bamtools: linter fixes (#7061)

Author: bernt-matthias

tool_collections/bamtools/bamtools/.lint_skip

@@ -160,26 +160,38 @@
     <tests>
         <test>
             <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
-            <param name="analysis_type_selector" value="convert"/>
-            <param name="format_type_selector" value="pileup"/>
-            <param name="reference_source_selector" value="history" />
-            <param name="mapqual" value="true" />
-            <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="convert"/>
+                <conditional name="format_type">
+                    <param name="format_type_selector" value="pileup"/>
+                    <conditional name="reference_source">
+                        <param name="reference_source_selector" value="history" />
+                        <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
+                    </conditional>
+                    <param name="mapqual" value="true" />
+                </conditional>
+            </conditional>
             <output name="out_file1" file="bamtools-convert-pileup.pu" />
         </test>
         <test>
             <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
-            <param name="analysis_type_selector" value="count"/>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="count"/>
+            </conditional>
             <output name="out_file1" file="bamtools-count.tab" />
         </test>
         <test>
             <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
-            <param name="analysis_type_selector" value="coverage"/>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="coverage"/>
+            </conditional>
             <output name="out_file1" file="bamtools-coverage.tab" />
         </test>
         <test>
             <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
-            <param name="analysis_type_selector" value="header"/>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="header"/>
+            </conditional>
             <output name="out_file1" file="bamtools-header.txt" />
         </test>
     </tests>

tool_collections/bamtools/bamtools/bamtools.xml

@@ -193,8 +193,14 @@ $json.dumps( $config, indent=4 )
     <tests>
         <test>
             <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
-            <param name="bam_property_selector" value="mapQuality"/>
-            <param name="bam_property_value" value="&gt;20"/>
+            <repeat name="conditions">
+                <repeat name="filters">
+                    <conditional name="bam_property">
+                        <param name="bam_property_selector" value="mapQuality"/>
+                        <param name="bam_property_value" value="&gt;20"/>
+                    </conditional>
+                </repeat>
+            </repeat>
             <output name="out_file1" ftype="bam" file="bamtools-test1.bam" />
         </test>
     </tests>

tool_collections/bamtools/bamtools_filter/.lint_skip

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">2.5.2</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <xml name="xrefs">
         <xrefs>
             <xref type="bio.tools">bamtools</xref>