Mercurial > repos > iuc > amrfinderplus

diff amrfinderplus.xml @ 7:7844dbe4f8e2 draft default tip

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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
line wrap: on
line diff
--- 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[