Mercurial > repos > iuc > meryl_arithmetic_kmers

annotate arithmetic-kmers.xml @ 1:ed66556da445 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 18:35:35 +0000
parents 50aca3a67e3e
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50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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1 <tool id="meryl_arithmetic_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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2 <description>apply arithmetic operations to k-mer counts</description>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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3 <macros>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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4 <import>macros.xml</import>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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5 </macros>
50aca3a67e3e 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"/>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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7 <xrefs>
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8 <xref type="bio.tools">meryl</xref>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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9 </xrefs>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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10 <expand macro="requirements"/>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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11 <version_command>meryl --version</version_command>
50aca3a67e3e 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[
50aca3a67e3e 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)) &&
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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14 mkdir -p ./temp_db/ &&
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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15 tar -xmf $input_meryldb_02 --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" -C ./temp_db/ &&
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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16 mv ./temp_db/* tmp.meryl &&
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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17 meryl
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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18 $arithmetic_operations
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19 $X
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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20 tmp.meryl
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21 output read-db.meryl &&
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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22 tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" read-db.meryl
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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23 ]]></command>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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24 <inputs>
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25 <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed">
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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26 <option value="increase">Increase: add x to the count of each k-mer</option>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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27 <option value="decrease">Decrease: subtract x from the count of each k-mer</option>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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28 <option value="multiply">Multiply: multiply the count of each k-mer by x</option>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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29 <option value="divide">Divide: divide the count of each k-mer by x</option>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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30 <option value="divide-round">Divide-round: divide the count of each k-mer by x and round the results</option>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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31 <option value="modulo">Modulo: set the count of each k-mer to the remainder of the count divided by x</option>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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32 </param>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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33 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset"/>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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34 <param name="X" type="integer" min="1" max="1000000" value="" optional="true" label="Operand"/>
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35 </inputs>
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36 <outputs>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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37 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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38 </outputs>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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39 <tests>
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40 <test expect_num_outputs="1">
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41 <param name="X" value="100000"/>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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42 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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43 <param name="arithmetic_operations" value="increase"/>
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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44 <output name="read_db" ftype="meryldb">
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45 <assert_contents>
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46 <has_size value="58946" delta="3000"/>
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47 <expand macro="meryldb_archive_assumptions"/>
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48 </assert_contents>
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49 </output>
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50 </test>
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51 <test expect_num_outputs="1">
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52 <param name="X" value="100"/>
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53 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
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54 <param name="arithmetic_operations" value="decrease"/>
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55 <output name="read_db" ftype="meryldb">
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56 <assert_contents>
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57 <has_size value="45595" delta="3000"/>
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58 <expand macro="meryldb_archive_assumptions"/>
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59 </assert_contents>
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60 </output>
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61 </test>
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62 <test expect_num_outputs="1">
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63 <param name="X" value="3"/>
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64 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
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65 <param name="arithmetic_operations" value="multiply"/>
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66 <output name="read_db" ftype="meryldb">
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67 <assert_contents>
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68 <has_size value="60645" delta="3000"/>
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69 <expand macro="meryldb_archive_assumptions"/>
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70 </assert_contents>
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71 </output>
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72 </test>
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73 <test expect_num_outputs="1">
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74 <param name="X" value="2"/>
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75 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
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76 <param name="arithmetic_operations" value="divide"/>
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77 <output name="read_db" ftype="meryldb">
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78 <assert_contents>
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79 <has_size value="58481" delta="3000"/>
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80 <expand macro="meryldb_archive_assumptions"/>
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81 </assert_contents>
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82 </output>
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83 </test>
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84 <test expect_num_outputs="1">
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85 <param name="X" value="2"/>
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86 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
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87 <param name="arithmetic_operations" value="divide-round"/>
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88 <output name="read_db" ftype="meryldb">
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89 <assert_contents>
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90 <has_size value="58236" delta="3000"/>
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91 <expand macro="meryldb_archive_assumptions"/>
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92 </assert_contents>
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93 </output>
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94 </test>
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95 <test expect_num_outputs="1">
50aca3a67e3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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96 <param name="X" value="3"/>
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97 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
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98 <param name="arithmetic_operations" value="modulo"/>
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99 <output name="read_db" ftype="meryldb">
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100 <assert_contents>
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101 <has_size value="36971" delta="3000"/>
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102 <expand macro="meryldb_archive_assumptions"/>
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103 </assert_contents>
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104 </output>
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105 </test>
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106 </tests>
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107 <help>
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108
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109 .. class:: infomark
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110
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111 **Purpose**
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112
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113 Meryl is the k-mer counter. This tool applies arithmetic operations on k-mer counts:
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114
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115 - Increase: add x to the count of each k-mer
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116 - Decrease: subsctract x from the count of each k-mer
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117 - Multiply: multiply the count of each k-mer by x
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118 - Divide: divide the count of each k-mer by x
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119 - Divide-round: divide the count of each k-mer by x and round th results
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120 - Modulo: set the count of each k-mer to the remainder of the count divided by x
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121 </help>
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122 <expand macro="citations"/>
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123 </tool>