Mercurial > repos > iuc > meryl_filter_kmers

annotate filter-kmers.xml @ 1:4f5b7b30ed7d 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 18:34:21 +0000
parents 956142499a02
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956142499a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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1 <tool id="meryl_filter_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
956142499a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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2 <description>filter k-mers</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
956142499a02 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"/>
956142499a02 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>
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9 </xrefs>
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10 <expand macro="requirements"/>
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11 <version_command>meryl --version</version_command>
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12 <command detect_errors="exit_code"><![CDATA[
956142499a02 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)) &&
956142499a02 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/ &&
956142499a02 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/ &&
956142499a02 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 &&
956142499a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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17 meryl
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18 $filter_operations
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19 #if $filter_type.type == 'times'
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20 $filter_type.N
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21 #elif $filter_type.type == 'frequency'
1
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22 distinct=$filter_type.distinct
0
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23 #end if
956142499a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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24 tmp.meryl
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25 output read-db.meryl &&
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26 tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" read-db.meryl
956142499a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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27 ]]></command>
956142499a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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28 <inputs>
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29 <param name="filter_operations" type="select" label="Filter operations" help="Select an operation to be executed">
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30 <option value="less-than">Less-than: return k-mers that occur fewer than a threshold value</option>
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31 <option value="greater-than">Greater-than: return k-mers that occur more than a threshold value</option>
956142499a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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32 <option value="equal-to">Equal-to: return k-mers that occur exactly a threshold value</option>
956142499a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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33 <option value="not-equal-to">Not-equal-to: return k-mers that do not occur exactly a threshold value</option>
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34 </param>
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35 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset"/>
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36 <conditional name="filter_type">
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37 <param name="type" type="select" label="Type of filtering">
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38 <option value="times">Return k-mers that occur N times in the input</option>
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39 <option value="frequency">Return k-mers occurring at specific frequencies</option>
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40 </param>
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41 <when value="times">
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42 <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Number of times in the input" help="Return k-mers that occur N times in the input."/>
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43 </when>
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44 <when value="frequency">
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45 <param name="distinct" type="float" min="0" max="1" value="0.9998" optional="true" label="Frequency" help="Return k-mers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)"/>
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46 </when>
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47 </conditional>
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48 </inputs>
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49 <outputs>
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50 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
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51 </outputs>
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52 <tests>
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53 <test expect_num_outputs="1">
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54 <conditional name="filter_type">
1
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55 <param name="type" value="times"/>
0
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56 <param name="N" value="100"/>
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57 </conditional>
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58 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
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59 <param name="filter_operations" value="less-than"/>
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60 <output name="read_db" ftype="meryldb">
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61 <assert_contents>
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62 <has_size value="32382" delta="3000"/>
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63 <expand macro="meryldb_archive_assumptions"/>
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64 </assert_contents>
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65 </output>
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66 </test>
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67 <test expect_num_outputs="1">
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68 <conditional name="filter_type">
1
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69 <param name="type" value="times"/>
0
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70 <param name="N" value="80"/>
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71 </conditional>
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72 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
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73 <param name="filter_operations" value="greater-than"/>
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74 <output name="read_db" ftype="meryldb">
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75 <assert_contents>
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76 <has_size value="50850" delta="3000"/>
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77 <expand macro="meryldb_archive_assumptions"/>
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78 </assert_contents>
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79 </output>
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80 </test>
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81 <test expect_num_outputs="1">
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82 <conditional name="filter_type">
1
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83 <param name="type" value="frequency"/>
0
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84 <param name="distinct" value="0.9998"/>
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85 </conditional>
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86 <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb"/>
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87 <param name="filter_operations" value="greater-than"/>
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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="1880" delta="1000"/>
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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">
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96 <conditional name="filter_type">
1
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97 <param name="type" value="times"/>
0
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98 <param name="N" value="100"/>
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99 </conditional>
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100 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
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101 <param name="filter_operations" value="equal-to"/>
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102 <output name="read_db" ftype="meryldb">
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103 <assert_contents>
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104 <has_size value="3073" delta="1000"/>
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105 <expand macro="meryldb_archive_assumptions"/>
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106 </assert_contents>
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107 </output>
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108 </test>
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109 <test expect_num_outputs="1">
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110 <conditional name="filter_type">
1
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111 <param name="type" value="times"/>
0
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112 <param name="N" value="100"/>
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113 </conditional>
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114 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
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115 <param name="filter_operations" value="not-equal-to"/>
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116 <output name="read_db" ftype="meryldb">
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117 <assert_contents>
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118 <has_size value="59719" delta="3000"/>
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119 <expand macro="meryldb_archive_assumptions"/>
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120 </assert_contents>
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121 </output>
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122 </test>
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123 </tests>
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124 <help>
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125
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126 .. class:: infomark
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127
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128 **Purpose**
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129
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130 Meryl is the k-mer counter. This tool can be used to filter k-mers.
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131
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132 - Less-than: return k-mers that occur fewer than N times in the input
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133 - Greater-than: return k-mers that occur more than N times in the input
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134 - Equal-to: return k-mers that occur exactly N times in the input
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135 - Not-equal-to: return k-mers that do not occur exactly N times in the input
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136
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137 </help>
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138 <expand macro="citations"/>
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139 </tool>