Mercurial > repos > iuc > meryl_arithmetic_kmers

comparison arithmetic-kmers.xml @ 0:50aca3a67e3e 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 16:42:28 +0000
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-1:000000000000 0:50aca3a67e3e
1 <tool id="meryl_arithmetic_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
2 <description>apply arithmetic operations to k-mer counts</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 mkdir -p ./temp_db/ &&
15 tar -xmf $input_meryldb_02 --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" -C ./temp_db/ &&
16 mv ./temp_db/* tmp.meryl &&
17 meryl
18 $arithmetic_operations
19 $X
20 tmp.meryl
21 output read-db.meryl &&
22 tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" read-db.meryl
23 ]]></command>
24 <inputs>
25 <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed">
26 <option value="increase">Increase: add x to the count of each k-mer</option>
27 <option value="decrease">Decrease: subtract x from the count of each k-mer</option>
28 <option value="multiply">Multiply: multiply the count of each k-mer by x</option>
29 <option value="divide">Divide: divide the count of each k-mer by x</option>
30 <option value="divide-round">Divide-round: divide the count of each k-mer by x and round the results</option>
31 <option value="modulo">Modulo: set the count of each k-mer to the remainder of the count divided by x</option>
32 </param>
33 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" help="Select a meryldb dataset"/>
34 <param name="X" type="integer" min="1" max="1000000" value="" optional="true" label="Operand"/>
35 </inputs>
36 <outputs>
37 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
38 </outputs>
39 <tests>
40 <test expect_num_outputs="1">
41 <param name="X" value="100000"/>
42 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
43 <param name="arithmetic_operations" value="increase"/>
44 <output name="read_db" ftype="meryldb">
45 <assert_contents>
46 <has_size value="58946" delta="3000"/>
47 <expand macro="meryldb_archive_assumptions"/>
48 </assert_contents>
49 </output>
50 </test>
51 <test expect_num_outputs="1">
52 <param name="X" value="100"/>
53 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
54 <param name="arithmetic_operations" value="decrease"/>
55 <output name="read_db" ftype="meryldb">
56 <assert_contents>
57 <has_size value="45595" delta="3000"/>
58 <expand macro="meryldb_archive_assumptions"/>
59 </assert_contents>
60 </output>
61 </test>
62 <test expect_num_outputs="1">
63 <param name="X" value="3"/>
64 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
65 <param name="arithmetic_operations" value="multiply"/>
66 <output name="read_db" ftype="meryldb">
67 <assert_contents>
68 <has_size value="60645" delta="3000"/>
69 <expand macro="meryldb_archive_assumptions"/>
70 </assert_contents>
71 </output>
72 </test>
73 <test expect_num_outputs="1">
74 <param name="X" value="2"/>
75 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
76 <param name="arithmetic_operations" value="divide"/>
77 <output name="read_db" ftype="meryldb">
78 <assert_contents>
79 <has_size value="58481" delta="3000"/>
80 <expand macro="meryldb_archive_assumptions"/>
81 </assert_contents>
82 </output>
83 </test>
84 <test expect_num_outputs="1">
85 <param name="X" value="2"/>
86 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
87 <param name="arithmetic_operations" value="divide-round"/>
88 <output name="read_db" ftype="meryldb">
89 <assert_contents>
90 <has_size value="58236" delta="3000"/>
91 <expand macro="meryldb_archive_assumptions"/>
92 </assert_contents>
93 </output>
94 </test>
95 <test expect_num_outputs="1">
96 <param name="X" value="3"/>
97 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
98 <param name="arithmetic_operations" value="modulo"/>
99 <output name="read_db" ftype="meryldb">
100 <assert_contents>
101 <has_size value="36971" delta="3000"/>
102 <expand macro="meryldb_archive_assumptions"/>
103 </assert_contents>
104 </output>
105 </test>
106 </tests>
107 <help>
108
109 .. class:: infomark
110
111 **Purpose**
112
113 Meryl is the k-mer counter. This tool applies arithmetic operations on k-mer counts:
114
115 - Increase: add x to the count of each k-mer
116 - Decrease: subsctract x from the count of each k-mer
117 - Multiply: multiply the count of each k-mer by x
118 - Divide: divide the count of each k-mer by x
119 - Divide-round: divide the count of each k-mer by x and round th results
120 - Modulo: set the count of each k-mer to the remainder of the count divided by x
121 </help>
122 <expand macro="citations"/>
123 </tool>