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* Add seqkit translate * Update tools/seqkit/seqkit_translate.xml Change name into argument Co-authored-by: Björn Grüning <[email protected]> * change name by argument and delete help * Delete test file --------- Co-authored-by: Björn Grüning <[email protected]>
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| <tool id="seqkit_translate" name="SeqKit translate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||
| <description>Translate nucleotid sequence to protein sequence</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="bio_tools"/> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| seqkit translate | ||
| '$input' | ||
| -o '$output' | ||
| #if $translate_or_remove_unknown.selector == 'trimming': | ||
| $translate_or_remove_unknown.trim | ||
| #elif $translate_or_remove_unknown.selector == 'translate': | ||
| $translate_or_remove_unknown.allow_unknown_codon | ||
| #end if | ||
| $append_frame | ||
| $clean | ||
| #if $frame | ||
| -f '$frame' | ||
| #end if | ||
| $init_codon_as_M | ||
| #if $transl_table | ||
| -T '$transl_table' | ||
| #end if | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/> | ||
| <param argument="--frame" type="select" multiple="true" label="Frame(s) to translate" > | ||
| <option value="1" selected="true">1 (default)</option> | ||
| <option value="2" selected="false">2</option> | ||
| <option value="3" selected="false">3</option> | ||
| <option value="-1" selected="false">-1</option> | ||
| <option value="-2" selected="false">-2</option> | ||
| <option value="-3" selected="false">-3</option> | ||
| <option value="6" selected="false">All 6 frames</option> | ||
| </param> | ||
| <param argument="--append-frame" type="boolean" truevalue="--append-frame" falsevalue="" checked="false" label="Append frame information to sequence ID ?" /> | ||
| <param argument="--transl-table" type="select" label="Translate table / genetic code to use" > | ||
| <option value="1" selected="true">1: The Standard Code (default)</option> | ||
| <option value="2" selected="false">2: The Vertebrate Mitochondrial Code</option> | ||
| <option value="3" selected="false">3: The Yeast Mitochondrial Code</option> | ||
| <option value="4" selected="false">4: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | ||
| <option value="5" selected="false">5: The Invertebrate Mitochondrial Code</option> | ||
| <option value="6" selected="false">6: The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> | ||
| <option value="9" selected="false">9: The Echinoderm and Flatworm Mitochondrial Code</option> | ||
| <option value="10" selected="false">10: The Euplotid Nuclear Code</option> | ||
| <option value="11" selected="false">11: The Bacterial, Archaeal and Plant Plastid Code</option> | ||
| <option value="12" selected="false">12: The Alternative Yeast Nuclear Code</option> | ||
| <option value="13" selected="false">13: The Ascidian Mitochondrial Code</option> | ||
| <option value="14" selected="false">14: The Alternative Flatworm Mitochondrial Code</option> | ||
| <option value="16" selected="false">16: Chlorophycean Mitochondrial Code</option> | ||
| <option value="21" selected="false">21: Trematode Mitochondrial Code</option> | ||
| <option value="22" selected="false">22: Scenedesmus obliquus Mitochondrial Code</option> | ||
| <option value="23" selected="false">23: Thraustochytrium Mitochondrial Code</option> | ||
| <option value="24" selected="false">24: Pterobranchia Mitochondrial Code</option> | ||
| <option value="25" selected="false">25: Candidate Division SR1 and Gracilibacteria Code</option> | ||
| <option value="26" selected="false">26: Pachysolen tannophilus Nuclear Code</option> | ||
| <option value="27" selected="false">27: Karyorelict Nuclear</option> | ||
| <option value="28" selected="false">28: Condylostoma Nuclear</option> | ||
| <option value="29" selected="false">29: Mesodinium Nuclear</option> | ||
| <option value="30" selected="false">30: Peritrich Nuclear</option> | ||
| <option value="31" selected="false">31: Blastocrithidia Nuclear</option> | ||
| </param> | ||
| <param argument="--clean" type="boolean" truevalue="--clean" falsevalue="" checked="false" label="Change all STOP codon positions from the '*' character to 'X' (an unknown residue) ?" /> | ||
| <conditional name="translate_or_remove_unknown" > | ||
| <param name="selector" type="select" label="Translate or remove unknown code ?" > | ||
| <option value="trimming">Remove all 'X' and '*' characters</option> | ||
| <option value="translate">Translate unknown code to 'X'</option> | ||
| </param> | ||
| <when value="trimming"> | ||
| <param argument="--trim" type="boolean" truevalue="--trim" falsevalue="" checked="false" label="Remove all 'X' and '*' characters from the right end of the translation" /> | ||
| </when> | ||
| <when value="translate"> | ||
| <param argument="--allow-unknown-codon" type="boolean" truevalue="--allow-unknown-codon" falsevalue="" checked="false" label="Translate unknown code to 'X' ?" /> | ||
| </when> | ||
| </conditional> | ||
| <param argument="--init-codon-as-M" type="boolean" truevalue="--init-codon-as-M" falsevalue="" checked="false" label="Translate initial codon at beginning to 'M'" /> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format_source="input" label="${input.name} translate (${tool.name})"/> | ||
| </outputs> | ||
| <tests> | ||
| <!-- 1. fastq --> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/> | ||
| <output decompress="true" name="output" file="translate_output3.fastq.gz" ftype="fastqsanger.gz"/> | ||
| </test> | ||
| <!-- 2. fasta --> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/> | ||
| <conditional name="translate_or_remove_unknown"> | ||
| <param name="allow_unknown_codon" value="true"/> | ||
| </conditional> | ||
| <param name="append_frame" value="true"/> | ||
| <param name="clean" value="true"/> | ||
| <param name="frame" value="2,3" /> | ||
| <param name="init_codon_as_M" value="true" /> | ||
| <param name="transl_table" value="3" /> | ||
| <output decompress="true" name="output" file="translate_output1.fasta.gz" ftype="fasta.gz"/> | ||
| </test> | ||
| <!-- 3. fastq + trim --> | ||
| <test expect_num_outputs="1"> | ||
| <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/> | ||
| <conditional name="translate_or_remove_unknown"> | ||
| <param name="trim" value="true" /> | ||
| </conditional> | ||
| <output decompress="true" name="output" file="translate_output2.fastq.gz" ftype="fastqsanger.gz"/> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| **What it does** | ||
|
|
||
| Translate DNA/RNA to protein sequence (supporting ambiguous bases) | ||
|
|
||
| </help> | ||
| <expand macro="citations"/> | ||
| </tool> |
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