Fix amrfinderplus linter errors and quoting (#7939)

* amrfinderplus: fix linter error

* fix quotes

Author: bernt-matthias

tools/amrfinderplus/.lint_skip

@@ -13,7 +13,7 @@
         #*======================================
                     CPU option
         ======================================*#
-        --threads \${GALAXY_SLOTS:-1}
+        --threads "\${GALAXY_SLOTS:-1}"
         #*======================================
                     DATABASE
         ======================================*#
@@ -22,29 +22,29 @@
                     INPUT TYPE
         ======================================*#
         #if $input_option.input_mode.input_select == 'nucleotide'
-            --nucleotide $input_option.input_mode.nucleotide_input
+            --nucleotide '$input_option.input_mode.nucleotide_input'
             #if $input_option.input_mode.nucleotide_flank5_size > 0
                 --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
                 --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
             #end if
             --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
         #elif $input_option.input_mode.input_select == 'protein'
-            --protein $input_option.input_mode.protein_input
+            --protein '$input_option.input_mode.protein_input'
             #if $input_option.input_mode.gff_annotation
-                --gff $input_option.input_mode.gff_annotation
+                --gff '$input_option.input_mode.gff_annotation'
             #end if
             #if $input_option.input_mode.annotation_format
                 --annotation_format $input_option.input_mode.annotation_format
             #end if
             --protein_output 'amrfinderplus_protein_output.fasta'
         #else
-            --nucleotide $input_option.input_mode.nucleotide_input
+            --nucleotide '$input_option.input_mode.nucleotide_input'
             #if $input_option.input_mode.nucleotide_flank5_size and $input_option.input_mode.nucleotide_flank5_size > 0
                 --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
                 --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
             #end if
-            --protein $input_option.input_mode.protein_input
-            --gff $input_option.input_mode.gff_annotation
+            --protein '$input_option.input_mode.protein_input'
+            --gff '$input_option.input_mode.gff_annotation'
             --annotation_format $input_option.input_mode.annotation_format
             --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
             --protein_output 'amrfinderplus_protein_output.fasta'
@@ -147,8 +147,7 @@
                     <param argument="--report_common"  type="boolean" truevalue="--report_common" falsevalue=""
                     label="Report proteins common to a taxonomy group (need the plus and organism options)"/> 
                 </when>
-                <when value="">
-                </when>
+                <when value=""/>
             </conditional>
         </section>
             <!-- OPTIONS -->
@@ -185,9 +184,9 @@
                 <option value="33">33 Cephalodiscidae mitochondrial</option>
             </param>
             <param argument="--plus"  type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report"/>
-            <param argument="--report_all_equal"  type="boolean" truevalue="--report_all_equal" falsevalue="" label="Report all equally-scoring BLAST and HMM matches"/> 
-            <param argument="--print_node"  type="boolean" truevalue="--print_node" falsevalue="" label="print hierarchy node (family)"/> 
-            <param argument="--name"  type="text" label="First column name" help="Text to be added as the first column 'name' to all rows of the report"/> 
+            <param argument="--report_all_equal" type="boolean" truevalue="--report_all_equal" falsevalue="" label="Report all equally-scoring BLAST and HMM matches"/> 
+            <param argument="--print_node" type="boolean" truevalue="--print_node" falsevalue="" label="print hierarchy node (family)"/> 
+            <param argument="--name" type="text" label="First column name" help="Text to be added as the first column 'name' to all rows of the report"/> 
         </section>
     </inputs>
     <outputs>
@@ -256,7 +255,6 @@
                 <param name="report_all_equal" value="true"/>
                 <param name="print_node" value="true"/>
                 <param name="name" value="test_2"/>
-                <param name="log" value="true"/>
             </section>
             <output name="amrfinderplus_report" ftype="tabular">
                 <assert_contents>