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comparison 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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-1:000000000000 0:a3af9d9727ad
1 <tool id="meryl_groups_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
2 <description>apply operations on k-mer databases</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_ontology"/>
7 <xrefs>
8 <xref type="bio.tools">meryl</xref>
9 </xrefs>
10 <expand macro="requirements"/>
11 <version_command>meryl --version</version_command>
12 <command detect_errors="exit_code"><![CDATA[
13 export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
14 #for $i,$mdb in enumerate($input_meryldb_02)
15 mkdir -p ./tmp_folder_$i/ &&
16 tar -xmf $mdb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" -C ./tmp_folder_$i &&
17 mv ./tmp_folder_$i/* db_'${i}'.meryl &&
18 #end for
19 meryl $groups_operations output read-db.meryl db_* &&
20 tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" read-db.meryl
21 ]]></command>
22 <inputs>
23 <param name="groups_operations" type="select" label="Operations on sets of k-mers" help="Select an operation to be executed">
24 <option value="union">Union: return k-mers that occur in any input</option>
25 <option value="union-min">Union-min: return k-mers that occur in any input, set the count to the minimum count</option>
26 <option value="union-max">Union-max: return k-mers that occur in any input, set the count to the maximum count</option>
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>
28 <option value="intersect">Intersect: return k-mers that occur in all inputs, set the count to the count in the first input</option>
29 <option value="intersect-min">Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count</option>
30 <option value="intersect-max">Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count</option>
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>
32 <option value="subtract">Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs</option>
33 <option value="difference">Difference: return k-mers that occur in the first input, but none of the other inputs</option>
34 <option value="symmetric-difference">Symmetric-difference: return k-mers that occur in exactly one input</option>
35 </param>
36 <param name="input_meryldb_02" type="data" multiple="true" format="meryldb" label="Input meryldb"/>
37 </inputs>
38 <outputs>
39 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
40 </outputs>
41 <tests>
42 <test expect_num_outputs="1">
43 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
44 <param name="groups_operations" value="union"/>
45 <output name="read_db" ftype="meryldb">
46 <assert_contents>
47 <has_size value="34918" delta="3000"/>
48 <expand macro="meryldb_archive_assumptions"/>
49 </assert_contents>
50 </output>
51 </test>
52 <test expect_num_outputs="1">
53 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
54 <param name="groups_operations" value="union-min"/>
55 <output name="read_db" ftype="meryldb">
56 <assert_contents>
57 <has_size value="59637" delta="3000"/>
58 <expand macro="meryldb_archive_assumptions"/>
59 </assert_contents>
60 </output>
61 </test>
62 <test expect_num_outputs="1">
63 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
64 <param name="groups_operations" value="union-max"/>
65 <output name="read_db" ftype="meryldb">
66 <assert_contents>
67 <has_size value="60705" delta="3000"/>
68 <expand macro="meryldb_archive_assumptions"/>
69 </assert_contents>
70 </output>
71 </test>
72 <test expect_num_outputs="1">
73 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
74 <param name="groups_operations" value="union-sum"/>
75 <output name="read_db" ftype="meryldb">
76 <assert_contents>
77 <has_size value="61311" delta="3000"/>
78 <expand macro="meryldb_archive_assumptions"/>
79 </assert_contents>
80 </output>
81 </test>
82 <test expect_num_outputs="1">
83 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
84 <param name="groups_operations" value="intersect"/>
85 <output name="read_db" ftype="meryldb">
86 <assert_contents>
87 <has_size value="16003" delta="3000"/>
88 <expand macro="meryldb_archive_assumptions"/>
89 </assert_contents>
90 </output>
91 </test>
92 <test expect_num_outputs="1">
93 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
94 <param name="groups_operations" value="intersect-min"/>
95 <output name="read_db" ftype="meryldb">
96 <assert_contents>
97 <has_size value="15413" delta="3000"/>
98 <expand macro="meryldb_archive_assumptions"/>
99 </assert_contents>
100 </output>
101 </test>
102 <test expect_num_outputs="1">
103 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
104 <param name="groups_operations" value="intersect-max"/>
105 <output name="read_db" ftype="meryldb">
106 <assert_contents>
107 <has_size value="15424" delta="3000"/>
108 <expand macro="meryldb_archive_assumptions"/>
109 </assert_contents>
110 </output>
111 </test>
112 <test expect_num_outputs="1">
113 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
114 <param name="groups_operations" value="intersect-sum"/>
115 <output name="read_db" ftype="meryldb">
116 <assert_contents>
117 <has_size value="15965" delta="3000"/>
118 <expand macro="meryldb_archive_assumptions"/>
119 </assert_contents>
120 </output>
121 </test>
122 <test expect_num_outputs="1">
123 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
124 <param name="groups_operations" value="subtract"/>
125 <output name="read_db" ftype="meryldb">
126 <assert_contents>
127 <has_size value="25728" delta="3000"/>
128 <expand macro="meryldb_archive_assumptions"/>
129 </assert_contents>
130 </output>
131 </test>
132 <test expect_num_outputs="1">
133 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
134 <param name="groups_operations" value="difference"/>
135 <output name="read_db" ftype="meryldb">
136 <assert_contents>
137 <has_size value="24666" delta="3000"/>
138 <expand macro="meryldb_archive_assumptions"/>
139 </assert_contents>
140 </output>
141 </test>
142 <test expect_num_outputs="1">
143 <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/>
144 <param name="groups_operations" value="symmetric-difference"/>
145 <output name="read_db" ftype="meryldb">
146 <assert_contents>
147 <has_size value="60385" delta="3000"/>
148 <expand macro="meryldb_archive_assumptions"/>
149 </assert_contents>
150 </output>
151 </test>
152 </tests>
153 <help>
154
155 .. class:: infomark
156
157 **Purpose**
158
159 Meryl is the k-mer counter. Apply operations on multiple k-mer databases.
160
161 - Union-min: return k-mers that occur in any input, set the count to the minimum count
162 - Union-max: return k-mers that occur in any input, set the count to the maximum count
163 - Union-sum: return k-mers that occur in any input, set the count to the sum of the counts
164 - Intersect: return k-mers that occur in all inputs, set the count to the count in the first input
165 - Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count
166 - Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count
167 - Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts
168 - Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs
169 - Difference: return k-mers that occur in the first input, but none of the other inputs
170 - Symmetric-difference: return k-mers that occur in exactly one input
171
172 </help>
173 <expand macro="citations"/>
174 </tool>