diff bicodon_counts_from_fasta.xml @ 0:e13169dca7c8 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bicodon_counts_from_fasta.xml	Mon Apr 11 20:36:48 2022 +0000
@@ -0,0 +1,99 @@
+<tool id="bicodon_counts_from_fasta" name="Get Codon and Bicodon frequency" version="@TOOL_VERSION@" profile="20.05">
+    <description>from FASTA files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <version_command>bicodon_counts_from_fasta.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        bicodon_counts_from_fasta.py
+            #if $ref.ref_source == 'cached':
+                --seq '${ref.ref_loc.fields.path}'
+            #elif $ref.ref_source == 'history':
+                --seq '${ref.ref_file}'
+            #end if
+
+            --taxid '$taxid'
+
+            --organelle '$organelle'
+
+            --division '$division'
+
+            --assembly '$assembly'
+
+            --species '$species'
+
+            --translation_table '$translation_table'
+
+            --codon_out '$codon_out'
+
+            --bicodon_out '$bicodon_out'
+    ]]></command>
+    <inputs>
+        <conditional name="ref">
+            <param name="ref_source" type="select" label="Source for Sequence Data">
+                <option value="cached">Locally cached FASTA</option>
+                <option value="history" selected="True">History dataset FASTA</option>
+            </param>
+            <when value="cached">
+                <param argument="--seq" name="ref_loc" type="select" label="Select FASTA nucleotide sequences">
+                    <options from_data_table="all_fasta"/>
+                </param>
+            </when>
+            <when value="history">
+                <param argument="--seq" name="ref_file" type="data" format="fasta" label="FASTA nucleotide sequences"/>
+            </when>
+        </conditional>
+        <param argument="--taxid" type="text" value="9606" label="Taxonomy ID to list in output" help="9606 is Homo sapiens (human)"/>
+        <param argument="--organelle" type="text" value="genomic" label="Organelle to list in output" help="genomic is default"/>
+        <param argument="--division" type="text" value="custom" label="Division to list in output" help="custom is default"/>
+        <param argument="--assembly" type="text" value="hg38" label="Assembly to list in output" help="hg38 is default"/>
+        <param argument="--species" type="text" value="Homo sapiens" label="Species to list in output" help="Homo sapiens is default"/>
+        <expand macro="translation_table_select_parameter"/>
+    </inputs>
+    <outputs>
+        <data name="codon_out" format="tabular" label="Get Codon and Bicodon frequency on ${on_string}: #if $ref.ref_source == 'cached' then $ref.ref_loc.fields.name else $ref.ref_file.name# codon usage output"/>
+        <data name="bicodon_out" format="tabular" label="Get Codon and Bicodon frequency on ${on_string}: #if $ref.ref_source == 'cached' then $ref.ref_loc.fields.name else $ref.ref_file.name# bicodon usage"/>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="ref">
+                <param name="ref_source" value="history"/>
+                <param name="ref_file" value="naltorfs_fasta_out.fasta" dbkey="hg38" ftype="fasta"/>
+            </conditional>
+            <param name="taxid" value="9606"/>
+            <param name="organelle" value="genomic"/>
+            <param name="division" value="custom"/>
+            <param name="assembly" value="hg38"/>
+            <param name="species" value="Homo sapiens"/>
+            <param name="translation_table" value="1"/>
+            <output name="codon_out" value="codon_out.tabular"/>
+            <output name="bicodon_out" value="bicodon_out.tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Calculate Codon and Bicodon (Codon Pair) usage frequency from FASTA files.
+
+Output is designed to mimic that from 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).
+
+Translation table identifiers are based upon NCBI standards (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).
+
+Example of CoCoPUTs style codon output, the majority of codons have been removed in this example, for brevity:
+
+  +-----------+-----------+-------+--------------+-----------+-------------------+-------+----------+-----+-----+-----+-----+-----+
+  | Division  | Assembly  | Taxid | Species      | Organelle | Translation Table | # CDS | # Codons | aaa | aac | aag | aat | ... |
+  +===========+===========+=======+==============+===========+===================+=======+==========+=====+=====+=====+=====+=====+
+  | custom    | hg38      | 9606  | Homo sapiens | genomic   | 1                 | 4     | 859      | 14  | 13  |  29 | 8   | ... |
+  +-----------+-----------+-------+--------------+-----------+-------------------+-------+----------+-----+-----+-----+-----+-----+
+
+Example of CoCoPUTs style bicodon output, 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>