annotate emboss_trimseq.xml @ 14:2e0fb4bc860e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit fed02ef07e0a45f0d5a89cdca364607ab8da6cf9
author iuc
date Mon, 28 Jan 2019 11:22:18 -0500
parents 8992d258e42f
children
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8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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1 <tool id="EMBOSS: trimseq103" name="trimseq" version="@VERSION@.1">
10
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2 <description>Trim ambiguous bits off the ends of sequences</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>trimseq -sequence '$input1' -outseq '$out_file1' -window $window -percent $percent -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto</command>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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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="window" type="integer" value="1" label="Window size" />
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12 <param name="percent" type="float" value="100.0" label="Threshold of the percentage ambiguity" />
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13 <param name="strict" type="select" label="Trim all ambiguity codes">
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14 <option value="no">No</option>
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15 <option value="yes">Yes</option>
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16 </param>
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17 <param name="star" type="select" label="In protein sequences, trim off not only X's, but also the *'s">
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18 <option value="no">No</option>
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19 <option value="yes">Yes</option>
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20 </param>
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21 <param name="left" type="select" label="Trim at the start">
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22 <option value="yes">Yes</option>
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23 <option value="no">No</option>
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24 </param>
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25 <param name="right" type="select" label="Trim at the end">
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26 <option value="yes">Yes</option>
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27 <option value="no">No</option>
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28 </param>
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29 <param name="out_format1" type="select" label="Output sequence file format">
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30 <option value="fasta">FASTA (m)</option>
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31 <option value="acedb">ACeDB (m)</option>
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32 <option value="asn1">ASN.1 (m)</option>
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33 <option value="clustal">Clustal (m)</option>
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34 <option value="codata">CODATA (m)</option>
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35 <option value="embl">EMBL (m)</option>
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36 <option value="fitch">Fitch (m)</option>
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37 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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38 <option value="genbank">GENBANK (m)</option>
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39 <option value="gff">GFF (m)</option>
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40 <option value="hennig86">Hennig86 (m)</option>
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41 <option value="ig">Intelligenetics (m)</option>
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42 <option value="jackknifer">Jackknifer (m)</option>
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43 <option value="jackknifernon">Jackknifernon (m)</option>
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44 <option value="mega">Mega (m)</option>
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45 <option value="meganon">Meganon (m)</option>
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46 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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47 <option value="pir">NBRF (PIR) (m)</option>
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48 <option value="ncbi">NCBI style FASTA (m)</option>
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49 <option value="nexus">Nexus/PAUP (m)</option>
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50 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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51 <option value="phylip">PHYLIP interleaved (m)</option>
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52 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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53 <option value="selex">SELEX (m)</option>
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54 <option value="staden">Staden (s)</option>
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55 <option value="strider">DNA strider (m)</option>
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56 <option value="swiss">SwisProt entry (m)</option>
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57 <option value="text">Plain sequence (s)</option>
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58 <option value="treecon">Treecon (m)</option>
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59 </param>
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60 </inputs>
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61 <outputs>
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62 <data name="out_file1" format="fasta" />
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="input1" value="2.fasta"/>
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67 <param name="window" value="1"/>
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68 <param name="percent" value="100.0"/>
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69 <param name="strict" value="no"/>
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70 <param name="star" value="no"/>
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71 <param name="left" value="yes"/>
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72 <param name="right" value="yes"/>
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73 <param name="out_format1" value="fasta"/>
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74 <output name="out_file1" file="emboss_trimseq_out.fasta"/>
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75 </test>
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76 </tests>
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77 <help>
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78 .. class:: warningmark
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79
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80 The input dataset needs to be sequences.
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81
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82 -----
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83
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84 You can view the original documentation here_.
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85
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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86 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/trimseq.html
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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87 </help>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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88 <expand macro="citations" />
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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89 </tool>