[2] | 1 | <tool id="EMBOSS: trimest102" name="trimest" version="5.0.0">
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| 2 | <description>Trim poly-A tails off EST sequences</description>
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| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 4 | <command>trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
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| 5 | -auto</command>
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| 6 | <inputs>
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| 7 | <param format="fasta" name="input1" type="data">
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| 8 | <label>Sequences</label>
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| 9 | </param>
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| 10 | <param name="minlength" size="4" type="text" value="4">
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| 11 | <label>Minimum length that a poly-A (or poly-T) tail must have before it is removed</label>
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| 12 | </param>
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| 13 | <param name="mismatches" size="4" type="text" value="1">
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| 14 | <label>Number of fewer mismatched non-A bases in a poly-A tail</label>
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| 15 | </param>
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| 16 | <param name="reverse" type="select">
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| 17 | <label>Change the sequence to the forward sense when it is written out</label>
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| 18 | <option value="yes">Yes</option>
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| 19 | <option value="no">No</option>
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| 20 | </param>
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| 21 | <param name="tolower" type="select">
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| 22 | <label>Mask poly-A by converting to lowercase</label>
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| 23 | <option value="no">No</option>
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| 24 | <option value="yes">Yes</option>
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| 25 | </param>
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| 26 | <param name="fiveprime" type="select">
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| 27 | <label>Inspect 5' end of the sequence for poly-T tails</label>
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| 28 | <option value="yes">Yes</option>
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| 29 | <option value="no">No</option>
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| 30 | </param>
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| 31 | <param name="out_format1" type="select">
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| 32 | <label>Output Sequence File Format</label>
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| 33 | <option value="fasta">FASTA (m)</option>
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| 34 | <option value="acedb">ACeDB (m)</option>
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| 35 | <option value="asn1">ASN.1 (m)</option>
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| 36 | <option value="clustal">Clustal (m)</option>
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| 37 | <option value="codata">CODATA (m)</option>
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| 38 | <option value="embl">EMBL (m)</option>
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| 39 | <option value="fitch">Fitch (m)</option>
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| 40 | <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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| 41 | <option value="genbank">GENBANK (m)</option>
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| 42 | <option value="gff">GFF (m)</option>
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| 43 | <option value="hennig86">Hennig86 (m)</option>
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| 44 | <option value="ig">Intelligenetics (m)</option>
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| 45 | <option value="jackknifer">Jackknifer (m)</option>
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| 46 | <option value="jackknifernon">Jackknifernon (m)</option>
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| 47 | <option value="mega">Mega (m)</option>
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| 48 | <option value="meganon">Meganon (m)</option>
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| 49 | <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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| 50 | <option value="pir">NBRF (PIR) (m)</option>
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| 51 | <option value="ncbi">NCBI style FASTA (m)</option>
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| 52 | <option value="nexus">Nexus/PAUP (m)</option>
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| 53 | <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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| 54 | <option value="phylip">PHYLIP interleaved (m)</option>
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| 55 | <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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| 56 | <option value="selex">SELEX (m)</option>
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| 57 | <option value="staden">Staden (s)</option>
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| 58 | <option value="strider">DNA strider (m)</option>
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| 59 | <option value="swiss">SwisProt entry (m)</option>
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| 60 | <option value="text">Plain sequence (s)</option>
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| 61 | <option value="treecon">Treecon (m)</option>
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| 62 | </param>
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| 63 | </inputs>
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| 64 | <outputs>
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| 65 | <data format="fasta" name="out_file1" />
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| 66 | </outputs> |
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| 67 | <tests> |
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| 68 | <test> |
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| 69 | <param name="input1" value="2.fasta"/> |
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| 70 | <param name="minlength" value="4"/> |
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| 71 | <param name="mismatches" value="1"/> |
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| 72 | <param name="reverse" value="yes"/> |
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| 73 | <param name="tolower" value="no"/> |
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| 74 | <param name="fiveprime" value="yes"/> |
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| 75 | <param name="out_format1" value="fasta"/> |
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| 76 | <output name="out_file1" file="emboss_trimest_out.fasta"/> |
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| 77 | </test> |
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| 78 | </tests>
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| 79 | <code file="emboss_format_corrector.py" />
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| 80 | <help> |
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| 81 | |
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| 82 | .. class:: warningmark |
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| 83 | |
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| 84 | The input dataset needs to be sequences. |
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| 85 | |
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| 86 | ----- |
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| 87 | |
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| 88 | You can view the original documentation here_. |
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| 89 | |
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| 90 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimest.html |
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| 91 | </help> |
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| 92 | </tool> |
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