Mercurial > repos > devteam > emboss_5

annotate emboss_newseq.xml @ 12:ace31bbde4c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9d484642914b581ce35f254466b849d3c4c2c06c
author iuc
date Thu, 23 Feb 2017 09:43:32 -0500
parents 0e2484b6829b
children 27c43fb015f0
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11
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
iuc
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1 <tool id="EMBOSS: newseq59" name="newseq" version="5.0.0">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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2 <description>Type in a short new sequence</description>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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3 <macros>
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4 <import>macros.xml</import>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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5 </macros>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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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>
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9 <![CDATA[
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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10 newseq
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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11 -outseq '$out_file1'
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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12 -name '$seqname'
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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13 -description '$description'
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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14 -type $type
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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15 -sequence '$sequence'
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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16 -osformat5 $out_format1
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17 -auto
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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18 ]]>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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19 </command>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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20 <inputs>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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21 <param name="seqname" type="text" value="" label="Name of of the sequence" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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22 <param name="description" type="text" value="" label="Description of the sequence" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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23 <param name="type" type="select" label="Type of sequence">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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24 <option value="N">Nucleic</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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25 <option value="P">Protein</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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26 </param>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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27 <param name="sequence" type="text" value="" label="The sequence itself" />
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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28 <param name="out_format1" type="select" label="Output sequence file format">
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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29 <option value="fasta">FASTA (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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30 <option value="acedb">ACeDB (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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31 <option value="asn1">ASN.1 (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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32 <option value="clustal">Clustal (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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33 <option value="codata">CODATA (m)</option>
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34 <option value="embl">EMBL (m)</option>
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35 <option value="fitch">Fitch (m)</option>
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36 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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37 <option value="genbank">GENBANK (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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38 <option value="gff">GFF (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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39 <option value="hennig86">Hennig86 (m)</option>
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40 <option value="ig">Intelligenetics (m)</option>
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41 <option value="jackknifer">Jackknifer (m)</option>
0e2484b6829b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
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42 <option value="jackknifernon">Jackknifernon (m)</option>
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43 <option value="mega">Mega (m)</option>
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44 <option value="meganon">Meganon (m)</option>
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45 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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46 <option value="pir">NBRF (PIR) (m)</option>
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47 <option value="ncbi">NCBI style FASTA (m)</option>
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48 <option value="nexus">Nexus/PAUP (m)</option>
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49 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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50 <option value="phylip">PHYLIP interleaved (m)</option>
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51 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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52 <option value="selex">SELEX (m)</option>
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53 <option value="staden">Staden (s)</option>
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54 <option value="strider">DNA strider (m)</option>
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55 <option value="swiss">SwisProt entry (m)</option>
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56 <option value="text">Plain sequence (s)</option>
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57 <option value="treecon">Treecon (m)</option>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <data name="out_file1" format="fasta" />
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="seqname" value="cytoc"/>
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66 <param name="description" value="fragment_of_cytochrome_c"/>
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67 <param name="type" value="N"/>
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68 <param name="sequence" value="KKKEERADLIAY"/>
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69 <param name="out_format1" value="fasta"/>
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70 <output name="out_file1" file="emboss_newseq_out.fasta"/>
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71 </test>
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72 </tests>
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73 <help>
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74 You can view the original documentation here_.
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75
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76 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/newseq.html
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77 </help>
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78 <expand macro="citations" />
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79 </tool>