Mercurial > repos > iuc > meryl_count_kmers

annotate count-kmers.xml @ 0:e377b0f8efda draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
author iuc
date Tue, 08 Oct 2024 16:42:39 +0000
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children 52cfaa8d7b1c
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0
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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1 <tool id="meryl_count_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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2 <description>count k-mers</description>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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3 <macros>
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4 <import>macros.xml</import>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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5 </macros>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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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>
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9 </xrefs>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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10 <expand macro="requirements"/>
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11 <version_command>meryl --version</version_command>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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12 <command detect_errors="exit_code"><![CDATA[
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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13 export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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14 #if $options_kmer_size.kmer_size == 'estimate'
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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15 #from math import log
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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16 #set size=int(log(int($options_kmer_size.genome_size)*(1-float($options_kmer_size.collision_rate))/float($options_kmer_size.collision_rate))/log(4))
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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17 #elif $options_kmer_size.kmer_size == 'provide'
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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18 #set size=$options_kmer_size.input_kmer_size
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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19 #end if
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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20 ln -s '$input_reads' ./input.${input_reads.ext} &&
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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21
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22 meryl
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23 $count_operation
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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24 k=$size
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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25 memory=\$GALAXY_MEMORY_GB
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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26 threads=\${GALAXY_SLOTS:-1}
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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27 ./input.${input_reads.ext}
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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28 output read-db.meryl &&
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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29 echo 'K-mer size: ${size}' &&
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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30 tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" read-db.meryl
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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31 ]]></command>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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32 <inputs>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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33 <param name="count_operation" type="select" label="Count operations" help="Select an operation to be executed">
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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34 <option value="count">Count: count the occurrences of canonical k-mers</option>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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35 <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option>
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36 <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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37 </param>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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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."/>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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39 <conditional name="options_kmer_size">
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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40 <param name="kmer_size" type="select" label="K-mer size selector">
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41 <option value="provide">Set a k-mer size</option>
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42 <option value="estimate">Estimate the best k-mer size</option>
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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43 </param>
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44 <when value="provide">
e377b0f8efda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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45 <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G).."/>
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46 </when>
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47 <when value="estimate">
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48 <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided."/>
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49 <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001."/>
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50 </when>
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51 </conditional>
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52 </inputs>
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53 <outputs>
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54 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
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55 </outputs>
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56 <tests>
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57 <test expect_num_outputs="1">
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58 <conditional name="options_kmer_size">
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59 <param name="kmer_size" value="provide"/>
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60 <param name="input_kmer_size" value="7"/>
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61 </conditional>
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62 <param name="input_reads" value="child.fasta"/>
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63 <param name="count_operation" value="count"/>
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64 <output name="read_db" ftype="meryldb">
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65 <assert_contents>
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66 <has_size value="23404" delta="3000"/>
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67 <expand macro="meryldb_archive_assumptions"/>
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68 </assert_contents>
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69 </output>
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70 <assert_stdout>
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71 <has_line line="K-mer size: 7"/>
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72 </assert_stdout>
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73 </test>
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74 <test expect_num_outputs="1">
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75 <conditional name="options_kmer_size">
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76 <param name="kmer_size" value="provide"/>
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77 <param name="input_kmer_size" value="7"/>
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78 </conditional>
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79 <param name="input_reads" value="child.fasta.gz" ftype="fasta.gz"/>
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80 <param name="count_operation" value="count"/>
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81 <output name="read_db" ftype="meryldb">
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82 <assert_contents>
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83 <has_size value="22700" delta="3000"/>
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84 <expand macro="meryldb_archive_assumptions"/>
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85 </assert_contents>
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86 </output>
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87 <assert_stdout>
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88 <has_line line="K-mer size: 7"/>
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89 </assert_stdout>
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90 </test>
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91 <test expect_num_outputs="1">
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92 <conditional name="options_kmer_size">
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93 <param name="kmer_size" value="provide"/>
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94 <param name="input_kmer_size" value="7"/>
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95 </conditional>
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96 <param name="input_reads" value="child.fastq.gz" ftype="fastqsanger.gz"/>
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97 <param name="count_operation" value="count"/>
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98 <output name="read_db" ftype="meryldb">
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99 <assert_contents>
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100 <has_size value="23155" delta="3000"/>
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101 <expand macro="meryldb_archive_assumptions"/>
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102 </assert_contents>
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103 </output>
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104 <assert_stdout>
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105 <has_line line="K-mer size: 7"/>
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106 </assert_stdout>
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107 </test>
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108 </tests>
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109 <help>
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110
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111 .. class:: infomark
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112
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113 **Purpose**
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114
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115 Meryl is the k-mer counter. This tool can be used to count kmers.
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116
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117 - Count: count the occurrences of canonical k-mers
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118 - Count-forward: count the occurreces of forward k-mers
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119 - Count-reverse: count the occurreces of reverse k-mers
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120 </help>
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121 <expand macro="citations"/>
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122 </tool>