# HG changeset patch
# User stephenshank
# Date 1687969348 0
# Node ID 48a6ea2de0da07c64ee535243d384da81b46f7f7

planemo upload commit 3a0a853d0f21f2eac12b959d1eba7ee9fa289cc3-dirty

diff -r 000000000000 -r 48a6ea2de0da bamtocov.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtocov.xml	Wed Jun 28 16:22:28 2023 +0000
@@ -0,0 +1,49 @@
+<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>
diff -r 000000000000 -r 48a6ea2de0da regal.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/regal.xml	Wed Jun 28 16:22:28 2023 +0000
@@ -0,0 +1,41 @@
+<tool id="regal" name="Read-based evaluation of Genome Assemblies" version="1.0" profile="21.05">
+    <description>Assembly statistics from a BED coverage file</description>
+    <requirements>
+        <requirement type="package" version="0.0.1">assemblyqc</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+      regal -c $bed -a $ref -o $json -p $percentiles 
+        ]]>
+    </command>
+    <inputs>
+        <param argument="bed" type="data" format="bed" label="BED file" help="BED file containing coverage."/>
+        <param argument="ref" type="data" format="fasta" label="FASTA file" help="FASTA file of existing assembly."/>
+        <param argument="percentiles" type="text" label="Percentiles" help="Percentiles for assembly statistics (comma delimited)."/>
+    </inputs>
+    <outputs>
+        <data name="json" format="json" label="${tool.name} on ${on_string}: Assembly JSON"></data>
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+
+ .. class:: infomark
+
+**Purpose**
+
+Calculate some statistics associated to assembly quality.
+
+------
+
+ .. class:: infomark
+
+**Outputs**
+
+This tool generates a JSON file containing contiguous regions and assembly statistics based on the
+reads that were used to produce a given assembly.
+    ]]>
+    </help>
+    <citations>
+    </citations>
+</tool>
+