| Next changeset 1:7a5eaa19e92f (2021-05-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 16b63814cb85eff8e8f2486c99bb4d187d43e2fe" |
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added:
pretext_snapshot.xml test-data/fullmap1.jpg test-data/fullmap2.bmp test-data/map.pretext test-data/snapshot1.jpg test-data/snapshot2.jpg test-data/snapshot3.jpg |
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| diff -r 000000000000 -r 02b21260faf4 pretext_snapshot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pretext_snapshot.xml Mon Apr 05 17:27:18 2021 +0000 |
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| b'@@ -0,0 +1,190 @@\n+<tool id="pretext_snapshot" name="Pretext Snapshot" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">\n+ <macros>\n+ <token name="@WRAPPER_VERSION@">0.0.3</token>\n+ <token name="@VERSION_SUFFIX@">galaxy0</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@WRAPPER_VERSION@">pretextsnapshot</requirement>\n+ <requirement type="package" version="1.601">rename</requirement>\n+ </requirements>\n+ <version_command>PretextSnapshot --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ PretextSnapshot -m $input\n+ -f $formats.outformat\n+ #if $formats.outformat == \'jpeg\':\n+ --jpegQuality $formats.jpegQuality\n+ #end if\n+ -r $resolution\n+ -c $colormap\n+ --sequences \'$sequences\'\n+ --minTexels $mintexels\n+ #if $grid.showGrid == \'yes\':\n+ --gridSize $grid.gridsize\n+ --gridColour $grid.gridcolor\n+ #else:\n+ --gridSize 0\n+ #end if\n+ \'${sequencenames}\'\n+ -o output\n+ --prefix pretext_snapshot\n+ #if $formats.outformat == \'jpeg\':\n+ && find ./output/* | rename -s .jpeg .jpg\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <param name="input" type="data" argument="--map" format="pretext" label="Input Pretext map file"/>\n+ <conditional name="formats">\n+ <param name="outformat" argument="-f" type="select" label="Output image format" help="Format of output image">\n+ <option value="png" selected="true"/>\n+ <option value="bmp"/>\n+ <option value="jpeg"/>\n+ </param>\n+ <when value="png"/>\n+ <when value="bmp"/>\n+ <when value="jpeg">\n+ <param name="jpegQuality" argument="--jpegQuality" type="integer" label="JPEG quality factor" value="80" min="0" max="100" help="An integer between 1 and 100, default 80. Larger values result in increased image quality and file size."/>\n+ </when>\n+ </conditional>\n+ <param name="resolution" argument="-r" type="integer" label="Output image resolution" min="1" value="1000" help="Image resolution, a positive integer, default 1080. For non-square images this will be the resolution of the longest dimension."/>\n+ <param name="colormap" argument=\'-c\' type="integer" label="Color Map" value="5" min="0" max="30" help="Color map based on list available in the help section"/>\n+ <param name="sequences" argument="--sequences" type="text" label="Sequence specification string" value="=full, =all" help="Each entry, except for \'=all\', corresponds to one output image. More information available in the help section.">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.ascii_letters,string.digits">\n+ <add value="="/>\n+ <add value="_"/>\n+ <add value=" "/>\n+ <add value=","/>\n+ <add value="["/>\n+ <add value="]"/>\n+ <add value="{"/>\n+ <add value="}"/>\n+ <add value="#"/>\n+ <add value="<"/>\n+ <add value=">"/>\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param name="mintexels" argument="--minTexels" type="integer" min="1" label="Min Texels" value="64" help="Minimum map texels per image (along a single dimension), a positive integer, Output images over too small a range that violate this minimum will not be created."/>\n+ <conditional name="grid">\n+ <param name="showGrid" label="Show grid?" type="boolean" truevalue="yes" falsevalue="no"/>\n+ <when value="yes">\n+ <param name="gridsize" argument="--gridSize" type="integer" label="Grid size" value="1" min="1" help="Width i'..b'--+-------------------------------+\n+ |1. Black Body |12. Blue-Orange Divergent |23. Orange-Green-Blue-Gray |\n+ +---------------------------------------+-------------------------------+-------------------------------+\n+ |2. Kindlmann |13. Brown 1 |24. Purple 1 |\n+ +---------------------------------------+-------------------------------+-------------------------------+\n+ |3. Extended Kindlmann |14. Brown 2 |25. Purple 2 |\n+ +---------------------------------------+-------------------------------+-------------------------------+\n+ |4. Three Wave Yellow-Grey-Blue |15. Brown 3 |26. Red 1 |\n+ +---------------------------------------+-------------------------------+-------------------------------+\n+ |5. Three Wave Blue-Green-Yellow |16. Green 1 |27. Red 2 |\n+ +---------------------------------------+-------------------------------+-------------------------------+\n+ |6. Four Wave Grey-Red-Green |17. Green 2 |28. Red 3 |\n+ +---------------------------------------+-------------------------------+-------------------------------+\n+ |7. Five Wave Yellow-Brown-Blue |18. Green 3 |29. Yellow 1 |\n+ +---------------------------------------+-------------------------------+-------------------------------+\n+ |8. Blue 1 |19. Green 4 |30. Yellow 2 |\n+ +---------------------------------------+-------------------------------+-------------------------------+\n+ |9. Blue 2 |20. Mellow Rainbow | |\n+ +---------------------------------------+-------------------------------+-------------------------------+\n+ |10. Blue 3 |21. Orange 1 | |\n+ +---------------------------------------+-------------------------------+-------------------------------+\n+\n+\n+ **Sequence strings:**\n+ \n+ * --sequences "=full"\n+\n+ * Creates a single image of the full contact map.\n+\n+ * --sequences "=full, =all"\n+\n+ * Creates an image of the full contact map, plus an image of each sequence.\n+\n+ * --sequences "seq_0"\n+\n+ * Creates a single image of the sequence named "seq_0"\n+\n+ * --sequences "seq_0, seq_1 > seq_2"\n+\n+ * Creates an image of seq_0, and an image from the start of seq_1 to the end of seq_2\n+\n+ * --sequences "seq_0[1000000] > seq_3"\n+\n+ * Creates an image starting 1Mbp into seq_0, ending at the end of seq_3\n+\n+ * --sequences "{seq_0, seq_1}"\n+\n+ * Create an single image of the off-diagonal region between seq_0 and seq_1, \n+ * i.e. the inter-sequence map of seq_0 and seq_1.\n+\n+ * --sequences "{seq_2[2000000] > seq_4[1000000] , seq_0[3000000] > seq_1[4000000]} , seq_0 > seq_10"\n+\n+ * Creates two images. The first is the off-diagonal region between 2Mbp into seq_2 and 1Mbp into seq_4 along the x-dimension, and 3Mbp into seq_0 and 4Mbp into seq_1 along the y-dimension.\n+ * The second image is the diagonal region between the start of seq_0 and the end of seq_10.\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">\n+ @misc{Harry_et_al,\n+ Author={Harry, E},\n+ title={Paired REad TEXTure Snapshot: Command line image generator for Pretext contact maps.},\n+ url = {https://github.com/wtsi-hpag/PretextSnapshot},}\n+ </citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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