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annotate emboss_extractseq.xml @ 11:1b6538ec8b56 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 09:43:47 -0500
parents d49956b87f7e
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: extractseq35" name="extractseq" version="5.0.0">
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2 <description>Extract regions from 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>extractseq -sequence '$input1' -outseq '$out_file1' -regions '$regions' -separate $separate -osformat2 $out_format1 -auto</command>
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9 <inputs>
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10 <param name="input1" type="data" format="data" label="Sequences" />
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11 <param name="regions" type="text" value="1-9999999" label="Regions to extract" />
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12 <param name="separate" type="select" label="Write each specified region as a separate sequence">
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13 <option value="no">No</option>
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14 <option value="yes">Yes</option>
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15 </param>
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16 <param name="out_format1" type="select" label="Output sequence file format">
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17 <option value="fasta">FASTA (m)</option>
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18 <option value="acedb">ACeDB (m)</option>
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19 <option value="asn1">ASN.1 (m)</option>
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20 <option value="clustal">Clustal (m)</option>
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21 <option value="codata">CODATA (m)</option>
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22 <option value="embl">EMBL (m)</option>
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23 <option value="fitch">Fitch (m)</option>
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24 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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25 <option value="genbank">GENBANK (m)</option>
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26 <option value="gff">GFF (m)</option>
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27 <option value="hennig86">Hennig86 (m)</option>
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28 <option value="ig">Intelligenetics (m)</option>
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29 <option value="jackknifer">Jackknifer (m)</option>
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30 <option value="jackknifernon">Jackknifernon (m)</option>
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31 <option value="mega">Mega (m)</option>
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32 <option value="meganon">Meganon (m)</option>
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33 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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34 <option value="pir">NBRF (PIR) (m)</option>
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35 <option value="ncbi">NCBI style FASTA (m)</option>
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36 <option value="nexus">Nexus/PAUP (m)</option>
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37 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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38 <option value="phylip">PHYLIP interleaved (m)</option>
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39 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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40 <option value="selex">SELEX (m)</option>
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41 <option value="staden">Staden (s)</option>
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42 <option value="strider">DNA strider (m)</option>
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43 <option value="swiss">SwisProt entry (m)</option>
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44 <option value="text">Plain sequence (s)</option>
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45 <option value="treecon">Treecon (m)</option>
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46 </param>
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47 </inputs>
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48 <outputs>
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49 <data name="out_file1" format="fasta" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="input1" value="2.fasta"/>
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54 <param name="regions" value="1-9999999"/>
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55 <param name="separate" value="no"/>
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56 <param name="out_format1" value="fasta"/>
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57 <output name="out_file1" file="emboss_extractseq_out.fasta"/>
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58 </test>
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59 </tests>
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60 <help>
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61 You can view the original documentation here_.
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62
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63 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/extractseq.html
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64 </help>
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65 <expand macro="citations" />
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66 </tool>