Mercurial > repos > iuc > ucsc_twobittofa

annotate twobittofa.xml @ 0:d025a40bbff1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
author iuc
date Fri, 19 Aug 2016 06:30:41 -0400
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children 4a81db403bd9
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d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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1 <tool id="ucsc-twobittofa" name="twoBitToFa" version="@WRAPPER_VERSION@">
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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2 <macros>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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3 <token name="@WRAPPER_VERSION@">332</token>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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4 </macros>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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6 <description>Convert all or part of .2bit file to fasta</description>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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7
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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8 <requirements>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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9 <requirement type="package" version="@WRAPPER_VERSION@">ucsc-twobittofa</requirement>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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10 </requirements>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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11
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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12 <version_command><![CDATA[ echo "@WRAPPER_VERSION@" ]]></version_command>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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13
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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14 <command>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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15 <![CDATA[
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16 twoBitToFa
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17 '$twobit_input'
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18 '$fasta_output'
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19
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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20 #if $seq
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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21 -seq='$seq'
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22 #end if
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23
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24 #if $start
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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25 -start=$start
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26 #end if
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27
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28 #if $end
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29 -end=$end
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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30 #end if
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31
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32 #if $seqList
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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33 -seqList='$seqList'
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34 #end if
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35
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36 $noMask
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37 ]]>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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38 </command>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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39
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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40 <inputs>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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41 <param name="twobit_input" type="data" format="twobit"
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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42 label="Input TwoBit file" help=""/>
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43
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44 <param argument="-seq" type="text" label="Restrict this to just one sequence
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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45 (Optional)" help="" optional="True"/>
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46
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47 <param argument="-start" type="integer" label="Start at given position in
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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48 sequence (Optional)" help="Zero-based" optional="True"/>
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49
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50 <param argument="-end" type="integer" label="End at given position in
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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51 sequence (Optional)" help="Non-inclusive" optional="True"/>
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52
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53 <param argument="-seqList" type="data" format="txt"
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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54 label="File containing list of the desired sequence names (Optional)"
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55 help="It must be in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189
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56 where coordinates are half-open zero-based, i.e. [start,end)"
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57 optional="True"/>
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58
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59 <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue=""
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60 checked="false" label="Convert sequence to all upper case?" help=""/>
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61 </inputs>
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62
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63 <outputs>
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64 <data format="fasta" name="fasta_output"/>
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65 </outputs>
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66
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67 <tests>
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68 <test>
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69 <param name="twobit_input" value="input.2bit"/>
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70 <output name="fasta_output" file="output.fasta" />
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71 </test>
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72 </tests>
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73
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74 <help><![CDATA[
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75 **What it does**
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76
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77 twoBitToFa is a tool to convert all or part of .2bit file to fasta.
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78
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79 For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html/>`_.
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80
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81 ]]></help>
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82
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83 <citations>
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84 </citations>
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85 </tool>