| Previous changeset 2:53dd00a4ab68 (2023-03-28) Next changeset 4:392811378515 (2024-11-19) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit d4e8bcb01de330e345970d3df6b75392c7fe2275 |
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modified:
blobtoolkit.xml macros.xml test-data/test01_blobdir.tar.gz test-data/test02_blobdir.tar.gz |
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added:
test-data/blobdir.tgz test-data/output.svg test-data/output_cumulative.svg test-data/output_legend.svg test-data/test02_blob.svg |
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| diff -r 53dd00a4ab68 -r 8c2167481e72 blobtoolkit.xml --- a/blobtoolkit.xml Tue Mar 28 15:17:19 2023 +0000 +++ b/blobtoolkit.xml Fri Jul 26 16:15:35 2024 +0000 |
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| b'@@ -1,5 +1,5 @@\n <tool id="blobtoolkit" name="BlobToolKit" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">\n- <description>genome assembly QC</description>\n+ <description>Genome Assembly QC</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n@@ -22,7 +22,14 @@\n --taxid $mode_conditional.taxid\n --taxdump \'./taxdump\'\n \'./Blobdir\'\n+ \n && tar -C ./Blobdir -zcvf Blobdir.tgz .\n+\n+ #else if $mode_conditional.selector == \'plot\'\n+ mkdir -p blobtk_files && \n+ tar -xvf \'$blobdir_input\' -C blobtk_files &&\n+ blobtk plot --blobdir blobtk_files --view \'$plot_view\'\n+ \n #else if $mode_conditional.selector == \'add\'\n mkdir -p \'./Blobdir\' &&\n mkdir -p \'./taxdump\' &&\n@@ -97,6 +104,11 @@\n #end if\n $mode_conditional.advanced_options.replace\n \'./Blobdir\'\n+\n+ #if $mode_conditional.blobtk_plot_options.blobtk_plot == \'yes\'\n+ && blobtk plot --blobdir \'./Blobdir\' --view $blobtk_plot_options.plot_view\n+ #end if\n+ \n && tar -C ./Blobdir -zcvf Blobdir.tgz .\n \n #else if $mode_conditional.selector == \'filter\'\n@@ -156,8 +168,14 @@\n #end if\n ./Blobdir\n #end if\n+\n+ #if $mode_conditional.blobtk_plot_options.blobtk_plot == \'yes\'\n+ && blobtk plot --blobdir ./Blobdir --view $blobtk_plot_options.plot_view\n+ #end if\n+\n && tar -C ./Blobdir -zcvf Blobdir.tgz .\n #end if\n+\n ]]></command>\n <inputs>\n <conditional name="mode_conditional">\n@@ -165,6 +183,7 @@\n <option value="create">Create a BlobToolKit dataset</option>\n <option value="add">Add data to a BlobToolKit dataset</option>\n <option value="filter">Edit a BlobToolKit dataset</option>\n+ <option value="plot">Plot a BlobToolKit dataset</option>\n </param>\n <when value="create">\n <param argument="--fasta" type="data" format="fasta" label="Genome assembly file" help="FASTA sequence file" />\n@@ -217,6 +236,7 @@\n <param argument="--text-no-array" type="boolean" truevalue="--text-no-array" falsevalue="" checked="false" label="Prevent duplicated identifiers" \n help="Prevent fields in files with duplicate identifiers being loaded as array fields" />\n </expand>\n+ <expand macro="blobtk_plotting"></expand>\n <section name="advanced_options" title="Advanced options">\n <param argument="--blobdb" type="data" format="json" optional="true" label="Blobtools v1 database" help="This file should have been generated with the previous Blobtools tool version"/>\n <param argument="--synonyms" type="data" format="tsv" optional="true" label="Identifier and sinonyms" help="TSV file containing current identifiers and synonyms"/>\n@@ -295,6 +315,16 @@\n <validator type="regex">[0-9a-zA-Z]+</validator>\n </param>\n </section>\n+ <expand macro="blobtk_plotting"></expand>\n+ </when>\n+ <when value="plot">\n+ <param name="blobdir_input" type="data" format="tgz" label="Select the blobdir tar.gz file generated from blobtools"/>\n+ <param name="plot_view" type="select" label="Select the view type for the plot">\n+ <option value="blob" selected="true">Blob view</option>\n+ <option value="cumulative">Cumulative view</option>\n+ <option value="legend">Legend view</option>\n+ <option value="snail">Snail view</option>\n+ </param>\n </when>\n </conditional>\n </inputs>\n@@ -302,8 +332,18 @@\n '..b' <param name="plot_view" value="blob"/>\n+ </conditional>\n </conditional>\n <output name="blobdir" file="test02_blobdir.tar.gz" compare="sim_size" delta="100"/>\n+ <output name="output_svg" file="test02_blob.svg" compare="sim_size" delta="100"/>\n </test>\n+ <!-- Test 03: Testing blobtoolkit with filtering and plotting disabled -->\n <test expect_num_outputs="1">\n <conditional name="mode_conditional">\n <param name="selector" value="filter"/>\n@@ -350,12 +397,16 @@\n <param name="remove_selector" value="--all"/>\n </section>\n </conditional>\n+ <conditional name="blobtk_plot_options">\n+ <param name="blobtk_plot" value="no"/>\n+ </conditional>\n <output name="blobdir">\n <assert_contents>\n <has_size value="620" delta="50"/>\n </assert_contents>\n </output>\n </test>\n+ <!-- Test 04: Testing blobtoolkit with filter with list and fasta filtering -->\n <test expect_num_outputs="1">\n <conditional name="mode_conditional">\n <param name="selector" value="filter"/>\n@@ -368,12 +419,55 @@\n <param name="remove_selector" value="--all"/>\n </section>\n </conditional>\n+ <conditional name="blobtk_plot_options">\n+ <param name="blobtk_plot" value="no"/>\n+ </conditional>\n <output name="blobdir">\n <assert_contents>\n <has_size value="620" delta="50"/>\n </assert_contents>\n </output>\n </test>\n+ <!-- Test 05: Testing blobtoolkit blob plot -->\n+ <test expect_num_outputs="1">\n+ <conditional name="mode_conditional">\n+ <param name="selector" value="plot"/>\n+ <param name="blobdir_input" value="blobdir.tgz"/>\n+ <param name="plot_view" value="blob"/>\n+ </conditional>\n+ <output name="output_svg" ftype="svg" file="output.svg" compare="sim_size"/>\n+ </test>\n+ <!-- Test 06 :Testing blobtoolkit Snail plot -->\n+ <test expect_num_outputs="1">\n+ <conditional name="mode_conditional">\n+ <param name="selector" value="plot"/>\n+ <param name="blobdir_input" value="blobdir.tgz"/>\n+ <param name="plot_view" value="snail"/>\n+ </conditional>\n+ <output name="output_svg" ftype="svg">\n+ <assert_contents>\n+ <has_text text="Log10 scaffold count (total 242)"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test 07: Testing blobtoolkit legend plot -->\n+ <test expect_num_outputs="1">\n+ <conditional name="mode_conditional">\n+ <param name="selector" value="plot"/>\n+ <param name="blobdir_input" value="blobdir.tgz"/>\n+ <param name="plot_view" value="legend"/>\n+ </conditional>\n+ <output name="output_svg" ftype="svg" file="output_legend.svg" compare="sim_size"/>\n+ </test>\n+ <!-- Test 08: Testing blobtoolkit Cumulative plot -->\n+ <test expect_num_outputs="1">\n+ <conditional name="mode_conditional">\n+ <param name="selector" value="plot"/>\n+ <param name="blobdir_input" value="blobdir.tgz"/>\n+ <param name="plot_view" value="cumulative"/>\n+ </conditional>\n+ <output name="output_svg" ftype="svg" file="output_cumulative.svg" compare="sim_size"/>\n+ </test>\n </tests>\n <help><![CDATA[\n BlobToolKit is a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. It can be used to process assembly, \n' |
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| diff -r 53dd00a4ab68 -r 8c2167481e72 macros.xml --- a/macros.xml Tue Mar 28 15:17:19 2023 +0000 +++ b/macros.xml Fri Jul 26 16:15:35 2024 +0000 |
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| @@ -1,10 +1,10 @@ <macros> <token name="@TOOL_VERSION@">4.0.7</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <xml name="requirements"> <requirements> - <container type="docker">genomehubs/blobtoolkit:@TOOL_VERSION@</container> + <container type="docker">quay.io/biocontainers/blobtoolkit:4.3.11</container> </requirements> </xml> <xml name="citations"> @@ -46,4 +46,21 @@ <xml name="macro_taxdump"> <param argument="--taxdump" type="data" format="tar,gz,tgz" label="NCBI taxdump directory" help="It requires to use the last taxdump version. You can find more information about it in the help section."/> </xml> + <xml name="blobtk_plotting"> + <conditional name="blobtk_plot_options"> + <param name="blobtk_plot" type="select" label="Do you want to plot the dataset"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="plot_view" type="select" label="Select the view type for the plot"> + <option value="blob" selected="true">Blob view</option> + <option value="cumulative">Cumulative view</option> + <option value="legend">Legend view</option> + <option value="snail">Snail view</option> + </param> + </when> + <when value="no"></when> + </conditional> + </xml> </macros> |
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| diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/blobdir.tgz |
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| Binary file test-data/blobdir.tgz has changed |
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| diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/output.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.svg Fri Jul 26 16:15:35 2024 +0000 |
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| diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/output_cumulative.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_cumulative.svg Fri Jul 26 16:15:35 2024 +0000 |
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| diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/output_legend.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_legend.svg Fri Jul 26 16:15:35 2024 +0000 |
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| b |
| diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/test01_blobdir.tar.gz |
| b |
| Binary file test-data/test01_blobdir.tar.gz has changed |
| b |
| diff -r 53dd00a4ab68 -r 8c2167481e72 test-data/test02_blob.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test02_blob.svg Fri Jul 26 16:15:35 2024 +0000 |
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