Mercurial > repos > iuc > ucsc_twobittofa

annotate twobittofa.xml @ 2:356dc923f8d3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 6f82cbc16053cecdf58d15a8d0fcdeac7991abaf
author iuc
date Thu, 25 Jan 2018 12:07:29 -0500
parents 4a81db403bd9
children 8067dfa00ed2
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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@">
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2 <description>Convert all or part of .2bit file to FASTA</description>
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3 <macros>
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356dc923f8d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 6f82cbc16053cecdf58d15a8d0fcdeac7991abaf
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4 <token name="@WRAPPER_VERSION@">357</token>
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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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5 </macros>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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6 <requirements>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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7 <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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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 <version_command><![CDATA[ echo "@WRAPPER_VERSION@" ]]></version_command>
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10 <command><![CDATA[
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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11 twoBitToFa
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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12 '$twobit_input'
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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13 '$fasta_output'
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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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15 #if $seq
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16 -seq='$seq'
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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17 #end if
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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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19 #if str($start)
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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20 -start=$start
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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21 #end if
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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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22
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23 #if str($end)
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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24 -end=$end
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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25 #end if
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26
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27 #if $seqList
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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28 -seqList='$seqList'
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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29 #end if
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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31 $noMask
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32 ]]></command>
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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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34 <inputs>
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35 <param name="twobit_input" type="data" format="twobit" label="Input TwoBit file" />
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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36 <param argument="-seq" type="text" optional="true" label="Restrict this to just one sequence" help="Optional" />
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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37 <param argument="-start" type="integer" optional="true" label="Start at given position in sequence" help="Zero-based, optional"/>
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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38 <param argument="-end" type="integer" optional="true" label="End at given position in sequence" help="Non-inclusive, optional" />
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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39 <param argument="-seqList" type="data" format="txt" optional="true"
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40 label="File containing list of the desired sequence names (Optional)"
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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41 help="It must be in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189
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42 where coordinates are half-open zero-based, i.e. [start,end)" />
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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43 <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue="" checked="false" label="Convert sequence to all upper case?" />
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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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44 </inputs>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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45 <outputs>
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46 <data name="fasta_output" format="fasta" />
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="twobit_input" value="input.2bit"/>
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51 <output name="fasta_output" file="output.fasta" />
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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52 </test>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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53 </tests>
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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54 <help><![CDATA[
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55 **What it does**
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56
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57 twoBitToFa is a tool to convert all or part of .2bit file to FASTA.
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58
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59 For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.
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60 ]]></help>
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61 <citations>
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62 </citations>
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63 </tool>