--- a/coverageBed.xml	Thu Mar 02 08:52:08 2023 +0000
+++ b/coverageBed.xml	Sat May 18 23:28:38 2024 +0000
@@ -1,13 +1,13 @@
-<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="bio_tools" />
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
-        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
     </expand>
-    <expand macro="stdio" />
+    <expand macro="stdio"/>
     <command><![CDATA[
 bedtools coverage
 $d
@@ -41,95 +41,83 @@
 > '$output'
     ]]></command>
     <inputs>
-        <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
+        <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
         <conditional name="reduce_or_iterate">
             <param name="reduce_or_iterate_selector" type="select" label="Combined or separate output files">
                 <option value="iterate" selected="true">One output file per 'input B' file</option>
                 <option value="reduce">Single output containing results for all 'input B' files</option>
             </param>
             <when value="iterate">
-                <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@"
-                       label="File B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
+                <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
             </when>
             <when value="reduce">
-                <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" multiple="true"
-                       label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
+                <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" multiple="true"/>
             </when>
         </conditional>
-        <expand macro="split" />
-        <param name="strandedness" argument="-s" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
-            help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand"/>
-        <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
-            label="Report the depth at each position in each A feature"
-            help="Positions reported are one based. Each position and depth follow the complete B feature" />
-        <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false"
-            label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
-            help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth" />
-        <param name="mean" argument="-mean" type="boolean" label="Mean depth" truevalue="-mean" falsevalue="" checked="false"
-            help="Report the mean depth of all positions in each A feature."/>
-        <expand macro="overlap" name="overlap_a" />
-        <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" />
-        <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
-            label="Require that the fraction overlap be reciprocal for A AND B."
-            help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B" />
-        <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
-            label="Require that the minimum fraction be satisfied for A OR B."
-            help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of  B is covered. Without -e, both fractions would have to be satisfied" />
+        <expand macro="split"/>
+        <param name="strandedness" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness" help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand"/>
+        <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" label="Report the depth at each position in each A feature" help="Positions reported are one based. Each position and depth follow the complete B feature"/>
+        <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false" label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A" help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth"/>
+        <param argument="-mean" type="boolean" truevalue="-mean" falsevalue="" checked="false" label="Mean depth" help="Report the mean depth of all positions in each A feature."/>
+        <expand macro="overlap" name="overlap_a"/>
+        <expand macro="overlap" name="overlap_b" argument="-F" fracof="B"/>
+        <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Require that the fraction overlap be reciprocal for A AND B." help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B"/>
+        <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Require that the minimum fraction be satisfied for A OR B." help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of  B is covered. Without -e, both fractions would have to be satisfied"/>
         <!-- -sorted -g  -->
-        <expand macro="sorted" />
+        <expand macro="sorted"/>
     </inputs>
     <outputs>
         <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
     </outputs>
     <tests>
         <test>
-            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
-            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
-            <output name="output" file="coverageBed_result1.bed" ftype="bed" />
+            <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
+            <param name="inputB" value="coverageBedB.bed" ftype="bed"/>
+            <output name="output" file="coverageBed_result1.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="multiCov1.bed" ftype="bed" />
-            <param name="inputB" value="srma_in3.bam" ftype="bam" />
+            <param name="inputA" value="multiCov1.bed" ftype="bed"/>
+            <param name="inputB" value="srma_in3.bam" ftype="bam"/>
             <param name="sorted" value="true"/>
-            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
+            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="multiCov1.bed" ftype="bed" />
-            <param name="reduce_or_iterate_selector" value="reduce" />
-            <param name="inputB" value="srma_in3.bam" ftype="bam" />
+            <param name="inputA" value="multiCov1.bed" ftype="bed"/>
+            <param name="reduce_or_iterate_selector" value="reduce"/>
+            <param name="inputB" value="srma_in3.bam" ftype="bam"/>
             <param name="sorted" value="true"/>
-            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
+            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
-            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
-            <param name="overlap_b" value="1"  />
-            <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />
+            <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
+            <param name="inputB" value="coverageBedB.bed" ftype="bed"/>
+            <param name="overlap_b" value="1"/>
+            <output name="output" file="coverageBed_result2_F1.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
-            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
-            <param name="overlap_a" value="1E-5"  />
-            <param name="reciprocal_overlap" value="true"  />
-            <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
+            <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
+            <param name="inputB" value="coverageBedB.bed" ftype="bed"/>
+            <param name="overlap_a" value="1E-5"/>
+            <param name="reciprocal_overlap" value="true"/>
+            <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="multiCov1.bed" ftype="bed" />
-            <param name="reduce_or_iterate_selector" value="reduce" />
-            <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam" />
+            <param name="inputA" value="multiCov1.bed" ftype="bed"/>
+            <param name="reduce_or_iterate_selector" value="reduce"/>
+            <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam"/>
             <param name="sorted" value="true"/>
-            <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed" />
+            <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
-            <param name="inputB" value="coverageBed.bam" ftype="bam" />
-            <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
+            <param name="inputA" value="coverageBedA2.bed" ftype="bed"/>
+            <param name="inputB" value="coverageBed.bam" ftype="bam"/>
+            <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
-            <param name="inputB" value="coverageBed.bam" ftype="bam" />
+            <param name="inputA" value="coverageBedA2.bed" ftype="bed"/>
+            <param name="inputB" value="coverageBed.bam" ftype="bam"/>
             <param name="mean" value="true"/>
-            <output name="output" file="mean_coverage.bed" ftype="bed" />
+            <output name="output" file="mean_coverage.bed" ftype="bed"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -155,5 +143,5 @@
 
 @REFERENCES@
     ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>