--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lofreq_alnqual.xml	Tue Dec 17 17:26:09 2019 -0500
@@ -0,0 +1,98 @@
+<tool id="lofreq_alnqual" name="Add LoFreq alignment quality scores" version="@WRAPPER_VERSION@0">
+    <description>to aligned read SAM/BAM records</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @PREPARE_REF@
+        lofreq alnqual -b ${alnqual_choice.extended_baq} ${alnqual_choice.alnquals_to_use} $recompute_all '$reads' '$reference_fasta_fn' > '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" name="reads" format="bam" label="Reads" />
+        <expand macro="reference_interface" />
+        <expand macro="handle_alnqual" mode="Add" />
+        <param argument="-r" name="recompute_all" type="boolean" truevalue="-r" falsevalue=""
+        label="Overwrite exisitng values with newly computed ones" />
+    </inputs>
+    <outputs>
+        <data name="output" format="bam" label="${tool.name} to ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <output name="output" file="alnqual-out1.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <conditional name="alnqual_choice">
+                <param name="alnquals_to_use" value="-B" />
+            </conditional>
+            <output name="output" file="alnqual-out2.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <conditional name="alnqual_choice">
+                <param name="alnquals_to_use" value="-A" />
+            </conditional>
+            <output name="output" file="alnqual-out3.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <conditional name="alnqual_choice">
+                <param name="extended_baq" value="false" />
+            </conditional>
+            <output name="output" file="alnqual-out4.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <param name="recompute" value="true" />
+            <output name="output" file="alnqual-out5.bam" />
+        </test>
+    </tests>
+    <help><![CDATA[
+lofreq alnqual: add base- and indel-alignment qualities (BAQ, IDAQ) to
+aligned read records
+
+.. class:: infomark
+
+   **What it does**
+
+This tool can compute base- and/or indel-alignment quality scores for aligned
+reads in SAM/BAM format and store these scores under the custom tags ``lb``
+(for the base alignment qualities, ``ai`` (insertion alignment qualities) and
+``ad`` (deletion alignment qualities), which it will add to its output BAM.
+
+These tags and their scores can be reused by LoFreq call, which can
+incorporate them into its model for variant quality calculation.
+
+.. class:: warning
+
+   **Do not realign** your reads after adding alignment qualities to them since
+   the scores would not be updated in the process!
+
+Notes:
+
+- While LoFreq call can optionally calculate the exact same scores on the fly
+  if needed, having the scores added to the aligned read records is going to
+  save computation time with repeated variant calling from the same input data.
+
+- The base alignment quality scores have the same meaning as in samtools, but
+  are expressed as absolute scores, not as base quality offsets like with the
+  `BQ` tag generated by samtools.
+
+- `ai` and `ad` tags, if requested, will only be added to reads containing
+  insertions/deletions.
+    ]]></help>
+    <expand macro="citations" />
+</tool>