Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_est2genome.xml @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| 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: est2genome32" name="est2genome" version="5.0.0"> | |
| 2 <description>Align EST and genomic DNA sequences</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty | |
| 5 $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command> | |
| 6 <inputs> | |
| 7 <param format="fasta" name="input1" type="data"> | |
| 8 <label>EST sequence(s)</label> | |
| 9 </param> | |
| 10 <param format="data" name="input2" type="data"> | |
| 11 <label>Genomic sequence</label> | |
| 12 </param> | |
| 13 <param name="match" size="4" type="text" value="1"> | |
| 14 <label>Score for matching two bases</label> | |
| 15 </param> | |
| 16 <param name="mismatch" size="4" type="text" value="1"> | |
| 17 <label>Cost for mismatching two bases</label> | |
| 18 </param> | |
| 19 <param name="gappenalty" size="4" type="text" value="2"> | |
| 20 <label>Cost for deleting a single base in either sequence, excluding introns</label> | |
| 21 </param> | |
| 22 <param name="intronpenalty" size="4" type="text" value="40"> | |
| 23 <label>Cost for an intron, independent of length</label> | |
| 24 </param> | |
| 25 <param name="splicepenalty" size="4" type="text" value="20"> | |
| 26 <label>Cost for an intron, independent of length and starting/ending on donor-acceptor sites</label> | |
| 27 </param> | |
| 28 <param name="minscore" size="4" type="text" value="30"> | |
| 29 <label>Exclude alignments with scores below this threshold score</label> | |
| 30 </param> | |
| 31 <param name="reverse" type="select"> | |
| 32 <label>Reverse the orientation of the EST sequence</label> | |
| 33 <option value="no">No</option> | |
| 34 <option value="yes">Yes</option> | |
| 35 </param> | |
| 36 <param name="splice" type="select"> | |
| 37 <label>Use donor and acceptor splice sites</label> | |
| 38 <option value="yes">Yes</option> | |
| 39 <option value="no">No</option> | |
| 40 </param> | |
| 41 <param name="mode" type="select"> | |
| 42 <label>Comparison mode</label> | |
| 43 <option value="both">Both strands</option> | |
| 44 <option value="forward">Forward strand only</option> | |
| 45 <option value="reverse">Reverse strand only</option> | |
| 46 </param> | |
| 47 <param name="best" type="select"> | |
| 48 <label>Only best comparisons</label> | |
| 49 <option value="yes">Yes</option> | |
| 50 <option value="no">No</option> | |
| 51 </param> | |
| 52 <param name="shuffle" size="4" type="text" value="0"> | |
| 53 <label>Shuffle</label> | |
| 54 </param> | |
| 55 <param name="seed" size="4" type="text" value="20825"> | |
| 56 <label>Random number seed</label> | |
| 57 </param> | |
| 58 <param name="align" type="select"> | |
| 59 <label>Show the alignment</label> | |
| 60 <option value="no">No</option> | |
| 61 <option value="yes">Yes</option> | |
| 62 </param> | |
| 63 <param name="width" size="4" type="text" value="50"> | |
| 64 <label>Alignment width</label> | |
| 65 </param> | |
| 66 </inputs> | |
| 67 <outputs> | |
| 68 <data format="est2genome" name="out_file1" /> | |
| 69 </outputs> | |
| 70 <tests> | |
| 71 <test> | |
| 72 <param name="input1" value="2.fasta"/> | |
| 73 <param name="input2" value="1.fasta"/> | |
| 74 <param name="match" value="1"/> | |
| 75 <param name="mismatch" value="1"/> | |
| 76 <param name="match" value="1"/> | |
| 77 <param name="gappenalty" value="2"/> | |
| 78 <param name="intronpenalty" value="40"/> | |
| 79 <param name="splicepenalty" value="20"/> | |
| 80 <param name="minscore" value="30"/> | |
| 81 <param name="reverse" value="no"/> | |
| 82 <param name="splice" value="yes"/> | |
| 83 <param name="mode" value="both"/> | |
| 84 <param name="best" value="yes"/> | |
| 85 <param name="shuffle" value="0"/> | |
| 86 <param name="seed" value="20825"/> | |
| 87 <param name="align" value="no"/> | |
| 88 <param name="width" value="50"/> | |
| 89 <output name="out_file1" file="emboss_est2genome_out.est2genome"/> | |
| 90 </test> | |
| 91 </tests> | |
| 92 <help> | |
| 93 .. class:: warningmark | |
| 94 | |
| 95 The input dataset needs to be sequences. | |
| 96 | |
| 97 ----- | |
| 98 | |
| 99 You can view the original documentation here_. | |
| 100 | |
| 101 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html | |
| 102 </help> | |
| 103 </tool> |