Mercurial > repos > iuc > ucsc_twobittofa

annotate twobittofa.xml @ 5:e9bbe2f71784 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa commit f23db5c2e7b9360148eff9c3227c57c0b7c379a8
author iuc
date Mon, 28 Oct 2024 07:09:20 +0000
parents 3c6f9e8a4c17
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3c6f9e8a4c17 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa commit 303002db06287fb25306020c4391626842f52162
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1 <tool id="ucsc-twobittofa" name="twoBitToFa" version="@TOOL_VERSION@" profile="22.05">
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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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e9bbe2f71784 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa commit f23db5c2e7b9360148eff9c3227c57c0b7c379a8
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4 <token name="@TOOL_VERSION@">472</token>
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5 </macros>
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8067dfa00ed2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit e021ee7a5b682d6f513ca053138acf9bb5d2b4b2"
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6 <xrefs>
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7 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
8067dfa00ed2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit e021ee7a5b682d6f513ca053138acf9bb5d2b4b2"
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">ucsc-twobittofa</requirement>
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11 </requirements>
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8067dfa00ed2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit e021ee7a5b682d6f513ca053138acf9bb5d2b4b2"
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12 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
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13 <command><![CDATA[
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14 twoBitToFa
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15 '$twobit_input'
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16 '$fasta_output'
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18 #if $seq
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19 -seq='$seq'
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20 #end if
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1
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22 #if str($start)
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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23 -start=$start
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24 #end if
0
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1
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26 #if str($end)
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27 -end=$end
4a81db403bd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
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28 #end if
0
d025a40bbff1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 454df102c5630d90af25d1b9ff8050a6c7b82ffc
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1
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30 #if $seqList
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31 -seqList='$seqList'
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32 #end if
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34 $noMask
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35 ]]></command>
0
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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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37 <inputs>
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38 <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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39 <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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40 <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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41 <param argument="-end" type="integer" optional="true" label="End at given position in sequence" help="Non-inclusive, optional" />
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42 <param argument="-seqList" type="data" format="txt" optional="true"
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43 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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44 help="It must be in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189
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45 where coordinates are half-open zero-based, i.e. [start,end)" />
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46 <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue="" checked="false" label="Convert sequence to all upper case?" />
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47 </inputs>
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48 <outputs>
1
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49 <data name="fasta_output" 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="twobit_input" value="input.2bit"/>
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54 <output name="fasta_output" file="output.fasta" />
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 **What it does**
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59
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60 `twoBitToFa`_ is a tool to convert all or part of .2bit file to FASTA.
0
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61
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62 For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.
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64 For implementation details see twoBitToFa's `source code`_.
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65
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66 .. _twoBitToFa: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
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67 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/utils/twoBitToFa/twoBitToFa.c
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68 ]]></help>
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69 <citations>
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70 <citation type="doi">10.1093/bib/bbs038</citation>
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71 </citations>
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72 </tool>