Mercurial > repos > iuc > ucsc_twobittofa

annotate twobittofa.xml @ 3:8067dfa00ed2 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit e021ee7a5b682d6f513ca053138acf9bb5d2b4b2"
author iuc
date Wed, 02 Feb 2022 13:56:20 +0000
parents 356dc923f8d3
children
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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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1 <tool id="ucsc-twobittofa" name="twoBitToFa" version="@TOOL_VERSION@">
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2 <description>Convert all or part of .2bit file to FASTA</description>
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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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3 <xrefs>
8067dfa00ed2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit e021ee7a5b682d6f513ca053138acf9bb5d2b4b2"
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4 <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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5 </xrefs>
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6 <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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7 <token name="@TOOL_VERSION@">377</token>
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8 </macros>
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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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17
1
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18 #if $seq
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19 -seq='$seq'
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20 #end if
0
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21
1
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22 #if str($start)
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23 -start=$start
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24 #end if
0
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25
1
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26 #if str($end)
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27 -end=$end
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28 #end if
0
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29
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" />
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39 <param argument="-seq" type="text" optional="true" label="Restrict this to just one sequence" help="Optional" />
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40 <param argument="-start" type="integer" optional="true" label="Start at given position in sequence" help="Zero-based, optional"/>
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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)"
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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
1
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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
1
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62 For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.
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63 ]]></help>
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64 <citations>
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65 </citations>
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66 </tool>