--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/codon_freq_from_bicodons.xml	Mon Apr 11 20:34:25 2022 +0000
@@ -0,0 +1,68 @@
+<tool id="codon_freq_from_bicodons" name="Get Codon frequency" version="@TOOL_VERSION@" profile="20.05">
+    <description>from bicodons</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <version_command>codon_freq_from_bicodons.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        codon_freq_from_bicodons.py
+
+            --bicodons '$bicodons'
+
+            --taxid '$taxid'
+
+            --organelle '$organelle'
+
+            --out '$out'
+
+            --aa_out '$aa_out'
+
+            #if $write_log:
+                > '$log'
+            #end if
+    ]]></command>
+    <inputs>
+        <param argument="--bicodons" type="data" format="tabular" label="Bicondon rates input" help="Formatted like CoCoPUTs."/>
+        <param argument="--taxid" type="text" value="9606" label="Taxonomy ID of interest" help="9606 is Homo sapiens (human)"/>
+        <param argument="--organelle" type="text" value="genomic" label="Organelle of interest" help="genomic is default"/>
+        <param name="write_log" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Create log file"/>
+    </inputs>
+    <outputs>
+        <data name="out" format="tabular" label="Get Codon frequency on ${on_string}: codon counts"/>
+        <data name="aa_out" format="tabular" label="Get Codon frequency on ${on_string}: amino acid counts"/>
+        <data name="log" format="txt" label="Get Codon frequency on ${on_string}: log">
+            <filter>write_log</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="3">
+            <param name="bicodons" value="bicodon_out.tabular"/>
+            <param name="taxid" value="9606"/>
+            <param name="organelle" value="genomic"/>
+            <param name="write_log" value="true"/>
+            <output name="out" value="codon_freq_from_bicodon.tabular"/>
+            <output name="aa_out" value="aa_freq_from_bicodon.tabular"/>
+            <output name="log" value="codon_freq_from_bicodon_log.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Get Codon frequency from bicodons.
+
+Input format should match that provided by CoCoPUTs (https://dnahive.fda.gov/dna.cgi?cmd=codon_usage&id=537&mode=cocoputs; e.g. https://dnahive.fda.gov/dna.cgi?cmd=objFile&ids=537&filename=Refseq_Bicod.tsv&raw=1).
+
+Input row of interest is selected by the combination of the provided taxid and organelle.
+
+Translation table identifiers are based upon NCBI standards (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).
+
+Example of CoCoPUTs style bicodon input, the majority of bicodons (codon pairs) have been removed in this example, for brevity:
+
+  +-----------+-----------+-------+--------------+-----------+-------------------+-------+---------------+--------+--------+--------+--------+-----+
+  | Division  | Assembly  | Taxid | Species      | Organelle | Translation Table | # CDS | # Codon Pairs | aaaaaa | aaaaac | aaaaag | aaaaat | ... |
+  +===========+===========+=======+==============+===========+===================+=======+===============+========+========+========+========+=====+
+  | custom    | hg38      | 9606  | Homo sapiens | genomic   | 1                 | 4     | 859           | 0      | 0      |     0  | 1      | ... |
+  +-----------+-----------+-------+--------------+-----------+-------------------+-------+---------------+--------+--------+--------+--------+-----+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>