diff bamtocov.xml @ 0:48a6ea2de0da draft default tip

planemo upload commit 3a0a853d0f21f2eac12b959d1eba7ee9fa289cc3-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtocov.xml	Wed Jun 28 16:22:28 2023 +0000
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+<tool id="bamtocov" name="BAM to Coverage" version="1.0" profile="21.05">
+    <description>Get a BED file of coverage from a BAM</description>
+    <requirements>
+        <requirement type="package" version="2.7.0">bamtocov</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        bamtocov '$bam' > '$bed'
+        ]]>
+    </command>
+    <inputs>
+        <param argument="bam" type="data" format="bam" label="BAM file" help="BAM file to get coverage from."/>
+    </inputs>
+    <outputs>
+        <data name="bed" format="bed" label="${tool.name} on ${on_string}: Coverage"></data>
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+
+ .. class:: infomark
+
+**Purpose**
+
+Calculate coverage from a BAM file.
+
+------
+
+ .. class:: infomark
+
+**Outputs**
+
+This tool generates a BED file containing coverage information from the associated BAM file.
+    ]]>
+    </help>
+    <citations>
+        <citation type="bibtex">
+          @article{birolo2022bamtocov,
+              title={BamToCov: an efficient toolkit for sequence coverage calculations},
+              author={Birolo, Giovanni and Telatin, Andrea},
+              journal={Bioinformatics},
+              volume={38},
+              number={9},
+              pages={2617--2618},
+              year={2022},
+              publisher={Oxford University Press}
+            }
+        </citation>
+    </citations>
+</tool>