Mercurial > repos > iuc > meryl_groups_kmers

annotate groups-kmers.xml @ 0:a3af9d9727ad 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 16:42:51 +0000
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0
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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1 <tool id="meryl_groups_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
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2 <description>apply operations on k-mer databases</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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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>
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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[
a3af9d9727ad 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)) &&
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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14 #for $i,$mdb in enumerate($input_meryldb_02)
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15 mkdir -p ./tmp_folder_$i/ &&
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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16 tar -xmf $mdb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" -C ./tmp_folder_$i &&
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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17 mv ./tmp_folder_$i/* db_'${i}'.meryl &&
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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18 #end for
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19 meryl $groups_operations output read-db.meryl db_* &&
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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20 tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" read-db.meryl
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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21 ]]></command>
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22 <inputs>
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23 <param name="groups_operations" type="select" label="Operations on sets of k-mers" help="Select an operation to be executed">
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24 <option value="union">Union: return k-mers that occur in any input</option>
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25 <option value="union-min">Union-min: return k-mers that occur in any input, set the count to the minimum count</option>
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26 <option value="union-max">Union-max: return k-mers that occur in any input, set the count to the maximum count</option>
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27 <option value="union-sum">Union-sum: return k-mers that occur in any input, set the count to the sum of the counts</option>
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28 <option value="intersect">Intersect: return k-mers that occur in all inputs, set the count to the count in the first input</option>
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29 <option value="intersect-min">Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count</option>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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30 <option value="intersect-max">Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count</option>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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31 <option value="intersect-sum">Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts</option>
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32 <option value="subtract">Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs</option>
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33 <option value="difference">Difference: return k-mers that occur in the first input, but none of the other inputs</option>
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34 <option value="symmetric-difference">Symmetric-difference: return k-mers that occur in exactly one input</option>
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35 </param>
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36 <param name="input_meryldb_02" type="data" multiple="true" format="meryldb" label="Input meryldb"/>
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37 </inputs>
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38 <outputs>
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39 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
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40 </outputs>
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41 <tests>
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42 <test expect_num_outputs="1">
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43 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
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44 <param name="groups_operations" value="union"/>
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45 <output name="read_db" ftype="meryldb">
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46 <assert_contents>
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47 <has_size value="34918" delta="3000"/>
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48 <expand macro="meryldb_archive_assumptions"/>
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49 </assert_contents>
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50 </output>
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51 </test>
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52 <test expect_num_outputs="1">
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53 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
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54 <param name="groups_operations" value="union-min"/>
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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="59637" 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="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
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64 <param name="groups_operations" value="union-max"/>
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65 <output name="read_db" ftype="meryldb">
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66 <assert_contents>
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67 <has_size value="60705" delta="3000"/>
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68 <expand macro="meryldb_archive_assumptions"/>
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69 </assert_contents>
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70 </output>
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71 </test>
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72 <test expect_num_outputs="1">
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73 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
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74 <param name="groups_operations" value="union-sum"/>
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75 <output name="read_db" ftype="meryldb">
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76 <assert_contents>
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77 <has_size value="61311" delta="3000"/>
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78 <expand macro="meryldb_archive_assumptions"/>
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79 </assert_contents>
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80 </output>
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81 </test>
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82 <test expect_num_outputs="1">
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83 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
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84 <param name="groups_operations" value="intersect"/>
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iuc
parents:
diff changeset
85 <output name="read_db" ftype="meryldb">
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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86 <assert_contents>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
parents:
diff changeset
87 <has_size value="16003" delta="3000"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
parents:
diff changeset
88 <expand macro="meryldb_archive_assumptions"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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89 </assert_contents>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
parents:
diff changeset
90 </output>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
parents:
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91 </test>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
parents:
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92 <test expect_num_outputs="1">
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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diff changeset
93 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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94 <param name="groups_operations" value="intersect-min"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
parents:
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95 <output name="read_db" ftype="meryldb">
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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96 <assert_contents>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
parents:
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97 <has_size value="15413" delta="3000"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
parents:
diff changeset
98 <expand macro="meryldb_archive_assumptions"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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99 </assert_contents>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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100 </output>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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101 </test>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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102 <test expect_num_outputs="1">
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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103 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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104 <param name="groups_operations" value="intersect-max"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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105 <output name="read_db" ftype="meryldb">
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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106 <assert_contents>
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iuc
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107 <has_size value="15424" delta="3000"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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108 <expand macro="meryldb_archive_assumptions"/>
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109 </assert_contents>
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110 </output>
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111 </test>
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112 <test expect_num_outputs="1">
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113 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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114 <param name="groups_operations" value="intersect-sum"/>
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115 <output name="read_db" ftype="meryldb">
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116 <assert_contents>
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117 <has_size value="15965" delta="3000"/>
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iuc
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118 <expand macro="meryldb_archive_assumptions"/>
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119 </assert_contents>
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120 </output>
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121 </test>
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iuc
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122 <test expect_num_outputs="1">
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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123 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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124 <param name="groups_operations" value="subtract"/>
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iuc
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125 <output name="read_db" ftype="meryldb">
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iuc
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126 <assert_contents>
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iuc
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127 <has_size value="25728" delta="3000"/>
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iuc
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128 <expand macro="meryldb_archive_assumptions"/>
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129 </assert_contents>
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130 </output>
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131 </test>
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132 <test expect_num_outputs="1">
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iuc
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133 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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134 <param name="groups_operations" value="difference"/>
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iuc
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135 <output name="read_db" ftype="meryldb">
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136 <assert_contents>
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iuc
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137 <has_size value="24666" delta="3000"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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138 <expand macro="meryldb_archive_assumptions"/>
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139 </assert_contents>
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140 </output>
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141 </test>
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142 <test expect_num_outputs="1">
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143 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
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144 <param name="groups_operations" value="symmetric-difference"/>
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iuc
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145 <output name="read_db" ftype="meryldb">
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146 <assert_contents>
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iuc
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147 <has_size value="60385" delta="3000"/>
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148 <expand macro="meryldb_archive_assumptions"/>
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149 </assert_contents>
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150 </output>
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151 </test>
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152 </tests>
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153 <help>
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154
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155 .. class:: infomark
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156
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iuc
parents:
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157 **Purpose**
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158
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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159 Meryl is the k-mer counter. Apply operations on multiple k-mer databases.
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160
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161 - Union-min: return k-mers that occur in any input, set the count to the minimum count
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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162 - Union-max: return k-mers that occur in any input, set the count to the maximum count
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163 - Union-sum: return k-mers that occur in any input, set the count to the sum of the counts
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164 - Intersect: return k-mers that occur in all inputs, set the count to the count in the first input
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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165 - Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count
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iuc
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166 - Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count
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iuc
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167 - Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts
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168 - Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs
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169 - Difference: return k-mers that occur in the first input, but none of the other inputs
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170 - Symmetric-difference: return k-mers that occur in exactly one input
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171
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172 </help>
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173 <expand macro="citations"/>
a3af9d9727ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
iuc
parents:
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174 </tool>