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80 lines
3.4 KiB
XML
80 lines
3.4 KiB
XML
<tool id="EMBOSS: trimest102" name="trimest">
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<description>Trim poly-A tails off EST sequences</description>
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<command>trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
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-auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>Sequences</label>
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</param>
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<param name="minlength" size="4" type="text" value="4">
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<label>Minimum length that a poly-A (or poly-T) tail must have before it is removed</label>
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</param>
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<param name="mismatches" size="4" type="text" value="1">
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<label>Number of fewer mismatched non-A bases in a poly-A tail</label>
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</param>
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<param name="reverse" type="select">
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<label>Change the sequence to the forward sense when it is written out</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="tolower" type="select">
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<label>Mask poly-A by converting to lowercase</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="fiveprime" type="select">
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<label>Inspect 5' end of the sequence for poly-T tails</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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</inputs>
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<outputs>
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<data format="fasta" name="out_file1" />
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</outputs>
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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/4.0/emboss/apps/trimest.html
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</help>
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</tool>
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