Mercurial > repos > iuc > meryl_count_kmers

annotate count-kmers.xml @ 2:e893b7452150 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
author iuc
date Sun, 09 Nov 2025 18:36:47 +0000
parents bb6774c6aeaf
children
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a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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1 <tool id="meryl_count_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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2 <description>count k-mers</description>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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3 <macros>
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4 <import>macros.xml</import>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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5 </macros>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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6 <expand macro="edam_ontology"/>
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7 <xrefs>
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8 <xref type="bio.tools">meryl</xref>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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9 </xrefs>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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10 <expand macro="requirements"/>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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11 <version_command>meryl --version</version_command>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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12 <command detect_errors="exit_code"><![CDATA[
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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13 export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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14 #if $options_kmer_size.kmer_size == 'estimate'
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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15 #from math import log
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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16 #set size=int(log(int($options_kmer_size.genome_size)*(1-float($options_kmer_size.collision_rate))/float($options_kmer_size.collision_rate))/log(4))
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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17 #elif $options_kmer_size.kmer_size == 'provide'
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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18 #set size=$options_kmer_size.input_kmer_size
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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19 #end if
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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20 ln -s '$input_reads' ./input.${input_reads.ext} &&
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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21
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22 meryl
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23 $count_operation
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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24 k=$size
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25 memory=\$GALAXY_MEMORY_GB
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26 threads=\${GALAXY_SLOTS:-1}
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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27 ./input.${input_reads.ext}
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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28 output read-db.meryl &&
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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29 echo 'K-mer size: ${size}' &&
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30 tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" read-db.meryl
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a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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31 ]]></command>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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32 <inputs>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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33 <param name="count_operation" type="select" label="Count operations" help="Select an operation to be executed">
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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34 <option value="count">Count: count the occurrences of canonical k-mers</option>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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35 <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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36 <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option>
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37 </param>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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38 <param name="input_reads" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Input sequences" help="Select your reads in FASTA/FASTQ format."/>
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e893b7452150 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
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39 <expand macro="kmer_param"/>
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a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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40 </inputs>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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41 <outputs>
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42 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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43 </outputs>
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44 <tests>
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45 <test expect_num_outputs="1">
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46 <conditional name="options_kmer_size">
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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47 <param name="kmer_size" value="provide"/>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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48 <param name="input_kmer_size" value="7"/>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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49 </conditional>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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50 <param name="input_reads" value="child.fasta"/>
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51 <param name="count_operation" value="count"/>
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52 <output name="read_db" ftype="meryldb">
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53 <assert_contents>
1
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54 <has_size value="23404" delta="3000"/>
0
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55 <expand macro="meryldb_archive_assumptions"/>
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56 </assert_contents>
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57 </output>
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58 <assert_stdout>
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59 <has_line line="K-mer size: 7"/>
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60 </assert_stdout>
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61 </test>
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62 <test expect_num_outputs="1">
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63 <conditional name="options_kmer_size">
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64 <param name="kmer_size" value="provide"/>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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65 <param name="input_kmer_size" value="7"/>
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66 </conditional>
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67 <param name="input_reads" value="child.fasta.gz" ftype="fasta.gz"/>
a33c838729c5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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68 <param name="count_operation" value="count"/>
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69 <output name="read_db" ftype="meryldb">
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70 <assert_contents>
1
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71 <has_size value="22700" delta="3000"/>
0
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72 <expand macro="meryldb_archive_assumptions"/>
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73 </assert_contents>
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74 </output>
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75 <assert_stdout>
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76 <has_line line="K-mer size: 7"/>
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77 </assert_stdout>
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78 </test>
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79 <test expect_num_outputs="1">
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80 <conditional name="options_kmer_size">
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81 <param name="kmer_size" value="provide"/>
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82 <param name="input_kmer_size" value="7"/>
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83 </conditional>
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84 <param name="input_reads" value="child.fastq.gz" ftype="fastqsanger.gz"/>
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85 <param name="count_operation" value="count"/>
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86 <output name="read_db" ftype="meryldb">
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87 <assert_contents>
1
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88 <has_size value="23155" delta="3000"/>
0
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89 <expand macro="meryldb_archive_assumptions"/>
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90 </assert_contents>
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91 </output>
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92 <assert_stdout>
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93 <has_line line="K-mer size: 7"/>
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94 </assert_stdout>
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95 </test>
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96 </tests>
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97 <help>
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98
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99 .. class:: infomark
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100
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101 **Purpose**
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102
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103 Meryl is the k-mer counter. This tool can be used to count kmers.
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104
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105 - Count: count the occurrences of canonical k-mers
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106 - Count-forward: count the occurreces of forward k-mers
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107 - Count-reverse: count the occurreces of reverse k-mers
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108 </help>
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109 <expand macro="citations"/>
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110 </tool>