| Previous changeset 3:43f9ca23c132 (2021-04-24) Next changeset 5:3852f36e3154 (2025-09-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3 |
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modified:
macros.xml mash_sketch.xml test-data/test_01_mash_sketch.msh test-data/test_02_mash_sketch.msh test-data/test_03_mash_sketch.msh test-data/test_04_mash_sketch.msh test-data/test_05_mash_sketch.msh test-data/test_06_mash_sketch.msh test-data/test_07_mash_sketch.msh |
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added:
test-data/ERR024951_seqtk_sample_1000_1.fastq.gz test-data/ERR024951_seqtk_sample_1000_2.fastq.gz test-data/m64326e_231117_100511.hifi_reads.bc2068--bc2068.msh test-data/m64326e_231130_052019.hifi_reads.bc2068--bc2068.msh |
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| diff -r 43f9ca23c132 -r c73c3dfe1af8 macros.xml --- a/macros.xml Sat Apr 24 13:28:53 2021 +0000 +++ b/macros.xml Thu Sep 11 10:22:17 2025 +0000 |
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| @@ -1,13 +1,17 @@ <macros> <token name="@TOOL_VERSION@">2.3</token> - <token name="@INTYPES@"> - fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz - </token> + <token name="@PROFILE@">23.2</token> + <token name="@INTYPES@">fasta,fasta.gz,fastqsanger,fastqsanger.gz</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">mash</requirement> </requirements> </xml> + <xml name="xref"> + <xrefs> + <xref type="bio.tools">mash</xref> + </xrefs> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1186/s13059-016-0997-x</citation> |
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| diff -r 43f9ca23c132 -r c73c3dfe1af8 mash_sketch.xml --- a/mash_sketch.xml Sat Apr 24 13:28:53 2021 +0000 +++ b/mash_sketch.xml Thu Sep 11 10:22:17 2025 +0000 |
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| @@ -1,10 +1,9 @@ -<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy0" profile="19.01"> - <description> - Create a reduced representation of a sequence or set of sequences, based on min-hashes - </description> +<tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> + <description>Create a reduced sequence representation based on min-hashes</description> <macros> <import>macros.xml</import> </macros> + <expand macro="xref"/> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ @@ -78,7 +77,7 @@ <data name="sketch" format="msh" from_work_dir="sketch.msh"/> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <conditional name="reads_assembly"> <param name="reads_assembly_selector" value="reads"/> <conditional name="reads_input"> @@ -88,40 +87,40 @@ </conditional> <output name="sketch" file="test_01_mash_sketch.msh" compare="sim_size" /> </test> - <test> + <test expect_num_outputs="1"> <conditional name="reads_assembly"> <param name="reads_assembly_selector" value="reads"/> <conditional name="reads_input"> <param name="reads_input_selector" value="single"/> <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/> - <param name="minimum_kmer_copies" value="10"/> </conditional> + <param name="minimum_kmer_copies" value="10"/> </conditional> <output name="sketch" file="test_02_mash_sketch.msh" compare="sim_size" /> </test> - <test> + <test expect_num_outputs="1"> <conditional name="reads_assembly"> <param name="reads_assembly_selector" value="reads"/> <conditional name="reads_input"> <param name="reads_input_selector" value="single"/> <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/> - <param name="target_coverage" value="1"/> </conditional> + <param name="target_coverage" value="1"/> </conditional> <output name="sketch" file="test_03_mash_sketch.msh" compare="sim_size" /> </test> - <test> + <test expect_num_outputs="1"> <conditional name="reads_assembly"> <param name="reads_assembly_selector" value="reads"/> <conditional name="reads_input"> <param name="reads_input_selector" value="single"/> <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/> - <param name="genome_size" value="1000"/> </conditional> + <param name="genome_size" value="1000"/> </conditional> <output name="sketch" file="test_04_mash_sketch.msh" compare="sim_size" /> </test> - <test> + <test expect_num_outputs="1"> <conditional name="reads_assembly"> <param name="reads_assembly_selector" value="reads"/> <conditional name="reads_input"> @@ -132,7 +131,7 @@ <param name="sketch_size" value="500"/> <output name="sketch" file="test_05_mash_sketch.msh" compare="sim_size" /> </test> - <test> + <test expect_num_outputs="1"> <conditional name="reads_assembly"> <param name="reads_assembly_selector" value="reads"/> <conditional name="reads_input"> @@ -143,7 +142,7 @@ <param name="kmer_size" value="17"/> <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" /> </test> - <test> + <test expect_num_outputs="1"> <conditional name="reads_assembly"> <param name="reads_assembly_selector" value="reads"/> <conditional name="reads_input"> @@ -154,7 +153,7 @@ <param name="prob_threshold" value="0.1"/> <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" /> </test> - <test> + <test expect_num_outputs="1"> <conditional name="reads_assembly"> <param name="reads_assembly_selector" value="assembly"/> <param name="assembly" value="test_assembly.fasta"/> |
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