Mercurial > repos > iuc > seqtk

annotate seqtk_seq.xml @ 11:8511b6d85fc7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit c819f01ae147fb23a1e5e91cee3626b6a19b9e03
author iuc
date Wed, 09 Jul 2025 19:23:11 +0000
parents a019807f4e67
children
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_seq" name="seqtk_seq" version="@TOOL_VERSION@+galaxy1" profile="22.05">
3
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3 <description>common transformation of FASTA/Q</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="bio_tools"/>
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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 seq -q $q
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12 -X $X
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13 #if $n:
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14 -n '$n'
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15 #end if
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16 -l $l
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17 -Q $Q
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18 -s $s
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19 -f $f
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20 #if $M:
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21 -M '$M'
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22 #end if
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23 -L $L
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24 $c
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25 #if $direction != 'forward'
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26 $direction
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27 #end if
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28 $A
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29 $C
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30 $N
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31 $x1
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32 $x2
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33 #if $in_file.is_of_type('fastqillumina')
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34 -V
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35 #end if
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36 '$in_file'
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37 @CONDITIONAL_GZIP_OUT@
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38 ]]></command>
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39 <configfiles>
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40 <configfile filename="outputs.json">
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41 #if $A and $in_file.is_of_type('fasta.gz', 'fastq.gz')
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42 #set $ext = "fasta.gz"
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43 #elif $A
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44 #set $ext = "fasta"
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45 #else
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46 #set $ext = $in_file.ext
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47 #end if
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48 {"default": {"ext": "$ext"}}
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49 </configfile>
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50 </configfiles>
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51 <inputs>
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52 <expand macro="in_faq"/>
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53 <param argument="-q" type="integer" value="0" label="Mask bases with quality lower than INT" />
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54 <param argument="-X" type="integer" value="255" label="Mask bases with quality higher than INT" />
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55 <param argument="-n" type="text" value="" label="Masked bases converted to CHAR; leave empty for lowercase masking" />
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56 <param argument="-l" type="integer" value="0" label="Number of residues per line; 0 for 2^32-1" />
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57 <param argument="-Q" type="integer" value="33" label="Quality shift: ASCII-INT gives base quality" help="Only applied during comparison to quality thresholds for masking" />
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58 <param argument="-s" type="integer" value="11" label="Random seed" help="Effective with -f" />
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59 <param argument="-f" type="float" value="1" label="Sample fraction of sequences" />
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60 <param argument="-M" type="data" format="bed,txt" optional="true" label="Mask regions in BED or name list file" />
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61 <param argument="-L" type="integer" value="0" label="Drop sequences with length shorter than INT" />
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62 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Mask complement region" help="Effective with -M" />
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63 <param name="direction" type="select" optional="false" label="Output complement">
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64 <option value="forward" selected="true">Forward only (Default)</option>
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65 <option value="-r">Reverse only (-r)</option>
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66 <option value="-R">Forward and Reverse (-R)</option>
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67 </param>
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68 <param argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Force FASTA output (discard quality)" />
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69 <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false" label="Drop comments at the header lines" />
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70 <param argument="-N" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Drop sequences containing ambiguous bases" />
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71 <param name="x1" argument="-1" type="boolean" truevalue="-1" falsevalue="" checked="false" label="Output the 2n-1 reads only" />
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72 <param name="x2" argument="-2" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Output the 2n reads only" />
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73 </inputs>
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74 <outputs provided_metadata_file="outputs.json">
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75 <data name="default" format="auto" label="${tool.name} on ${on_string}" />
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76 </outputs>
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77
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78 <tests>
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79 <!-- This is a sorry excuse for a test for a tool which does way more
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80 than it should, but upstream decided to put a TON of functionality
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81 into a single tool rather than using the single responsibility
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82 principle. -->
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83 <test expect_num_outputs="1">
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84 <param name="in_file" value="seqtk_seq.fa"/>
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85 <param name="direction" value="-r"/>
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86 <param name="n" value=""/>
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87 <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
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88 </test>
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89 <test expect_num_outputs="1">
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90 <param name="in_file" value="seqtk_seq.fa.gz" ftype="fasta.gz"/>
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91 <param name="direction" value="-r"/>
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92 <param name="n" value=""/>
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93 <output name="default" file="seqtk_seq_revcom.fa.gz" ftype="fasta.gz"/>
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94 </test>
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95 <test expect_num_outputs="1">
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96 <param name="in_file" value="seqtk_seq.fa"/>
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97 <param name="direction" value="-R"/>
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98 <param name="n" value=""/>
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99 <output name="default" file="seqtk_seq_revcom_forw.fa" ftype="fasta"/>
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100 </test>
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101 <test expect_num_outputs="1">
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102 <param name="in_file" value="seqtk_trimfq.fq" ftype="fastq"/>
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103 <param name="A" value="True" />
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104 <output name="default" file="seqtk_seq_A.fasta" ftype="fasta"/>
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105 </test>
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106 <test expect_num_outputs="1">
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107 <param name="in_file" value="seqtk_trimfq.fq.gz" ftype="fastq.gz"/>
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108 <param name="A" value="True" />
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109 <output name="default" file="seqtk_seq_A.fasta.gz" ftype="fasta.gz"/>
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110 </test>
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111 </tests>
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112 <help><![CDATA[
0
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113 **What it does**
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114
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115 Various utilities for transforming FASTA/Q data
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116
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117 @ATTRIBUTION@
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118 ]]></help>
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119 <expand macro="citation" />
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120 </tool>