--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ivar_removereads.xml	Mon Mar 30 07:13:18 2020 -0400
@@ -0,0 +1,45 @@
+<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy0">
+    <description>Remove reads from trimmed BAM file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_bam' sorted.bam &&
+        ln -s '$primer_index' primers.txt &&
+        ln -s '$input_bed' bed.bed &&
+        ivar removereads 
+        -i sorted.bam 
+        -p removed_reads.bam
+        -t primers.txt 
+        -b bed.bed
+    ]]>    </command>
+    <inputs>
+        <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
+        <param name="primer_index" argument="-t" type="data" format="txt" label="Text file with primer indices separated by spaces" help="This is the output of getmasked command"/>
+        <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
+    </inputs>
+    <outputs>
+        <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="removed_reads.bam"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
+            <param name="primer_index" value="zika/primer_mismatchers_indices.txt"/>
+            <param name="input_bed" value="zika/db/zika_primers.bed"/>
+            <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        This command accepts an aligned and sorted BAM file trimmed using ivar trim
+        and removes the reads corresponding to the supplied primer indices, which is
+        the output of ivar getmasked command. Under the hood, ivar trim adds the
+        zero based primer index (based on the BED file) to the BAM auxillary data for
+        every read. Hence, ivar removereads will only work on BAM files that have
+        been trimmed using ivar trim.
+        
+        Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
+    ]]>    </help>
+    <expand macro="citations" />
+</tool>