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