Mercurial > repos > iuc > seqtk

annotate seqtk_subseq.xml @ 8:3da72230c066 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 690c73637e3b8be3a52fe3afc8ba6436c4bab46f"
author iuc
date Thu, 14 Oct 2021 09:22:39 +0000
parents a09586d5149a
children 4b494533146a
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_subseq" name="seqtk_subseq" version="@TOOL_VERSION@.1">
3
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3 <description>extract subsequences from FASTA/Q files</description>
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3da72230c066 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 690c73637e3b8be3a52fe3afc8ba6436c4bab46f"
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4 <expand macro="bio_tools"/>
3
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5 <macros>
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6 <import>macros.xml</import>
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7 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command><![CDATA[
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12 seqtk subseq
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13 $t
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14 -l $l
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15 '$in_file'
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16 #if $source.type == 'bed':
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17 '$in_bed'
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18 #else
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19 '$name_list'
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20 #end if
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21 #if $t == '-t':
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22 | awk 'BEGIN{print "chr\tunknown\tseq"}1'
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23 #end if
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24 @CONDITIONAL_GZIP_OUT@
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25 ]]></command>
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26 <inputs>
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27 <expand macro="in_faq"/>
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28 <conditional name="source">
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29 <param name="type" type="select" label="Select source of sequence choices">
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30 <option value="bed">BED</option>
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31 <option value="name">FASTA/Q ID list</option>
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32 </param>
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33 <when value="bed">
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34 <param name="in_bed" type="data" format="bed" label="Input BED file"/>
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35 </when>
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36 <when value="name">
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37 <param name="name_list" type="data" format="txt" label="Input ID list"/>
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38 </when>
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39 </conditional>
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40 <param argument="-t" type="boolean" truevalue="-t" falsevalue="" label="TAB delimited output" />
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41 <param argument="-l" type="integer" value="0" label="Sequence line length" />
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42 </inputs>
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43 <outputs>
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44 <data name="default" format_source="in_file" label="Selected sequences from $in_file.name">
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45 <change_format>
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46 <when input="t" value="-t" format="tabular"/>
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47 </change_format>
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48 </data>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="in_file" value="seqtk_subseq.fa"/>
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53 <param name="type" value="name"/>
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54 <param name="t" value="False" />
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55 <param name="name_list" value="seqtk_subseq_list.txt"/>
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56 <output name="default" file="seqtk_subseq.out" ftype="fasta"/>
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57 </test>
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58 <test>
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59 <param name="in_file" value="seqtk_subseq.fa.gz" ftype="fasta.gz"/>
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60 <param name="type" value="name"/>
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61 <param name="t" value="False" />
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62 <param name="name_list" value="seqtk_subseq_list.txt"/>
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63 <output name="default" file="seqtk_subseq.out.gz" ftype="fasta.gz"/>
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 **What it does**
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68
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69 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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70
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71 ::
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72
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73 # Input ID list
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74 seq1
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75
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76 # Input fasta
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77 >seq1
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78 ACGTMRWSYK
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79 >seq2
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80 RWSYKACGTM
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81
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82 results in
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83
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84 ::
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85
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86 # Output result
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87 >seq1
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88 ACGTMRWSYK
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89
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90 @ATTRIBUTION@
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91 ]]></help>
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92 <expand macro="citation" />
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93 </tool>