Mercurial > repos > iuc > seqtk

annotate seqtk_subseq.xml @ 6:288f7f69fe25 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
author iuc
date Fri, 06 Sep 2019 09:10:07 -0400
parents a09586d5149a
children 3da72230c066
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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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4 <macros>
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5 <import>macros.xml</import>
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6 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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10 <command><![CDATA[
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11 seqtk subseq
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12 $t
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13 -l $l
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14 '$in_file'
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15 #if $source.type == 'bed':
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16 '$in_bed'
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17 #else
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18 '$name_list'
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19 #end if
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20 #if $t == '-t':
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21 | awk 'BEGIN{print "chr\tunknown\tseq"}1'
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22 #end if
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23 @CONDITIONAL_GZIP_OUT@
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24 ]]></command>
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25 <inputs>
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26 <expand macro="in_faq"/>
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27 <conditional name="source">
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28 <param name="type" type="select" label="Select source of sequence choices">
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29 <option value="bed">BED</option>
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30 <option value="name">FASTA/Q ID list</option>
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31 </param>
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32 <when value="bed">
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33 <param name="in_bed" type="data" format="bed" label="Input BED file"/>
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34 </when>
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35 <when value="name">
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36 <param name="name_list" type="data" format="txt" label="Input ID list"/>
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37 </when>
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38 </conditional>
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39 <param argument="-t" type="boolean" truevalue="-t" falsevalue="" label="TAB delimited output" />
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40 <param argument="-l" type="integer" value="0" label="Sequence line length" />
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41 </inputs>
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42 <outputs>
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43 <data name="default" format_source="in_file" label="Selected sequences from $in_file.name">
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44 <change_format>
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45 <when input="t" value="-t" format="tabular"/>
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46 </change_format>
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47 </data>
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="in_file" value="seqtk_subseq.fa"/>
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52 <param name="type" value="name"/>
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53 <param name="t" value="False" />
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54 <param name="name_list" value="seqtk_subseq_list.txt"/>
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55 <output name="default" file="seqtk_subseq.out" ftype="fasta"/>
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56 </test>
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57 <test>
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58 <param name="in_file" value="seqtk_subseq.fa.gz" ftype="fasta.gz"/>
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59 <param name="type" value="name"/>
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60 <param name="t" value="False" />
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61 <param name="name_list" value="seqtk_subseq_list.txt"/>
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62 <output name="default" file="seqtk_subseq.out.gz" ftype="fasta.gz"/>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 **What it does**
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67
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68 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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69
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70 ::
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71
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72 # Input ID list
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73 seq1
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74
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75 # Input fasta
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76 >seq1
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77 ACGTMRWSYK
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78 >seq2
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79 RWSYKACGTM
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80
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81 results in
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82
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83 ::
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84
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85 # Output result
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86 >seq1
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87 ACGTMRWSYK
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88
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89 @ATTRIBUTION@
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90 ]]></help>
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91 <expand macro="citation" />
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92 </tool>