Mercurial > repos > iuc > codon_freq_from_bicodons

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
author iuc
date Mon, 11 Apr 2022 20:34:25 +0000
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60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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1 <tool id="codon_freq_from_bicodons" name="Get Codon frequency" version="@TOOL_VERSION@" profile="20.05">
60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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2 <description>from bicodons</description>
60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edam_ontology"/>
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7 <expand macro="requirements"/>
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8 <version_command>codon_freq_from_bicodons.py --version</version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 codon_freq_from_bicodons.py
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11
60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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12 --bicodons '$bicodons'
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60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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14 --taxid '$taxid'
60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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16 --organelle '$organelle'
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60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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18 --out '$out'
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60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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20 --aa_out '$aa_out'
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21
60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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22 #if $write_log:
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23 > '$log'
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24 #end if
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25 ]]></command>
60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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26 <inputs>
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27 <param argument="--bicodons" type="data" format="tabular" label="Bicondon rates input" help="Formatted like CoCoPUTs."/>
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28 <param argument="--taxid" type="text" value="9606" label="Taxonomy ID of interest" help="9606 is Homo sapiens (human)"/>
60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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29 <param argument="--organelle" type="text" value="genomic" label="Organelle of interest" help="genomic is default"/>
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30 <param name="write_log" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Create log file"/>
60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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31 </inputs>
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32 <outputs>
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33 <data name="out" format="tabular" label="Get Codon frequency on ${on_string}: codon counts"/>
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34 <data name="aa_out" format="tabular" label="Get Codon frequency on ${on_string}: amino acid counts"/>
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35 <data name="log" format="txt" label="Get Codon frequency on ${on_string}: log">
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36 <filter>write_log</filter>
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37 </data>
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38 </outputs>
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39 <tests>
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40 <test expect_num_outputs="3">
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41 <param name="bicodons" value="bicodon_out.tabular"/>
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42 <param name="taxid" value="9606"/>
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43 <param name="organelle" value="genomic"/>
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44 <param name="write_log" value="true"/>
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45 <output name="out" value="codon_freq_from_bicodon.tabular"/>
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46 <output name="aa_out" value="aa_freq_from_bicodon.tabular"/>
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47 <output name="log" value="codon_freq_from_bicodon_log.txt"/>
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48 </test>
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49 </tests>
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50 <help><![CDATA[
60e1f1caedad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
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51 Get Codon frequency from bicodons.
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52
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53 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).
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54
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55 Input row of interest is selected by the combination of the provided taxid and organelle.
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56
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57 Translation table identifiers are based upon NCBI standards (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).
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58
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59 Example of CoCoPUTs style bicodon input, the majority of bicodons (codon pairs) have been removed in this example, for brevity:
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60
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61 +-----------+-----------+-------+--------------+-----------+-------------------+-------+---------------+--------+--------+--------+--------+-----+
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62 | Division | Assembly | Taxid | Species | Organelle | Translation Table | # CDS | # Codon Pairs | aaaaaa | aaaaac | aaaaag | aaaaat | ... |
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63 +===========+===========+=======+==============+===========+===================+=======+===============+========+========+========+========+=====+
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64 | custom | hg38 | 9606 | Homo sapiens | genomic | 1 | 4 | 859 | 0 | 0 | 0 | 1 | ... |
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65 +-----------+-----------+-------+--------------+-----------+-------------------+-------+---------------+--------+--------+--------+--------+-----+
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66 ]]></help>
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67 <expand macro="citations"/>
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68 </tool>