--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_coverage.xml	Tue Sep 28 15:10:16 2021 +0000
@@ -0,0 +1,126 @@
+<tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <description>computes the depth at each position or region</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @PREPARE_IDX@
+        samtools coverage
+
+            #if $condition_input.input_pooling == "Yes":
+                ${ ' '.join( [ "'%s'" %  $x for $x in $condition_input.input] ) }
+            #else
+                '$condition_input.input'
+            #end if
+
+            -l $additional_options.min_read_length
+            -q $additional_options.min_mq
+            -Q $additional_options.min_bq
+
+            #set $filter = $additional_options.required_flags
+            @FLAGS@
+            -rf $flags
+
+            #set $filter = $additional_options.skipped_flags
+            @FLAGS@
+            -ff $flags
+
+            #if $condition_histogram.histogram_select == "yes"
+                -m
+                -w $condition_histogram.n_bins
+                #if $condition_histogram.region != "":
+                    -r '$condition_histogram.region'
+                #end if
+            #end if
+
+            -o '$output'
+    ]]></command>
+    <inputs>
+        <conditional name="condition_input">
+            <param name="input_pooling" type="select" label="Are you pooling bam files?" help="Calculate the coverage for multiple bam files" >
+                <option value="No" selected="True">No</option>
+                <option value="Yes">Yes</option>
+            </param>
+            <when value="No" >
+                <param name="input" type="data" format="bam" multiple="true" label="BAM file"/>
+            </when>
+            <when value="Yes">
+                <param name="input" type="data" format="bam" multiple="true" label="BAM files to be pooled"/>
+            </when>
+        </conditional>
+
+        <section name="additional_options" title="Additional Options" expanded="true">
+            <param name="min_read_length" argument="-l" type="integer" min="0" value="0" label="Minimum read length" help="Ignore reads shorter than INT base pairs (Default = 0)" />
+            <param name="min_mq" argument="-q" type="integer" min="0" value="0" label="Minimum mapping quality" help="Minimum mapping quality for an alignment to be used (Default = 0)" />
+            <param name="min_bq" argument="-Q" type="integer" min="0" value="0" label="Minimum base quality" help="Minimum base quality for a base to be considered (Default = 0)" />
+
+            <param name="required_flags" argument="--rf" type="select" multiple="True" label="Require that these flags are set">
+                <expand macro="flag_options" />
+            </param>
+
+            <param name="skipped_flags" argument="--ff" type="select" multiple="True" label="Exclude reads with any of the following flags set">
+                <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
+            </param>
+        </section>
+
+        <conditional name="condition_histogram">
+            <param name="histogram_select" argument="-m" type="select" label="Histogram" help="Show histogram instead of tabular output">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param name="n_bins" argument="-w" type="integer" min="1" value="100" label="Number of bins in histogram" help="Number of bins in histogram" />
+                <param name="region" argument="-r" type="text" value="" label="Show specified region" help="Show specified region. Format: chr:start-end." />
+            </when>
+            <when value="no" />
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="test_1.bam" ftype="bam" />
+            <output name="output" file="results_1.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input" value="test_1.bam" ftype="bam" />
+            <param name="histogram_select" value="yes" />
+            <param name="n_bins" value="50" />
+            <output name="output" file="results_2.txt" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input_pooling" value="Yes" />
+            <param name="input" value="test_1.bam,test_2.bam" ftype="bam" />
+            <param name="histogram_select" value="yes" />
+            <param name="n_bins" value="100" />
+            <output name="output" file="results_3.txt" ftype="tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool runs the ``samtools coverage`` command.
+
+Computes the depth at each position or region and draws an ASCII-art histogram or tabulated text. If you select to pool the bam files, then it calculates coverage for the combined files.
+
+The tabulated form uses the following headings:
+
+- rname	Reference name / chromosome
+- startpos	Start position
+- endpos	End position (or sequence length)
+- numreads	Number reads aligned to the region (after filtering)
+- covbases	Number of covered bases with depth >= 1
+- coverage	Proportion of covered bases [0..1]
+- meandepth	Mean depth of coverage
+- meanbaseq	Mean baseQ in covered region
+- meanmapq	Mean mapQ of selected reads
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>