| Previous changeset 1:840822c1e84a (2023-03-20) Next changeset 3:8c2167481e72 (2024-07-26) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 |
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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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| diff -r 840822c1e84a -r 53dd00a4ab68 blobtoolkit.xml --- a/blobtoolkit.xml Mon Mar 20 16:37:54 2023 +0000 +++ b/blobtoolkit.xml Tue Mar 28 15:17:19 2023 +0000 |
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| b'@@ -22,14 +22,16 @@\n --taxid $mode_conditional.taxid\n --taxdump \'./taxdump\'\n \'./Blobdir\'\n- && cp -r \'./taxdump\' \'./Blobdir/\'\n- && tar -zcf \'./Blobdir.tgz\' \'./Blobdir\'\n-\n+ && tar -C ./Blobdir -zcvf Blobdir.tgz .\n #else if $mode_conditional.selector == \'add\'\n+ mkdir -p \'./Blobdir\' &&\n+ mkdir -p \'./taxdump\' &&\n+ ln -s \'${mode_conditional.taxdump}\' \'taxdump.tar\' &&\n+ tar -xf \'taxdump.tar\' -C \'./taxdump\' &&\n #if $mode_conditional.blobdir.is_of_type("tgz")\n- tar -zxf \'${mode_conditional.blobdir}\' -C \'./\' &&\n+ tar -zxf \'${mode_conditional.blobdir}\' -C \'./Blobdir\' &&\n #else\n- tar -xf \'${mode_conditional.blobdir}\' -C \'./\' &&\n+ tar -xf \'${mode_conditional.blobdir}\' -C \'./Blobdir\' &&\n #end if\n #if $mode_conditional.busco\n ln -s \'${mode_conditional.busco}\' \'./busco_results.tab\' && \n@@ -50,7 +52,7 @@\n #end if\n blobtools add\n --threads \\${GALAXY_SLOTS:-8}\n- --taxdump \'./Blobdir/taxdump\'\n+ --taxdump \'./taxdump\'\n #if $mode_conditional.busco\n --busco \'./busco_results.tab\'\n #end if\n@@ -95,9 +97,15 @@\n #end if\n $mode_conditional.advanced_options.replace\n \'./Blobdir\'\n- && tar -zcf \'./Blobdir.tgz\' \'./Blobdir\'\n+ && tar -C ./Blobdir -zcvf Blobdir.tgz .\n \n #else if $mode_conditional.selector == \'filter\'\n+ mkdir -p \'./Blobdir\' &&\n+ #if $mode_conditional.blobdir.is_of_type("tgz")\n+ tar -zxf \'${mode_conditional.blobdir}\' -C \'./Blobdir\' &&\n+ #else\n+ tar -xf \'${mode_conditional.blobdir}\' -C \'./Blobdir\' &&\n+ #end if\n #if $mode_conditional.filter_options.list\n echo $mode_conditional.filter_options.list > id_list.txt &&\n #end if\n@@ -148,29 +156,7 @@\n #end if\n ./Blobdir\n #end if\n- && tar -zcf \'./Blobdir.tgz\' \'./Blobdir\'\n-\n- #else if $mode_conditional.selector == \'plots\'\n- #if $mode_conditional.blobdir.is_of_type("tgz")\n- tar -zxf \'${mode_conditional.blobdir}\' -C \'./\' &&\n- #else\n- tar -xf \'${mode_conditional.blobdir}\' -C \'./\' &&\n- #end if \n- blobtools view\n- --format $mode_conditional.format\n- --view \'blob\'\n- ./Blobdir\n- && mv ./Blobdir.blob.circle* ./Blobdir.blob.circle\n- && blobtools view\n- --format $mode_conditional.format\n- --view \'cumulative\'\n- ./Blobdir\n- && mv ./Blobdir.cumulative* Blobdir.cumulative\n- && blobtools view\n- --format $mode_conditional.format\n- --view \'snail\'\n- ./Blobdir\n- && mv ./Blobdir.snail* Blobdir.snail\n+ && tar -C ./Blobdir -zcvf Blobdir.tgz .\n #end if\n ]]></command>\n <inputs>\n@@ -179,16 +165,16 @@\n <option value="create">Create a BlobToolKit dataset</option>\n <option value="add">Add data to a BlobToolKit dataset</option>\n <option value="filter">Edit a BlobToolKit dataset</option>\n- <option value="plots">Generate plots</option>\n </param>\n <when value="create">\n <param argument="--fasta" type="data" format="fasta" label="Genome assembly file" help="FASTA sequence file" />\n <param argument="--meta" type="data" format="yaml" label="Metadata file" optional="true" help="Optional metadata dataset"/>\n <param argument="--taxid" type="integer" value="" label="NCBI taxonomy ID" help="Add ranks to metadata for a taxid"/>\n- '..b'k_dir="./Blobdir.snail" label="${tool.name} on ${on_string}: snail plot">\n- <filter>mode_conditional[\'selector\'] == \'plots\'</filter>\n- <change_format>\n- <when input="$mode_conditional.format" value="svg" format="svg"/>\n- </change_format>\n- </data>\n </outputs>\n <tests>\n <test expect_num_outputs="1">\n@@ -352,12 +312,13 @@\n <param name="taxid" value="801"/>\n <param name="taxdump" value="small_taxdump.tar.gz"/>\n </conditional>\n- <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="1500"/>\n+ <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="100"/>\n </test>\n <test expect_num_outputs="1">\n <conditional name="mode_conditional">\n <param name="selector" value="add"/>\n <param name="blobdir" value="test01_blobdir.tar.gz"/>\n+ <param name="taxdump" value="small_taxdump.tar.gz"/>\n <param name="busco" value="busco_full_table.tabular"/>\n <param name="cov" value="bam_file.bam"/>\n <param name="fasta" value="contig.fasta"/>\n@@ -374,7 +335,7 @@\n <param name="hits_cols" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue"/>\n </conditional>\n </conditional>\n- <output name="blobdir" file="test02_blobdir.tar.gz" compare="sim_size" delta="1500"/>\n+ <output name="blobdir" file="test02_blobdir.tar.gz" compare="sim_size" delta="100"/>\n </test>\n <test expect_num_outputs="1">\n <conditional name="mode_conditional">\n@@ -391,20 +352,10 @@\n </conditional>\n <output name="blobdir">\n <assert_contents>\n- <has_size value="672500" delta="1000"/>\n+ <has_size value="620" delta="50"/>\n </assert_contents>\n </output>\n </test>\n- <test expect_num_outputs="3">\n- <conditional name="mode_conditional">\n- <param name="selector" value="plots"/>\n- <param name="blobdir" value="test02_blobdir.tar.gz"/>\n- <param name="format" value="png"/>\n- </conditional>\n- <output name="plot_circle" file="test04_circle.png" ftype="png"/>\n- <output name="plot_cumulative" file="test04_cumulative.png" ftype="png"/>\n- <output name="plot_snail" file="test04_snail.png" ftype="png"/>\n- </test>\n <test expect_num_outputs="1">\n <conditional name="mode_conditional">\n <param name="selector" value="filter"/>\n@@ -419,7 +370,7 @@\n </conditional>\n <output name="blobdir">\n <assert_contents>\n- <has_size value="672497" delta="1000"/>\n+ <has_size value="620" delta="50"/>\n </assert_contents>\n </output>\n </test>\n@@ -427,6 +378,13 @@\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 read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility.\n+\n+.. class:: infomark\n+ \n+**NCBI taxdump directory**\n+\n+The taxdump database, provided by NCBI, includes the taxonomic lineage of taxa, information on type strains and material, and host information. The file **new_taxdump.tar.gz** can be downloaded from the taxonomy directory on the `FTP site <ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/>`_. \n+ \n ]]></help>\n <expand macro="citations"/>\n-</tool>\n\\ No newline at end of file\n+</tool>\n' |
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| diff -r 840822c1e84a -r 53dd00a4ab68 macros.xml --- a/macros.xml Mon Mar 20 16:37:54 2023 +0000 +++ b/macros.xml Tue Mar 28 15:17:19 2023 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">4.0.7</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> @@ -42,6 +42,8 @@ </when> <when value="disabled"/> </conditional> - + </xml> + <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> </macros> |
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| diff -r 840822c1e84a -r 53dd00a4ab68 test-data/test01_blobdir.tar.gz |
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| diff -r 840822c1e84a -r 53dd00a4ab68 test-data/test02_blobdir.tar.gz |
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| Binary file test-data/test02_blobdir.tar.gz has changed |