| Previous changeset 4:27d65c78863c (2022-03-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5 |
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modified:
kraken_taxonomy_report.xml |
| b |
| diff -r 27d65c78863c -r bfae8da6082c kraken_taxonomy_report.xml --- a/kraken_taxonomy_report.xml Sun Mar 20 16:39:48 2022 +0000 +++ b/kraken_taxonomy_report.xml Tue Mar 12 09:52:55 2024 +0000 |
| [ |
| b'@@ -1,8 +1,16 @@\n-<tool id="kraken_taxonomy_report" name="Kraken taxonomic report" version="0.0.3" profile="16.04">\n+<tool id="kraken_taxonomy_report" name="Kraken taxonomic report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="16.04">\n <description>view report of classification for multiple samples</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">0.0.3</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n+ </macros>\n+ <xrefs>\n+ <xref type="bio.tools">Kraken-Taxonomy-Report</xref>\n+ </xrefs>\n <requirements>\n <requirement type="package" version="1.66">biopython</requirement>\n </requirements>\n+\n <version_command>python \'${__tool_directory__}/kraken_taxonomy_report.py\' --version</version_command>\n <command><![CDATA[\n #for $input_classification in $classification:\n@@ -13,17 +21,17 @@\n python \'${__tool_directory__}/kraken_taxonomy_report.py\'\n \n --db \'${kraken_database.fields.name}\'\n-${show_zeros}\n-${header_line}\n+${show_zeros_param}\n+${header_line_param}\n ${otu_name}\n-${taxonomy}\n-${show_rank}\n-${intermediate}\n-${sanitize_names}\n-#if str( $cluster.cluster ):\n- --cluster ${cluster.cluster}\n+${taxo}\n+${rank}\n+${intermediate_rank}\n+${sanitize_names_param}\n+#if str( $cluster.cluster_param ):\n+ --cluster ${cluster.cluster_param}\n #else:\n- ${cluster.summation}\n+ ${cluster.summ}\n #end if\n \n --output \'${output_report}\'\n@@ -38,8 +46,8 @@\n ]]></command>\n <inputs>\n <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />\n- <param checked="False" falsevalue="" argument="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" />\n- <param checked="True" falsevalue="" argument="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" />\n+ <param checked="False" falsevalue="" argument="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros_param" truevalue="--show-zeros" type="boolean" />\n+ <param checked="True" falsevalue="" argument="--header-line" label="Display a header line indicating sample IDs" name="header_line_param" truevalue="--header-line" type="boolean" />\n <param label="Select a Kraken database" name="kraken_database" type="select" help="Select the same database used to classify reads">\n <options from_data_table="kraken_databases">\n <validator message="No Kraken databases are available" type="no_options" />\n@@ -50,12 +58,12 @@\n <option value="--name-long">Taxonified Name</option>\n <option value="--name-id">Node ID</option>\n </param>\n- <param checked="True" falsevalue="" argument="--sanitize-names" label="Sanitize Names" name="sanitize_names" truevalue="--sanitize-names" type="boolean" help="Replace special chars (\\t| |\\||\\.;) with underscore (_)" />\n- <param checked="False" falsevalue="" argument="--show-rank" label="Output Rank Name in (second to) last column" name="show_rank" truevalue="--show-rank" type="boolean" />\n- <param checked="False" falsevalue="" argument="--taxonomy" label="Output taxonomy in last column" name="taxonomy" truevalue="--taxonomy" type="boolean" />\n- <param checked="True" falsevalue="" argument="--intermediate" label="Display intermediate ranks" name="intermediate" truevalue="--intermediate" type="boolean" />\n+ <param checked="True" falsevalue="" argument="--sanitize-names" label="Sanitize Names" name="sanitize_names_param" truevalue="--sanitize-names" type="boolean" help="Replace special chars (\\t| |\\||\\.;) with underscore (_)" />\n+ <param checked="False" falsevalue="" argument="--show-rank" label="Output Rank Name in (second to) last column" name="rank" truevalue="--show-rank" type="boolean" />\n+ <param checked="False" falsevalue="" argument'..b'st expect_num_outputs="2">\n <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>\n- <param name="show_zeros" value="True"/>\n- <param name="header_line" value="True"/>\n+ <param name="show_zeros_param" value="True"/>\n+ <param name="header_line_param" value="True"/>\n <param name="kraken_database" value="test_db"/>\n <param name="otu_name" value=""/>\n- <param name="sanitize_names" value="True"/>\n- <param name="show_rank" value="True"/>\n- <param name="taxonomy" value="True"/>\n- <param name="intermediate" value="True"/>\n+ <param name="sanitize_names_param" value="True"/>\n+ <param name="rank" value="True"/>\n+ <param name="taxo" value="True"/>\n+ <param name="intermediate_rank" value="True"/>\n <conditional name="cluster">\n- <param name="cluster" value=""/>\n- <param name="summation" value="False"/>\n+ <param name="cluster_param" value=""/>\n+ <param name="summ" value="False"/>\n </conditional>\n <param name="tree" value="True"/>\n <output name="output_report" file="output_abundance_2.tabular" ftype="tabular"/>\n <output name="output_tree" file="output_tree_1.newick" />\n </test>\n- <test>\n+ <test expect_num_outputs="2">\n <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>\n- <param name="show_zeros" value="True"/>\n- <param name="header_line" value="True"/>\n+ <param name="show_zeros_param" value="True"/>\n+ <param name="header_line_param" value="True"/>\n <param name="kraken_database" value="test_db"/>\n <param name="otu_name" value=""/>\n- <param name="sanitize_names" value="True"/>\n- <param name="show_rank" value="True"/>\n- <param name="taxonomy" value="True"/>\n- <param name="intermediate" value="False"/>\n+ <param name="sanitize_names_param" value="True"/>\n+ <param name="rank" value="True"/>\n+ <param name="taxo" value="True"/>\n+ <param name="intermediate_rank" value="False"/>\n <conditional name="cluster">\n- <param name="cluster" value="Species"/>\n+ <param name="cluster_param" value="Species"/>\n </conditional>\n <param name="tree" value="True"/>\n <output name="output_report" file="output_abundance_3.tabular" ftype="tabular"/>\n <output name="output_tree" file="output_tree_3.newick" />\n </test>\n- <test>\n+ <test expect_num_outputs="2">\n <param name="classification" value="input_kraken_1.tabular,input_kraken_2.tabular" ftype="tabular"/>\n- <param name="show_zeros" value="True"/>\n- <param name="header_line" value="True"/>\n+ <param name="show_zeros_param" value="True"/>\n+ <param name="header_line_param" value="True"/>\n <param name="kraken_database" value="test_db"/>\n <param name="otu_name" value=""/>\n- <param name="sanitize_names" value="True"/>\n- <param name="show_rank" value="True"/>\n- <param name="taxonomy" value="True"/>\n- <param name="intermediate" value="False"/>\n+ <param name="sanitize_names_param" value="True"/>\n+ <param name="rank" value="True"/>\n+ <param name="taxo" value="True"/>\n+ <param name="intermediate_rank" value="False"/>\n <conditional name="cluster">\n- <param name="cluster" value="Species"/>\n+ <param name="cluster_param" value="Species"/>\n </conditional>\n <param name="tree" value="True"/>\n <output name="output_report" file="output_abundance_4.tabular" ftype="tabular"/>\n' |