Mercurial > repos > bgruening > blobtoolkit
changeset 3:8c2167481e72 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit d4e8bcb01de330e345970d3df6b75392c7fe2275
| author | bgruening |
|---|---|
| date | Fri, 26 Jul 2024 16:15:35 +0000 |
| parents | 53dd00a4ab68 |
| children | |
| files | blobtoolkit.xml macros.xml test-data/blobdir.tgz test-data/output.svg test-data/output_cumulative.svg test-data/output_legend.svg test-data/test01_blobdir.tar.gz test-data/test02_blob.svg test-data/test02_blobdir.tar.gz |
| diffstat | 9 files changed, 1335 insertions(+), 4 deletions(-) [+] |
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--- a/blobtoolkit.xml Tue Mar 28 15:17:19 2023 +0000 +++ b/blobtoolkit.xml Fri Jul 26 16:15:35 2024 +0000 @@ -1,5 +1,5 @@ <tool id="blobtoolkit" name="BlobToolKit" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>genome assembly QC</description> + <description>Genome Assembly QC</description> <macros> <import>macros.xml</import> </macros> @@ -22,7 +22,14 @@ --taxid $mode_conditional.taxid --taxdump './taxdump' './Blobdir' + && tar -C ./Blobdir -zcvf Blobdir.tgz . + + #else if $mode_conditional.selector == 'plot' + mkdir -p blobtk_files && + tar -xvf '$blobdir_input' -C blobtk_files && + blobtk plot --blobdir blobtk_files --view '$plot_view' + #else if $mode_conditional.selector == 'add' mkdir -p './Blobdir' && mkdir -p './taxdump' && @@ -97,6 +104,11 @@ #end if $mode_conditional.advanced_options.replace './Blobdir' + + #if $mode_conditional.blobtk_plot_options.blobtk_plot == 'yes' + && blobtk plot --blobdir './Blobdir' --view $blobtk_plot_options.plot_view + #end if + && tar -C ./Blobdir -zcvf Blobdir.tgz . #else if $mode_conditional.selector == 'filter' @@ -156,8 +168,14 @@ #end if ./Blobdir #end if + + #if $mode_conditional.blobtk_plot_options.blobtk_plot == 'yes' + && blobtk plot --blobdir ./Blobdir --view $blobtk_plot_options.plot_view + #end if + && tar -C ./Blobdir -zcvf Blobdir.tgz . #end if + ]]></command> <inputs> <conditional name="mode_conditional"> @@ -165,6 +183,7 @@ <option value="create">Create a BlobToolKit dataset</option> <option value="add">Add data to a BlobToolKit dataset</option> <option value="filter">Edit a BlobToolKit dataset</option> + <option value="plot">Plot a BlobToolKit dataset</option> </param> <when value="create"> <param argument="--fasta" type="data" format="fasta" label="Genome assembly file" help="FASTA sequence file" /> @@ -217,6 +236,7 @@ <param argument="--text-no-array" type="boolean" truevalue="--text-no-array" falsevalue="" checked="false" label="Prevent duplicated identifiers" help="Prevent fields in files with duplicate identifiers being loaded as array fields" /> </expand> + <expand macro="blobtk_plotting"></expand> <section name="advanced_options" title="Advanced options"> <param argument="--blobdb" type="data" format="json" optional="true" label="Blobtools v1 database" help="This file should have been generated with the previous Blobtools tool version"/> <param argument="--synonyms" type="data" format="tsv" optional="true" label="Identifier and sinonyms" help="TSV file containing current identifiers and synonyms"/> @@ -295,6 +315,16 @@ <validator type="regex">[0-9a-zA-Z]+</validator> </param> </section> + <expand macro="blobtk_plotting"></expand> + </when> + <when value="plot"> + <param name="blobdir_input" type="data" format="tgz" label="Select the blobdir tar.gz file generated from blobtools"/> + <param name="plot_view" type="select" label="Select the view type for the plot"> + <option value="blob" selected="true">Blob view</option> + <option value="cumulative">Cumulative view</option> + <option value="legend">Legend view</option> + <option value="snail">Snail view</option> + </param> </when> </conditional> </inputs> @@ -302,8 +332,18 @@ <data name="blobdir" format="tgz" from_work_dir="./Blobdir.tgz" label="${tool.name} on ${on_string}: Blobdir.tgz"> <filter>mode_conditional['selector'] == 'create' or mode_conditional['selector'] == 'add' or mode_conditional['selector'] == 'filter'</filter> </data> + <data name="output_svg" format="svg" from_work_dir="output.svg" label="${tool.name} on ${on_string}: Output Plot"> + <filter> + (( + (mode_conditional['selector'] == 'add' and mode_conditional['blobtk_plot_options']['blobtk_plot'] == 'yes') or + (mode_conditional['selector'] == 'filter' and mode_conditional['blobtk_plot_options']['blobtk_plot'] == 'yes') or + (mode_conditional['selector'] == 'plot') + )) + </filter> + </data> </outputs> <tests> + <!-- Test 01: Testing blobtoolkit with create with no plotting enabled --> <test expect_num_outputs="1"> <conditional name="mode_conditional"> <param name="selector" value="create"/> @@ -314,7 +354,8 @@ </conditional> <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="100"/> </test> - <test expect_num_outputs="1"> + <!-- Test 02: Testing blobtoolkit with add with plotting enabled --> + <test expect_num_outputs="2"> <conditional name="mode_conditional"> <param name="selector" value="add"/> <param name="blobdir" value="test01_blobdir.tar.gz"/> @@ -334,9 +375,15 @@ <param name="hit_count" value="10"/> <param name="hits_cols" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue"/> </conditional> + <conditional name="blobtk_plot_options"> + <param name="blobtk_plot" value="yes"/> + <param name="plot_view" value="blob"/> + </conditional> </conditional> <output name="blobdir" file="test02_blobdir.tar.gz" compare="sim_size" delta="100"/> + <output name="output_svg" file="test02_blob.svg" compare="sim_size" delta="100"/> </test> + <!-- Test 03: Testing blobtoolkit with filtering and plotting disabled --> <test expect_num_outputs="1"> <conditional name="mode_conditional"> <param name="selector" value="filter"/> @@ -350,12 +397,16 @@ <param name="remove_selector" value="--all"/> </section> </conditional> + <conditional name="blobtk_plot_options"> + <param name="blobtk_plot" value="no"/> + </conditional> <output name="blobdir"> <assert_contents> <has_size value="620" delta="50"/> </assert_contents> </output> </test> + <!-- Test 04: Testing blobtoolkit with filter with list and fasta filtering --> <test expect_num_outputs="1"> <conditional name="mode_conditional"> <param name="selector" value="filter"/> @@ -368,12 +419,55 @@ <param name="remove_selector" value="--all"/> </section> </conditional> + <conditional name="blobtk_plot_options"> + <param name="blobtk_plot" value="no"/> + </conditional> <output name="blobdir"> <assert_contents> <has_size value="620" delta="50"/> </assert_contents> </output> </test> + <!-- Test 05: Testing blobtoolkit blob plot --> + <test expect_num_outputs="1"> + <conditional name="mode_conditional"> + <param name="selector" value="plot"/> + <param name="blobdir_input" value="blobdir.tgz"/> + <param name="plot_view" value="blob"/> + </conditional> + <output name="output_svg" ftype="svg" file="output.svg" compare="sim_size"/> + </test> + <!-- Test 06 :Testing blobtoolkit Snail plot --> + <test expect_num_outputs="1"> + <conditional name="mode_conditional"> + <param name="selector" value="plot"/> + <param name="blobdir_input" value="blobdir.tgz"/> + <param name="plot_view" value="snail"/> + </conditional> + <output name="output_svg" ftype="svg"> + <assert_contents> + <has_text text="Log10 scaffold count (total 242)"/> + </assert_contents> + </output> + </test> + <!-- Test 07: Testing blobtoolkit legend plot --> + <test expect_num_outputs="1"> + <conditional name="mode_conditional"> + <param name="selector" value="plot"/> + <param name="blobdir_input" value="blobdir.tgz"/> + <param name="plot_view" value="legend"/> + </conditional> + <output name="output_svg" ftype="svg" file="output_legend.svg" compare="sim_size"/> + </test> + <!-- Test 08: Testing blobtoolkit Cumulative plot --> + <test expect_num_outputs="1"> + <conditional name="mode_conditional"> + <param name="selector" value="plot"/> + <param name="blobdir_input" value="blobdir.tgz"/> + <param name="plot_view" value="cumulative"/> + </conditional> + <output name="output_svg" ftype="svg" file="output_cumulative.svg" compare="sim_size"/> + </test> </tests> <help><![CDATA[ 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,
--- a/macros.xml Tue Mar 28 15:17:19 2023 +0000 +++ b/macros.xml Fri Jul 26 16:15:35 2024 +0000 @@ -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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