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annotate seqtk_subseq.xml @ 16:48a51c72f5e7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author iuc
date Wed, 17 Oct 2018 05:58:58 -0400
parents 16f2535c08bf
children 069c8f0695ee
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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[
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10 seqtk subseq
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11 $t
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12 -l $l
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13 '$in_file'
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14 #if $source.type == 'bed':
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15 '$in_bed'
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16 #else
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17 '$name_list'
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18 #end if
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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 @CONDITIONAL_GZIP_OUT@
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23 ]]></command>
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24 <inputs>
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25 <expand macro="in_faq"/>
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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 ID list"/>
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36 </when>
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37 </conditional>
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38 <param argument="-t" type="boolean" truevalue="-t" falsevalue="" label="TAB delimited output" />
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39 <param argument="-l" type="integer" value="0" label="Sequence line length" />
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40 </inputs>
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41 <outputs>
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42 <data name="default" format_source="in_file" 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 <test>
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57 <param name="in_file" value="seqtk_subseq.fa.gz" ftype="fasta.gz"/>
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58 <param name="type" value="name"/>
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59 <param name="t" value="False" />
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60 <param name="name_list" value="seqtk_subseq_list.txt"/>
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61 <output name="default" file="seqtk_subseq.out.gz" ftype="fasta.gz"/>
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65 **What it does**
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66
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67 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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68
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69 ::
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70
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71 # Input ID list
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72 seq1
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73
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74 # Input fasta
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75 >seq1
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76 ACGTMRWSYK
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77 >seq2
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78 RWSYKACGTM
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79
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80 results in
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81
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82 ::
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83
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84 # Output result
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85 >seq1
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86 ACGTMRWSYK
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87
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88 @ATTRIBUTION@
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89 ]]></help>
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90 <expand macro="citation" />
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91 </tool>