--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ivar_getmasked.xml	Mon Mar 30 06:54:03 2020 -0400
@@ -0,0 +1,43 @@
+<tool id="ivar_getmasked" name="ivar getmasked" version="@VERSION@+galaxy0">
+    <description>Detect primer mismatches and get primer indices for the amplicon to be masked</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        ivar getmasked 
+        -i '$filtered_tsv' 
+        -b '$primers_bed'
+        -f '$primers_tsv'
+        -p masked_primers
+    ]]>    </command>
+    <inputs>
+        <param name="filtered_tsv" argument="-i" type="data" format="tabular,txt" label="Input filtered variants tsv generated from filtervariants"/>
+        <param name="primers_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
+        <param name="primers_tsv" argument="-f" type="data" format="tabular" label="Primer pair information file containing left and right primer names for the same amplicon"/>
+    </inputs>
+    <outputs>
+        <data name="masked" format="txt" label="${tool.name} on ${on_string} Output" from_work_dir="masked_primers.txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="filtered_tsv" value="zika/primers_Z52_consensus.tsv"/>
+            <param name="primers_bed" value="zika/db/zika_primers_consensus.bed"/>
+            <param name="primers_tsv" value="zika/db/pair_information.tsv"/>
+            <output name="masked" file="zika/primer_mismatchers_indices.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        iVar uses a .tsv file with variants to get the zero based indices (based on
+        the BED file) of mismatched primers. This command requires another .tsv file
+        with each line containing the left and right primer names separated by a
+        tab. This is used to get both the primers for an amplicon with a single
+        mismatched primer. The output is a text file with the zero based primer
+        indices delimited by a space. The output is written to a a text file using
+        the prefix provided.
+        
+        Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
+    ]]>    </help>
+    <expand macro="citations" />
+</tool>