| Previous changeset 4:6d5c8a6ceea0 (2025-09-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr commit 722ac223fd675de7cacf37e3236198725a9a64e3 |
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modified:
staramr_search.xml |
| b |
| diff -r 6d5c8a6ceea0 -r eaa563bd535a staramr_search.xml --- a/staramr_search.xml Tue Sep 09 15:45:23 2025 +0000 +++ b/staramr_search.xml Tue Oct 28 09:16:18 2025 +0000 |
| [ |
| b'@@ -1,9 +1,9 @@\n <tool id="staramr_search" name="staramr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes</description>\n <macros>\n- <token name="@TOOL_VERSION@">0.11.0</token>\n- <token name="@VERSION_SUFFIX@">3</token>\n- <token name="@PROFILE@">22.05</token>\n+ <token name="@TOOL_VERSION@">0.11.1</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">24.1</token>\n <xml name="element_assert" token_name="" token_text="">\n <element name="@NAME@">\n <assert_contents>\n@@ -104,7 +104,7 @@\n #end if\n ]]></command>\n <inputs>\n- <param name="hide_db_build" type="hidden" value="" />\n+ <param name="hide_db_build" type="hidden" value=""/>\n <param type="data" name="genomes" format="fasta" multiple="true"/>\n <param name="staramr_db_select" type="select" label="starAMR database">\n <options from_data_table="staramr_database">\n@@ -112,12 +112,12 @@\n </options>\n </param>\n <param argument="--pointfinder-organism" type="select" label="Enable scanning for point mutations using the PointFinder database" help="You can select one of the unvalidated PointFinder organisms to use for scanning for point mutations. These have not been fully validated as compatible with staramr so caution is recommended when interpreting results.">\n- <option value="disabled" selected="true">Disable PointFinder</option> \n+ <option value="disabled" selected="true">Disable PointFinder</option>\n <option value="campylobacter">Campylobacter (campylobacter)</option>\n <option value="enterococcus_faecalis">Enterococcus faecalis (enterococcus_faecalis)</option>\n <option value="enterococcus_faecium">Enterococcus faecium (enterococcus_faecium)</option>\n- <option value="escherichia_coli">Escherichia coli (escherichia_coli)</option> \n- <option value="helicobacter_pylori">Helicobacter pylori (helicobacter_pylori)</option> \n+ <option value="escherichia_coli">Escherichia coli (escherichia_coli)</option>\n+ <option value="helicobacter_pylori">Helicobacter pylori (helicobacter_pylori)</option>\n <option value="salmonella">Salmonella (salmonella)</option>\n <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organisms -->\n <option value="klebsiella">Unvalidated: Klebsiella (klebsiella) </option>\n@@ -127,18 +127,18 @@\n <option value="staphylococcus_aureus">Unvalidated: Staphylococcus aureus (staphylococcus_aureus)</option>\n </param>\n <section name="advanced" title="Advanced options" expanded="false">\n- <param argument="--pid-threshold" type="float" label="Percent identity threshold for BLAST" value="98.0" min="0" max="100" />\n- <param argument="--percent-length-overlap-resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0" min="0" max="100" />\n- <param argument="--percent-length-overlap-pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0" min="0" max="100" />\n- <param argument="--percent-length-overlap-plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0" min="0" max="100" />\n- <param argument="--genome-size-lower-bound" type="integer" label="The lower bound for our genome size for the quality metrics" value="4000000" min="0" />\n- <param argument="--genome-size-upper-bound" type="integer" label="The upper bound for our genome size for the quality metrics" value="6000000" min="0" />\n- <param argument="--'..b' </assert_contents>\n </output>\n </test>\n- <test expect_num_outputs="8"> <!-- TEST_10 -->\n- <param name="hide_db_build" value="true" />\n- <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />\n- <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502" /> \n- <param name="pointfinder_organism" value="disabled" />\n+ <test expect_num_outputs="8">\n+ <!-- TEST_10 -->\n+ <param name="hide_db_build" value="true"/>\n+ <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta"/>\n+ <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"/>\n+ <param name="pointfinder_organism" value="disabled"/>\n <section name="advanced">\n- <param name="pid_threshold" value="98.0" />\n- <param name="percent_length_overlap_resfinder" value="60.0" />\n- <param name="percent_length_overlap_pointfinder" value="95.0" />\n- <param name="percent_length_overlap_plasmidfinder" value="60.0" />\n- <param name="genome_size_lower_bound" value="1" />\n- <param name="genome_size_upper_bound" value="10" />\n- <param name="minimum_N50_value" value="10000" />\n- <param name="minimum_contig_length" value="300" />\n- <param name="unacceptable_number_contigs" value="1000" />\n- <param name="report_all_blast" value="False" />\n- <param name="exclude_negatives" value="False" />\n- <param name="exclude_resistance_phenotypes" value="False" />\n- <param name="mlst_scheme" value="auto" />\n+ <param name="pid_threshold" value="98.0"/>\n+ <param name="percent_length_overlap_resfinder" value="60.0"/>\n+ <param name="percent_length_overlap_pointfinder" value="95.0"/>\n+ <param name="percent_length_overlap_plasmidfinder" value="60.0"/>\n+ <param name="genome_size_lower_bound" value="1"/>\n+ <param name="genome_size_upper_bound" value="10"/>\n+ <param name="minimum_N50_value" value="10000"/>\n+ <param name="minimum_contig_length" value="300"/>\n+ <param name="unacceptable_number_contigs" value="1000"/>\n+ <param name="report_all_blast" value="False"/>\n+ <param name="exclude_negatives" value="False"/>\n+ <param name="exclude_resistance_phenotypes" value="False"/>\n+ <param name="mlst_scheme" value="auto"/>\n <conditional name="exclude_genes">\n- <param name="exclude_genes_condition" value="default" />\n+ <param name="exclude_genes_condition" value="default"/>\n </conditional>\n- <conditional name="complex_mutations">\n- <param name="complex_mutations_condition" value="default" />\n- </conditional>\n- <param name="plasmidfinder_type" value="include_all" />\n+ <param name="plasmidfinder_type" value="include_all"/>\n </section>\n <section name="output_files">\n <param name="output_selection" value="mlst_table,summary_table,detailed_summary_table,resfinder_table,plasmidfinder_table,settings_output,excel_output"/>\n </section>\n <output name="summary" ftype="tabular">\n <assert_contents>\n- <has_text_matching expression="Genome length is not within the acceptable length range \\[1,10\\]" />\n+ <has_text_matching expression="Genome length is not within the acceptable length range \\[1,10\\]"/>\n </assert_contents>\n </output>\n </test>\n' |