Mercurial > repos > iuc > amrfinderplus
diff amrfinderplus.xml @ 7:7844dbe4f8e2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
| author | iuc |
|---|---|
| date | Thu, 30 May 2024 13:07:03 +0000 |
| parents | 1920244e2895 |
| children |
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--- a/amrfinderplus.xml Tue Oct 31 14:47:37 2023 +0000 +++ b/amrfinderplus.xml Thu May 30 13:07:03 2024 +0000 @@ -8,7 +8,6 @@ <expand macro="biotools"/> <expand macro="requirements"/> <expand macro="version_command"/> - <command detect_errors="aggressive"><![CDATA[ amrfinder #*====================================== @@ -83,8 +82,9 @@ <!-- DB and file INPUT --> <section name="input_option" title="Input/Output options" expanded="true"> <param name="amrfinder_db_select" type="select" label="The amrfinderplus database"> - <options from_data_table="amrfinderplus_database"> - <validator message="No amrfinderplus database is available" type="no_options"/> + <options from_data_table="amrfinderplus_versioned_database"> + <filter type="static_value" value="3.12" column="db_version"/> + <validator message="No amrfinderplus database is available" type="no_options"/> </options> </param> <conditional name="input_mode"> @@ -209,18 +209,32 @@ <tests> <test expect_num_outputs="2"> <!-- TEST_1 simple nucleotide input --> <section name="input_option"> - <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> + <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> <conditional name="input_mode"> <param name="input_select" value="nucleotide"/> <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> </conditional> </section> - <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"/> + <output name="amrfinderplus_report" ftype="tabular"> + <assert_contents> + <has_n_columns n="22"/> + <has_n_lines n="8"/> + <has_text text="optrA"/> + <has_text text="WP_063854496"/> + <has_text text="WP_063843211"/> + </assert_contents> + </output> + <output name="nucleotide_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="142"/> + <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/> + <has_text text="TTGTCCAAAGCC"/> + </assert_contents> + </output> </test> <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"/> + <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> <conditional name="input_mode"> <param name="input_select" value="nucleotide"/> <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> @@ -235,22 +249,41 @@ </conditional> </section> <section name="options"> - <param name="ident_min" value="1"/> + <param name="ident_min" value="0.1"/> <param name="coverage_min" value="0.1"/> <param name="translation_table" value="11"/> <param name="plus" value="true"/> <param name="report_all_equal" value="true"/> <param name="print_node" value="true"/> <param name="name" value="test_2"/> - <param name="log" value="true"/> + <param name="log" value="true"/> </section> - <output name="amrfinderplus_report" value="test_2/amrfinderplus_results.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"/> + <output name="amrfinderplus_report" ftype="tabular"> + <assert_contents> + <has_n_columns n="24"/> + <has_n_lines n="13"/> + <has_text text="optrA"/> + <has_text text="WP_063854496"/> + </assert_contents> + </output> + <output name="nucleotide_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="267"/> + <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/> + <has_text text="TTGTCCAAAGCC"/> + </assert_contents> + </output> + <output name="nucleotide_flank5_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="298"/> + <has_text text=">contig_2:54987-57395 strand:- mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/> + <has_text text="TTGTCCAAAGCC"/> + </assert_contents> + </output> </test> <test expect_num_outputs="2"> <!-- TEST_3 nucleotide input and several options --> <section name="input_option"> - <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> + <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> <conditional name="input_mode"> <param name="input_select" value="nucleotide"/> <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> @@ -266,23 +299,51 @@ <section name="options"> <param name="report_all_equal" value="true"/> </section> - <output name="amrfinderplus_report" value="test_3/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> - <output name="nucleotide_output" value="test_3/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> + <output name="amrfinderplus_report" ftype="tabular"> + <assert_contents> + <has_n_columns n="22"/> + <has_n_lines n="9"/> + <has_text text="optrA"/> + <has_text text="WP_063854496"/> + <has_text text="WP_063856080"/> + </assert_contents> + </output> + <output name="nucleotide_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="142"/> + <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/> + <has_text text="TTGTCCAAAGCC"/> + </assert_contents> + </output> </test> <test expect_num_outputs="2"> <!-- TEST_4 simple protein input --> <section name="input_option"> - <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> + <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> <conditional name="input_mode"> <param name="input_select" value="protein"/> <param name="protein_input" value="enterococcus_faecalis.faa"/> </conditional> </section> - <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"/> + <output name="amrfinderplus_report" ftype="tabular"> + <assert_contents> + <has_n_columns n="18"/> + <has_n_lines n="7"/> + <has_text text="optrA"/> + <has_text text="WP_063854496"/> + <has_text text="WP_063856080"/> + </assert_contents> + </output> + <output name="protein_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="49"/> + <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/> + <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/> + </assert_contents> + </output> </test> <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"/> + <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> <conditional name="input_mode"> <param name="input_select" value="protein"/> <param name="protein_input" value="enterococcus_faecalis.faa"/> @@ -306,12 +367,26 @@ <param name="print_node" value="true"/> <param name="name" value="test_5"/> </section> - <output name="amrfinderplus_report" value="test_5/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> - <output name="protein_output" value="test_5/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> + <output name="amrfinderplus_report" ftype="tabular"> + <assert_contents> + <has_n_columns n="24"/> + <has_n_lines n="8"/> + <has_text text="optrA"/> + <has_text text="IDOBJL_14770"/> + <has_text text="WP_063856080"/> + </assert_contents> + </output> + <output name="nucleotide_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="49"/> + <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/> + <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/> + </assert_contents> + </output> </test> <test expect_num_outputs="2"> <!-- TEST_6 protein input and prokka annotation --> <section name="input_option"> - <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> + <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> <conditional name="input_mode"> <param name="input_select" value="protein"/> <param name="protein_input" value="PROKKA_05252023.faa"/> @@ -319,24 +394,50 @@ <param name="annotation_format" value="prokka"/> </conditional> </section> - <output name="amrfinderplus_report" value="test_6/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> - <output name="protein_output" value="test_6/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> + <output name="amrfinderplus_report" ftype="tabular"> + <assert_contents> + <has_n_columns n="22"/> + <has_n_lines n="7"/> + <has_text text="FODBOAIN_02586"/> + <has_text text="WP_063856395"/> + </assert_contents> + </output> + <output name="protein_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="49"/> + <has_text text=">FODBOAIN_02586 optrA ABC-F type ribosomal protection protein OptrA"/> + <has_text text="YSNLLLLFSGIIVISWLVTLNVYKHSQRDF"/> + </assert_contents> + </output> </test> <test expect_num_outputs="2"> <!-- TEST_7 protein input and genbank default annotation --> <section name="input_option"> - <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> + <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> <conditional name="input_mode"> <param name="input_select" value="protein"/> <param name="protein_input" value="input_ncbi.faa"/> <param name="gff_annotation" value="annotation_ncbi.gff3"/> </conditional> </section> - <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"/> + <output name="amrfinderplus_report" ftype="tabular"> + <assert_contents> + <has_n_columns n="22"/> + <has_n_lines n="4"/> + <has_text text="blaOXA"/> + <has_text text="WP_063855540"/> + </assert_contents> + </output> + <output name="protein_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="17"/> + <has_text text=">blaOXA-436_partial blaOXA OXA-48 family class D beta-lactamase"/> + <has_text text="SSNPDAAPVSS"/> + </assert_contents> + </output> </test> <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"/> + <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> <conditional name="input_mode"> <param name="input_select" value="nucl_prot"/> <param name="protein_input" value="enterococcus_faecalis.faa"/> @@ -351,13 +452,32 @@ <param name="organism" value="Enterococcus_faecalis"/> </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="amrfinderplus_report" ftype="tabular"> + <assert_contents> + <has_n_columns n="22"/> + <has_n_lines n="8"/> + <has_text text="IDOBJL_14770"/> + <has_text text="WP_063856080"/> + </assert_contents> + </output> + <output name="nucleotide_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="143"/> + <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/> + <has_text text="CTTATCTGTATAG"/> + </assert_contents> + </output> + <output name="protein_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="37"/> + <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/> + <has_text text="QEAGAGMSLLNFT"/> + </assert_contents> + </output> </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"/> + <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> <conditional name="input_mode"> <param name="input_select" value="nucl_prot"/> <param name="protein_input" value="e_faecalis_rast.faa"/> @@ -380,10 +500,34 @@ <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"/> + <output name="amrfinderplus_report" ftype="tabular"> + <assert_contents> + <has_n_columns n="24"/> + <has_n_lines n="2"/> + <has_text text="MUPIROCIN"/> + <has_text text="WP_063854488"/> + </assert_contents> + </output> + <output name="nucleotide_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="40"/> + <has_text text=">contig00019:27227-29524 strand:+ mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/> + <has_text text="ATCAGTCGTGAAATAGAA"/> + </assert_contents> + </output> + <output name="protein_output" ftype="fasta"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + <output name="mutation_all_report" ftype="tabular"> + <assert_contents> + <has_n_columns n="24"/> + <has_n_lines n="5"/> + <has_text text="23S_GA375AG"/> + <has_text text="NZ_CP04"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[