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74 lines
3.2 KiB
XML
74 lines
3.2 KiB
XML
<tool id="EMBOSS: coderet13" name="coderet" version="5.0.0">
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<description>Extract CDS, mRNA and translations from feature tables</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<!-- <command>coderet -seqall $input1 -outfile $out_file1 -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
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<command>coderet -seqall $input1 -outfile $out_file1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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<label>On query</label>
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</param>
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<!--
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<param name="cds" type="boolean" truevalue="yes" falsevalue="no" checked="true">
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<label>Extract CDS sequences</label>
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</param>
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<param name="mrna" type="select">
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<label>Extract mRNA sequences</label>
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<option value="yes">Yes</option>
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<option value="no">No</option>
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</param>
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<param name="translation" type="select">
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<label>Extract translated sequences</label>
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<option value="yes">Yes</option>
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<option value="no">No</option>
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</param>
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<param name="out_format1" type="select">
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<label>Output Sequence File Format</label>
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<option value="fasta">FASTA (m)</option>
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<option value="acedb">ACeDB (m)</option>
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<option value="asn1">ASN.1 (m)</option>
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<option value="clustal">Clustal (m)</option>
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<option value="codata">CODATA (m)</option>
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<option value="embl">EMBL (m)</option>
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<option value="fitch">Fitch (m)</option>
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<option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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<option value="genbank">GENBANK (m)</option>
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<option value="gff">GFF (m)</option>
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<option value="hennig86">Hennig86 (m)</option>
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<option value="ig">Intelligenetics (m)</option>
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<option value="jackknifer">Jackknifer (m)</option>
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<option value="jackknifernon">Jackknifernon (m)</option>
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<option value="mega">Mega (m)</option>
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<option value="meganon">Meganon (m)</option>
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<option value="msf">Wisconsin Package GCG's MSF (m)</option>
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<option value="pir">NBRF (PIR) (m)</option>
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<option value="ncbi">NCBI style FASTA (m)</option>
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<option value="nexus">Nexus/PAUP (m)</option>
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<option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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<option value="phylip">PHYLIP interleaved (m)</option>
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<option value="phylipnon">PHYLIP non-interleaved (m)</option>
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<option value="selex">SELEX (m)</option>
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<option value="staden">Staden (s)</option>
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<option value="strider">DNA strider (m)</option>
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<option value="swiss">SwisProt entry (m)</option>
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<option value="text">Plain sequence (s)</option>
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<option value="treecon">Treecon (m)</option>
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</param>
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-->
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</inputs>
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<outputs>
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<data format="coderet" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="2.fasta"/>
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<output name="out_file1" file="emboss_coderet_out.coderet"/>
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</test>
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</tests>
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<code file="emboss_format_corrector.py" />
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<help>
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/coderet.html
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</help>
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</tool>
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