Mercurial > repos > devteam > emboss_5

annotate emboss_revseq.xml @ 10:d49956b87f7e draft

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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
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children 8992d258e42f
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10
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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1 <tool id="EMBOSS: revseq82" name="revseq" version="5.0.0">
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2 <description>Reverse and complement a sequence</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <code file="emboss_format_corrector.py" />
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8 <command>revseq -sequence '$input1' -outseq '$out_file1' -reverse $reverse -complement $complement -osformat2 $out_format1 -auto</command>
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9 <inputs>
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10 <param name="input1" type="data" format="fasta" label="Sequences" />
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11 <param name="reverse" type="select" label="Reverse the sequence">
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12 <option value="yes">Yes</option>
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13 <option value="no">No</option>
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14 </param>
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15 <param name="complement" type="select" label="Complement the sequence">
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16 <option value="yes">Yes</option>
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17 <option value="no">No</option>
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18 </param>
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19 <param name="out_format1" type="select" label="Output sequence file format">
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20 <option value="fasta">FASTA (m)</option>
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21 <option value="acedb">ACeDB (m)</option>
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22 <option value="asn1">ASN.1 (m)</option>
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23 <option value="clustal">Clustal (m)</option>
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24 <option value="codata">CODATA (m)</option>
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25 <option value="embl">EMBL (m)</option>
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26 <option value="fitch">Fitch (m)</option>
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27 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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28 <option value="genbank">GENBANK (m)</option>
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29 <option value="gff">GFF (m)</option>
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30 <option value="hennig86">Hennig86 (m)</option>
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31 <option value="ig">Intelligenetics (m)</option>
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32 <option value="jackknifer">Jackknifer (m)</option>
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33 <option value="jackknifernon">Jackknifernon (m)</option>
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34 <option value="mega">Mega (m)</option>
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35 <option value="meganon">Meganon (m)</option>
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36 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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37 <option value="pir">NBRF (PIR) (m)</option>
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38 <option value="ncbi">NCBI style FASTA (m)</option>
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39 <option value="nexus">Nexus/PAUP (m)</option>
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40 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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41 <option value="phylip">PHYLIP interleaved (m)</option>
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42 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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43 <option value="selex">SELEX (m)</option>
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44 <option value="staden">Staden (s)</option>
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45 <option value="strider">DNA strider (m)</option>
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46 <option value="swiss">SwisProt entry (m)</option>
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47 <option value="text">Plain sequence (s)</option>
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48 <option value="treecon">Treecon (m)</option>
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49 </param>
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50 </inputs>
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51 <outputs>
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52 <data name="out_file1" format="fasta" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input1" value="2.fasta"/>
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57 <param name="reverse" value="yes"/>
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58 <param name="complement" value="yes"/>
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59 <param name="out_format1" value="fasta"/>
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60 <output name="out_file1" file="emboss_revseq_out.fasta"/>
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61 </test>
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62 </tests>
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63 <help>
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64 .. class:: warningmark
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65
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66 The input dataset needs to be sequences.
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67
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68 -----
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69
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70 You can view the original documentation here_.
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71
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72 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/revseq.html
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73 </help>
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74 <expand macro="citations" />
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75 </tool>