| Previous changeset 4:86dec4abcea8 (2021-04-24) Next changeset 6:23d6489e2604 (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_screen.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 86dec4abcea8 -r 0f9b62370529 macros.xml --- a/macros.xml Sat Apr 24 11:29:35 2021 +0000 +++ b/macros.xml Thu Sep 11 10:22:28 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 86dec4abcea8 -r 0f9b62370529 mash_screen.xml --- a/mash_screen.xml Sat Apr 24 11:29:35 2021 +0000 +++ b/mash_screen.xml Thu Sep 11 10:22:28 2025 +0000 |
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| @@ -1,10 +1,11 @@ -<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy3" profile="19.01"> - <description>determines how well query sequences are contained within a pool of sequences</description> +<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@"> + <description>Determine sequence conservation</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> - <expand macro="version_command" /> + <expand macro="xref"/> + <expand macro="requirements"/> + <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ #if str( $queries_input_source.queries_input_source_selector ) == "tool_data_table": ln -s '$queries_input_source.queries.fields.path' queries.msh && @@ -56,38 +57,49 @@ </param> </when> <when value="history"> - <param name="queries" type="data" format="msh" /> + <param name="queries" type="data" format="msh"/> </when> </conditional> - <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result" - help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/> - <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report" /> - <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report" /> + <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result" help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/> + <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report"/> + <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1." label="Maximum p-value to report"/> </inputs> <outputs> - <data name="output" format="tabular" /> + <data name="output" format="tabular"/> </outputs> <tests> - <test> - <param name="queries_input_source_selector" value="history"/> - <param name="queries" value="NZ_MYON01000010.1.msh"/> - <param name="pool_input_selector" value="single"/> - <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/> + <test expect_num_outputs="1"> + <conditional name="pool_input"> + <param name="pool_input_selector" value="single"/> + <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/> + </conditional> + <conditional name="queries_input_source"> + <param name="queries_input_source_selector" value="history"/> + <param name="queries" value="NZ_MYON01000010.1.msh"/> + </conditional> <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/> </test> - <test> - <param name="queries_input_source_selector" value="tool_data_table"/> - <param name="queries" value="test_sketch"/> - <param name="pool_input_selector" value="single"/> - <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/> + <test expect_num_outputs="1"> + <conditional name="pool_input"> + <param name="pool_input_selector" value="single"/> + <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/> + </conditional> + <conditional name="queries_input_source"> + <param name="queries_input_source_selector" value="tool_data_table"/> + <param name="queries" value="test_sketch"/> + </conditional> <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/> </test> - <test> - <param name="queries_input_source_selector" value="history"/> - <param name="queries" value="NZ_MYON01000010.1.msh"/> - <param name="pool_input_selector" value="paired"/> - <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/> - <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/> + <test expect_num_outputs="1"> + <conditional name="pool_input"> + <param name="pool_input_selector" value="paired"/> + <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/> + <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/> + </conditional> + <conditional name="queries_input_source"> + <param name="queries_input_source_selector" value="history"/> + <param name="queries" value="NZ_MYON01000010.1.msh"/> + </conditional> <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/> </test> </tests> |
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