Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_trimest.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="EMBOSS: trimest102" name="trimest" version="5.0.0"> | |
| 2 <description>Trim poly-A tails off EST sequences</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1 | |
| 5 -auto</command> | |
| 6 <inputs> | |
| 7 <param format="fasta" name="input1" type="data"> | |
| 8 <label>Sequences</label> | |
| 9 </param> | |
| 10 <param name="minlength" size="4" type="text" value="4"> | |
| 11 <label>Minimum length that a poly-A (or poly-T) tail must have before it is removed</label> | |
| 12 </param> | |
| 13 <param name="mismatches" size="4" type="text" value="1"> | |
| 14 <label>Number of fewer mismatched non-A bases in a poly-A tail</label> | |
| 15 </param> | |
| 16 <param name="reverse" type="select"> | |
| 17 <label>Change the sequence to the forward sense when it is written out</label> | |
| 18 <option value="yes">Yes</option> | |
| 19 <option value="no">No</option> | |
| 20 </param> | |
| 21 <param name="tolower" type="select"> | |
| 22 <label>Mask poly-A by converting to lowercase</label> | |
| 23 <option value="no">No</option> | |
| 24 <option value="yes">Yes</option> | |
| 25 </param> | |
| 26 <param name="fiveprime" type="select"> | |
| 27 <label>Inspect 5' end of the sequence for poly-T tails</label> | |
| 28 <option value="yes">Yes</option> | |
| 29 <option value="no">No</option> | |
| 30 </param> | |
| 31 <param name="out_format1" type="select"> | |
| 32 <label>Output Sequence File Format</label> | |
| 33 <option value="fasta">FASTA (m)</option> | |
| 34 <option value="acedb">ACeDB (m)</option> | |
| 35 <option value="asn1">ASN.1 (m)</option> | |
| 36 <option value="clustal">Clustal (m)</option> | |
| 37 <option value="codata">CODATA (m)</option> | |
| 38 <option value="embl">EMBL (m)</option> | |
| 39 <option value="fitch">Fitch (m)</option> | |
| 40 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option> | |
| 41 <option value="genbank">GENBANK (m)</option> | |
| 42 <option value="gff">GFF (m)</option> | |
| 43 <option value="hennig86">Hennig86 (m)</option> | |
| 44 <option value="ig">Intelligenetics (m)</option> | |
| 45 <option value="jackknifer">Jackknifer (m)</option> | |
| 46 <option value="jackknifernon">Jackknifernon (m)</option> | |
| 47 <option value="mega">Mega (m)</option> | |
| 48 <option value="meganon">Meganon (m)</option> | |
| 49 <option value="msf">Wisconsin Package GCG's MSF (m)</option> | |
| 50 <option value="pir">NBRF (PIR) (m)</option> | |
| 51 <option value="ncbi">NCBI style FASTA (m)</option> | |
| 52 <option value="nexus">Nexus/PAUP (m)</option> | |
| 53 <option value="nexusnon">Nexusnon/PAUPnon (m)</option> | |
| 54 <option value="phylip">PHYLIP interleaved (m)</option> | |
| 55 <option value="phylipnon">PHYLIP non-interleaved (m)</option> | |
| 56 <option value="selex">SELEX (m)</option> | |
| 57 <option value="staden">Staden (s)</option> | |
| 58 <option value="strider">DNA strider (m)</option> | |
| 59 <option value="swiss">SwisProt entry (m)</option> | |
| 60 <option value="text">Plain sequence (s)</option> | |
| 61 <option value="treecon">Treecon (m)</option> | |
| 62 </param> | |
| 63 </inputs> | |
| 64 <outputs> | |
| 65 <data format="fasta" name="out_file1" /> | |
| 66 </outputs> | |
| 67 <tests> | |
| 68 <test> | |
| 69 <param name="input1" value="2.fasta"/> | |
| 70 <param name="minlength" value="4"/> | |
| 71 <param name="mismatches" value="1"/> | |
| 72 <param name="reverse" value="yes"/> | |
| 73 <param name="tolower" value="no"/> | |
| 74 <param name="fiveprime" value="yes"/> | |
| 75 <param name="out_format1" value="fasta"/> | |
| 76 <output name="out_file1" file="emboss_trimest_out.fasta"/> | |
| 77 </test> | |
| 78 </tests> | |
| 79 <code file="emboss_format_corrector.py" /> | |
| 80 <help> | |
| 81 | |
| 82 .. class:: warningmark | |
| 83 | |
| 84 The input dataset needs to be sequences. | |
| 85 | |
| 86 ----- | |
| 87 | |
| 88 You can view the original documentation here_. | |
| 89 | |
| 90 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimest.html | |
| 91 </help> | |
| 92 </tool> |