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87 lines
3.9 KiB
XML
87 lines
3.9 KiB
XML
<tool id="EMBOSSchecktrans9" name="checktrans">
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<description>Reports STOP codons and ORF statistics of a protein</description>
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<command>checktrans -sequence $input1 -outfile $out_file1 -outseq $out_file2 -osformat3 $out_format2 -outfeat $out_file3 -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>On query</label>
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</param>
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<param name="orfml" size="4" type="text" value="100">
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<label>Minimum ORF Length to report</label>
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</param>
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<param name="addlast" type="select">
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<label>An asterisk in the protein sequence indicates the position of a STOP codon. Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there
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is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs</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_format2" 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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<param name="out_format3" type="select">
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<label>Output Feature File Format</label>
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<option value="gff">GFF</option>
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<option value="embl">EMBL</option>
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<option value="swiss">SwissProt</option>
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</param>
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</inputs>
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<outputs>
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<data format="checktrans" name="out_file1" />
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<data format="fasta" name="out_file2" />
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<data format="gff" name="out_file3" />
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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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<param name="orfml" value="100"/>
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<param name="addlast" value="yes"/>
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<param name="out_format2" value="fasta"/>
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<param name="out_format3" value="gff"/>
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<output name="out_file1" file="emboss_checktrans_out1.txt"/>
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<output name="out_file2" file="emboss_checktrans_out2.fasta"/>
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<output name="out_file3" file="emboss_checktrans_out3.gff"/>
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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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.. class:: warningmark
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The input dataset needs to be sequences.
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-----
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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/checktrans.html
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</help>
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</tool>
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