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1 <?xml version="1.0"?>
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2 <tool id="seqtk_subseq" name="seqtk_subseq" version="@WRAPPER_VERSION@.0">
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3 <description>extract subsequences from FASTA/Q files</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[seqtk subseq $t
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10 -l $l
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11 $in_file
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12
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13 #if $source.type == 'bed':
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14 $in_bed
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15 #else
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16 $name_list
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17 #end if
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18
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19 #if $t == '-t':
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20 | awk 'BEGIN{print "chr\tunknown\tseq"}1'
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21 #end if
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22
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23 > $default]]></command>
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24 <inputs>
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25 <param name="in_file" type="data" format="fasta,fastq" label="Input fasta/q file"/>
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26 <conditional name="source">
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27 <param name="type" type="select" label="Select source of sequence choices">
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28 <option value="bed">BED</option>
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29 <option value="name">FASTA/Q ID list</option>
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30 </param>
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31 <when value="bed">
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32 <param name="in_bed" type="data" format="bed" label="Input BED file"/>
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33 </when>
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34 <when value="name">
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35 <param name="name_list" type="data" format="txt" label="Input fasta file"/>
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36 </when>
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37 </conditional>
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38 <param label="TAB delimited output" help="(-t)" name="t" type="boolean" falsevalue="" truevalue="-t"/>
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39 <param label="sequence line length" help="(-l)" name="l" type="integer" value="0"/>
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40 </inputs>
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41 <outputs>
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42 <data format_source="in_file" hidden="false" name="default" label="Selected sequences from $in_file.name">
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43 <change_format>
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44 <when input="t" value="-t" format="tabular"/>
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45 </change_format>
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46 </data>
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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="in_file" value="seqtk_subseq.fa"/>
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51 <param name="type" value="name"/>
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52 <param name="t" value="False" />
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53 <param name="name_list" value="seqtk_subseq_list.txt"/>
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54 <output name="default" file="seqtk_subseq.out" ftype="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 Given a list of newline separated IDs from a fasta file, this will extract those named fasta sequences from the input file.
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61
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62 ::
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63
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64 # Input ID list
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65 seq1
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66
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67 # Input fasta
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68 >seq1
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69 ACGTMRWSYK
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70 >seq2
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71 RWSYKACGTM
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72
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73 results in
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74
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75 ::
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76
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77 # Output result
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78 >seq1
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79 ACGTMRWSYK
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80
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81 @ATTRIBUTION@
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82 ]]></help>
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83 </tool>
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