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1 <?xml version="1.0"?>
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2 <tool id="fa_to_twobit" name="faToTwoBit" version="1.0">
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3 <description>Converts a FASTA sequence file into a twoBit file</description>
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4
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5 <macros>
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6 <import>ucsc_macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements_twobit" />
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10
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 faToTwoBit
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14 "${fasta_input}" ${no_mask} ${strip_version} "${twobit_output}"
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="fasta_input" type="data" format="fasta" label="FASTA file" />
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19
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20 <param name="no_mask" type="boolean" checked="true"
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21 truevalue="-noMask" falsevalue=""
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22 label="Ignore lower-case masking in fa file"
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23 help="-noMask" />
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24
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25 <param name="strip_version" type="boolean" checked="true"
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26 truevalue="-stripVersion" falsevalue=""
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27 label="Strip off version number after '.' for GenBank accessions"
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28 help="-stripVersion" />
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29 </inputs>
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30 <outputs>
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31 <data name="twobit_output" format="twobit" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
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36 <output name="twobit_output" file="KB462401.unmasked.2bit" />
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37 </test>
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38 <test>
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39 <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
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40 <param name="no_mask" value="" />
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41 <output name="twobit_output" file="KB462401.masked.2bit" />
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42 </test>
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43 <test>
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44 <param name="fasta_input" value="KB462401.fa" ftype="fasta" />
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45 <param name="strip_version" value="" />
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46 <output name="twobit_output" file="KB462401.keepversion.2bit" />
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47 </test>
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48 </tests>
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49 <help>
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50 <![CDATA[
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51 **What it does**
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52
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53 faToTwoBit converts a DNA sequence file in FASTA format into a
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54 `twoBit Sequence Archive <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.
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55
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56 ]]></help>
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57
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58 <expand macro="citations" />
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59 </tool>
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