Mercurial > repos > iuc > amrfinderplus
diff amrfinderplus.xml @ 1:a37bb163d05d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit a93148583b30aebf45c816a5d671e710aeff6fbf
| author | iuc |
|---|---|
| date | Sat, 27 May 2023 19:51:49 +0000 |
| parents | a968af0a91f9 |
| children | 1920244e2895 |
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--- a/amrfinderplus.xml Fri May 26 09:19:12 2023 +0000 +++ b/amrfinderplus.xml Sat May 27 19:51:49 2023 +0000 @@ -218,7 +218,7 @@ <output name="amrfinderplus_report" value="test_1/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> <output name="nucleotide_output" value="test_1/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> </test> - <test expect_num_outputs="4"> <!-- TEST_2 nucleotide input and full options --> + <test expect_num_outputs="3"> <!-- TEST_2 nucleotide input and full options --> <section name="input_option"> <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> <conditional name="input_mode"> @@ -231,7 +231,6 @@ <conditional name="organism_conditionnal"> <param name="organism_select" value="add_organism"/> <param name="organism" value="Enterococcus_faecalis"/> - <param name="mutation_all" value="true"/> <param name="report_common" value="true"/> </conditional> </section> @@ -246,7 +245,6 @@ <param name="log" value="true"/> </section> <output name="amrfinderplus_report" value="test_2/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> - <output name="mutation_all_report" value="test_2/amrfinderplus_mutation_all.tsv" ftype="tabular" lines_diff="1"/> <output name="nucleotide_output" value="test_2/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> <output name="nucleotide_flank5_output" value="test_2/amrfinderplus_flanking_output.fasta" ftype="fasta" lines_diff="1"/> </test> @@ -282,7 +280,7 @@ <output name="amrfinderplus_report" value="test_4/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> <output name="protein_output" value="test_4/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> </test> - <test expect_num_outputs="3"> <!-- TEST_5 protein input and full options to gff3 and bakta --> + <test expect_num_outputs="2"> <!-- TEST_5 protein input and full options to gff3 and bakta --> <section name="input_option"> <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> <conditional name="input_mode"> @@ -296,7 +294,6 @@ <conditional name="organism_conditionnal"> <param name="organism_select" value="add_organism"/> <param name="organism" value="Enterococcus_faecalis"/> - <param name="mutation_all" value="true"/> <param name="report_common" value="true"/> </conditional> </section> @@ -310,7 +307,6 @@ <param name="name" value="test_5"/> </section> <output name="amrfinderplus_report" value="test_5/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> - <output name="mutation_all_report" value="test_5/amrfinderplus_mutation_all.tsv" ftype="tabular" lines_diff="1"/> <output name="protein_output" value="test_5/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> </test> <test expect_num_outputs="2"> <!-- TEST_6 protein input and prokka annotation --> @@ -338,7 +334,7 @@ <output name="amrfinderplus_report" value="test_7/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> <output name="protein_output" value="test_7/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> </test> - <test expect_num_outputs="4"> <!-- TEST_8 both protein and nucleotide input --> + <test expect_num_outputs="3"> <!-- TEST_8 both protein and nucleotide input --> <section name="input_option"> <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> <conditional name="input_mode"> @@ -353,14 +349,41 @@ <conditional name="organism_conditionnal"> <param name="organism_select" value="add_organism"/> <param name="organism" value="Enterococcus_faecalis"/> - <param name="mutation_all" value="true"/> - <param name="report_common" value="true"/> </conditional> </section> <output name="amrfinderplus_report" value="test_8/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> <output name="protein_output" value="test_8/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> <output name="nucleotide_output" value="test_8/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> - <output name="mutation_all_report" value="test_8/amrfinderplus_mutation_all.tsv" ftype="tabular" lines_diff="1"/> + </test> + <test expect_num_outputs="4"> <!-- TEST_9 rast annotation and mutation all results --> + <section name="input_option"> + <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> + <conditional name="input_mode"> + <param name="input_select" value="nucl_prot"/> + <param name="protein_input" value="e_faecalis_rast.faa"/> + <param name="nucleotide_input" value="e_faecalis_rast.fna"/> + <param name="gff_annotation" value="e_faecalis_rast.gff"/> + <param name="annotation_format" value="rast"/> + </conditional> + </section> + <section name="organism_options"> + <conditional name="organism_conditionnal"> + <param name="organism_select" value="add_organism"/> + <param name="organism" value="Enterococcus_faecalis"/> + <param name="mutation_all" value="true"/> + </conditional> + </section> + <section name="options"> + <param name="ident_min" value="0.1"/> + <param name="coverage_min" value="0.1"/> + <param name="plus" value="true"/> + <param name="print_node" value="true"/> + <param name="name" value="test_5"/> + </section> + <output name="amrfinderplus_report" value="test_9/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> + <output name="protein_output" value="test_9/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> + <output name="nucleotide_output" value="test_9/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> + <output name="mutation_all_report" value="test_9/amrfinderplus_mutation_all.tsv" ftype="tabular" lines_diff="1"/> </test> </tests> <help><![CDATA[