Mercurial > repos > devteam > emboss_5
comparison emboss_msbar.xml @ 10:d49956b87f7e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
| author | iuc |
|---|---|
| date | Wed, 08 Feb 2017 12:42:22 -0500 |
| parents | |
| children | 8992d258e42f |
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| 9:511429456d3c | 10:d49956b87f7e |
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| 1 <tool id="EMBOSS: msbar55" name="msbar" version="5.0.0.1"> | |
| 2 <description>Mutate sequence beyond all recognition</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <code file="emboss_format_corrector.py" /> | |
| 8 <command>msbar -sequence '$input1' -outseq '$out_file1' -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1 | |
| 9 -auto</command> | |
| 10 <inputs> | |
| 11 <param name="input1" type="data" format="fasta" label="Sequence 1" /> | |
| 12 <param name="count" type="integer" value="1" label="Number of times to perform the mutation operations" /> | |
| 13 <param name="point" type="select" label="Types of point mutations to perform"> | |
| 14 <option value="0">None</option> | |
| 15 <option value="1">Any of the following</option> | |
| 16 <option value="2">Insertions</option> | |
| 17 <option value="3">Deletions</option> | |
| 18 <option value="4">Changes</option> | |
| 19 <option value="5">Duplications</option> | |
| 20 <option value="6">Moves</option> | |
| 21 </param> | |
| 22 <param name="block" type="select" label="Types of block mutations to perform"> | |
| 23 <option value="0">None</option> | |
| 24 <option value="1">Any of the following</option> | |
| 25 <option value="2">Insertions</option> | |
| 26 <option value="3">Deletions</option> | |
| 27 <option value="4">Changes</option> | |
| 28 <option value="5">Duplications</option> | |
| 29 <option value="6">Moves</option> | |
| 30 </param> | |
| 31 <param name="codon" type="select" label="Types of codon mutations to perform" help="These are only done if the sequence is nucleic"> | |
| 32 <option value="0">None</option> | |
| 33 <option value="1">Any of the following</option> | |
| 34 <option value="2">Insertions</option> | |
| 35 <option value="3">Deletions</option> | |
| 36 <option value="4">Changes</option> | |
| 37 <option value="5">Duplications</option> | |
| 38 <option value="6">Moves</option> | |
| 39 </param> | |
| 40 <param name="inframe" type="select" label="Do 'codon' and 'block' operations in frame"> | |
| 41 <option value="no">No</option> | |
| 42 <option value="yes">Yes</option> | |
| 43 </param> | |
| 44 <param name="minimum" type="integer" value="1" label="Minimum size for a block mutation" /> | |
| 45 <param name="maximum" type="integer" value="10" label="Maximum size for a block mutation" /> | |
| 46 <param name="out_format1" type="select" label="Output sequence file format"> | |
| 47 <option value="fasta">FASTA (m)</option> | |
| 48 <option value="acedb">ACeDB (m)</option> | |
| 49 <option value="asn1">ASN.1 (m)</option> | |
| 50 <option value="clustal">Clustal (m)</option> | |
| 51 <option value="codata">CODATA (m)</option> | |
| 52 <option value="embl">EMBL (m)</option> | |
| 53 <option value="fitch">Fitch (m)</option> | |
| 54 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option> | |
| 55 <option value="genbank">GENBANK (m)</option> | |
| 56 <option value="gff">GFF (m)</option> | |
| 57 <option value="hennig86">Hennig86 (m)</option> | |
| 58 <option value="ig">Intelligenetics (m)</option> | |
| 59 <option value="jackknifer">Jackknifer (m)</option> | |
| 60 <option value="jackknifernon">Jackknifernon (m)</option> | |
| 61 <option value="mega">Mega (m)</option> | |
| 62 <option value="meganon">Meganon (m)</option> | |
| 63 <option value="msf">Wisconsin Package GCG's MSF (m)</option> | |
| 64 <option value="pir">NBRF (PIR) (m)</option> | |
| 65 <option value="ncbi">NCBI style FASTA (m)</option> | |
| 66 <option value="nexus">Nexus/PAUP (m)</option> | |
| 67 <option value="nexusnon">Nexusnon/PAUPnon (m)</option> | |
| 68 <option value="phylip">PHYLIP interleaved (m)</option> | |
| 69 <option value="phylipnon">PHYLIP non-interleaved (m)</option> | |
| 70 <option value="selex">SELEX (m)</option> | |
| 71 <option value="staden">Staden (s)</option> | |
| 72 <option value="strider">DNA strider (m)</option> | |
| 73 <option value="swiss">SwisProt entry (m)</option> | |
| 74 <option value="text">Plain sequence (s)</option> | |
| 75 <option value="treecon">Treecon (m)</option> | |
| 76 </param> | |
| 77 </inputs> | |
| 78 <outputs> | |
| 79 <data name="out_file1" format="fasta" /> | |
| 80 </outputs> | |
| 81 <tests> | |
| 82 <test> | |
| 83 <param name="input1" value="2.fasta"/> | |
| 84 <param name="count" value="1"/> | |
| 85 <param name="point" value="0"/> | |
| 86 <param name="block" value="0"/> | |
| 87 <param name="codon" value="0"/> | |
| 88 <param name="inframe" value="no"/> | |
| 89 <param name="minimum" value="1"/> | |
| 90 <param name="maximum" value="10"/> | |
| 91 <param name="out_format1" value="fasta"/> | |
| 92 <output name="out_file1" file="emboss_msbar_out.fasta"/> | |
| 93 </test> | |
| 94 </tests> | |
| 95 <help> | |
| 96 .. class:: warningmark | |
| 97 | |
| 98 The input dataset needs to be sequences. | |
| 99 | |
| 100 ----- | |
| 101 | |
| 102 You can view the original documentation here_. | |
| 103 | |
| 104 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/msbar.html | |
| 105 </help> | |
| 106 <expand macro="citations" /> | |
| 107 </tool> |