format="png" label="${tool.name} on ${on_string}: Comparison dotplot"/> <data name="output_csv" format="csv" label="${tool.name} on ${on_string}: Comparison metainformation"/> <data name="output_events" format="txt" label="${tool.name} on ${on_string}: Detected events"/> + <data name="output_events_png" format="png" label="${tool.name} on ${on_string}: Detected events plot"> + <filter>pngevents</filter> + </data> <data name="output_score" format="txt" label="${tool.name} on ${on_string}: Comparison score"/> </outputs> + <tests> <!-- test run w defaults (and non default for dimension) --> <test expect_num_outputs="5"> @@ -92,9 +106,9 @@ <output name="output_csv" file="mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.csv"/> <output name="output_events"> <assert_contents> - <has_text text="892758,898495"/> - <has_text text="x1,y1,x2,y2,len,event"/> + <has_text text="xStart,yStart,xEnd,yEnd,strand,approximate length,description"/> <has_text text="inverted transposition"/> + <has_text text="conserved block"/> </assert_contents> </output> <output name="output_score"> @@ -109,6 +123,25 @@ <has_text text="compute_score-nogrid.R"/> </assert_command> </test> + <test expect_num_outputs="6"> + <param name="query" value="mycoplasma-232.fasta"/> + <param name="db" value="mycoplasma-7422.fasta"/> + <param name="kmer" value="32"/> + <param name="diffuse" value="4"/> + <param name="dimension" value="1000"/> + <param name="grid" value=""/> + <param name="pngevents" value="pngevents"/> + <output name="output"/> + <output name="output_imagen"/> + <output name="output_csv"/> + <output name="output_events"/> + <output name="output_score"/> + <output name="output_events_png"> + <assert_contents> + <has_text text="PNG"/> + </assert_contents> + </output> + </test> </tests> <help> *CHROMEISTER* @@ -136,7 +169,10 @@ - Comparison matrix (plain text), i.e. a scaled matrix containing the number of unique and inexact hits per resolution cell. - A .png dotplot of the comparison with an automatic scoring distance (useful for classifying) and a grid (if enabled) separating the different sequences (chromosomes for instance) compared. - A .csv file including the coordinates of each sequence/chromosome contained within the query and reference sequences (useful for multi-fasta inputs). -- Events file. A text file where each row is a "Computational Synteny Block". This means that these events are Large-Scale Genome Rearrangements heuristically determined and classified as (Synteny block, transposition, inversion, ...). But this is only an informative labelling that only considers coordinates and does not employ genes nor other external information. +- Events file. A text file where each row is a "Computational Synteny Block". This means that these events are Large-Scale Genome Rearrangements heuristically determined and classified as conserved, transposed or inverted blocks. But this is only an informative labelling that only considers coordinates and does not employ genes nor other external information. A plot will be also available if enabled with option `Generate image of events` featuring the events that have been detected automatically. There is a color legend for each block, namely: + - Red: conserved blocks (close to the diagonal) + - Green: inverted blocks (reverse strand) + - Blue: transposed blocks (not reverted and not on the diagonal) </help> <citations> |
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| diff -r adea31d84cb9 -r 7e2fe094981e test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat --- a/test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat Fri Oct 02 18:23:26 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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0 0 0 0 0\n' |
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| diff -r adea31d84cb9 -r 7e2fe094981e test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.csv --- a/test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.csv Fri Oct 02 18:23:26 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -mycoplasma-7422.fasta (Y-Axis) -ID,header_name,length (bp),accumulated_length -1,gi|525903163|ref|NC_021831.1|,898495,898495 -# -mycoplasma-232.fasta (X-Axis) -ID,header_name,length (bp),accumulated_length -1,gi|54019969|ref|NC_006360.1|,892758,892758 -# |
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| diff -r adea31d84cb9 -r 7e2fe094981e test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.events.txt --- a/test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.events.txt Fri Oct 02 18:23:26 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -892758,898495 -x1,y1,x2,y2,len,event -10,15,60,75,60,synteny block -200,55,90,195,140,inverted transposition -80,165,55,215,50,inverted transposition -200,195,500,500,305,synteny block -0,0,0,0,0,Null event |
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| diff -r adea31d84cb9 -r 7e2fe094981e test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.filt.png |
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| Binary file test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.filt.png has changed |
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| diff -r adea31d84cb9 -r 7e2fe094981e test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.scr.txt --- a/test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.scr.txt Fri Oct 02 18:23:26 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -0.048 |
