Mercurial > repos > iuc > meryl_arithmetic_kmers

comparison arithmetic-kmers.xml @ 1:8d594609538e 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 16:43:43 +0000
parents 57343b69e9da
children
comparison
equal deleted inserted replaced
0:57343b69e9da 1:8d594609538e
10 <expand macro="requirements"/> 10 <expand macro="requirements"/>
11 <version_command>meryl --version</version_command> 11 <version_command>meryl --version</version_command>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) && 13 export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
14 mkdir -p ./temp_db/ && 14 mkdir -p ./temp_db/ &&
15 tar -zxf $input_meryldb_02 -C ./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 && 16 mv ./temp_db/* tmp.meryl &&
17 meryl 17 meryl
18 $arithmetic_operations 18 $arithmetic_operations
19 $X 19 $X
20 tmp.meryl 20 tmp.meryl
21 output read-db.meryl && 21 output read-db.meryl &&
22 tar -zcf read-db.meryldb read-db.meryl 22 tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" read-db.meryl
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed"> 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> 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> 27 <option value="decrease">Decrease: subtract x from the count of each k-mer</option>
41 <param name="X" value="100000"/> 41 <param name="X" value="100000"/>
42 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/> 42 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
43 <param name="arithmetic_operations" value="increase"/> 43 <param name="arithmetic_operations" value="increase"/>
44 <output name="read_db" ftype="meryldb"> 44 <output name="read_db" ftype="meryldb">
45 <assert_contents> 45 <assert_contents>
46 <has_size value="59500" delta="1000"/> 46 <has_size value="58946" delta="3000"/>
47 <expand macro="meryldb_archive_assumptions"/> 47 <expand macro="meryldb_archive_assumptions"/>
48 </assert_contents> 48 </assert_contents>
49 </output> 49 </output>
50 </test> 50 </test>
51 <test expect_num_outputs="1"> 51 <test expect_num_outputs="1">
52 <param name="X" value="100"/> 52 <param name="X" value="100"/>
53 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/> 53 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
54 <param name="arithmetic_operations" value="decrease"/> 54 <param name="arithmetic_operations" value="decrease"/>
55 <output name="read_db" ftype="meryldb"> 55 <output name="read_db" ftype="meryldb">
56 <assert_contents> 56 <assert_contents>
57 <has_size value="42313" delta="1000"/> 57 <has_size value="45595" delta="3000"/>
58 <expand macro="meryldb_archive_assumptions"/> 58 <expand macro="meryldb_archive_assumptions"/>
59 </assert_contents> 59 </assert_contents>
60 </output> 60 </output>
61 </test> 61 </test>
62 <test expect_num_outputs="1"> 62 <test expect_num_outputs="1">
63 <param name="X" value="3"/> 63 <param name="X" value="3"/>
64 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/> 64 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
65 <param name="arithmetic_operations" value="multiply"/> 65 <param name="arithmetic_operations" value="multiply"/>
66 <output name="read_db" ftype="meryldb"> 66 <output name="read_db" ftype="meryldb">
67 <assert_contents> 67 <assert_contents>
68 <has_size value="60530" delta="1000"/> 68 <has_size value="60645" delta="3000"/>
69 <expand macro="meryldb_archive_assumptions"/> 69 <expand macro="meryldb_archive_assumptions"/>
70 </assert_contents> 70 </assert_contents>
71 </output> 71 </output>
72 </test> 72 </test>
73 <test expect_num_outputs="1"> 73 <test expect_num_outputs="1">
74 <param name="X" value="2"/> 74 <param name="X" value="2"/>
75 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/> 75 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
76 <param name="arithmetic_operations" value="divide"/> 76 <param name="arithmetic_operations" value="divide"/>
77 <output name="read_db" ftype="meryldb"> 77 <output name="read_db" ftype="meryldb">
78 <assert_contents> 78 <assert_contents>
79 <has_size value="56200" delta="1000"/> 79 <has_size value="58481" delta="3000"/>
80 <expand macro="meryldb_archive_assumptions"/> 80 <expand macro="meryldb_archive_assumptions"/>
81 </assert_contents> 81 </assert_contents>
82 </output> 82 </output>
83 </test> 83 </test>
84 <test expect_num_outputs="1"> 84 <test expect_num_outputs="1">
85 <param name="X" value="2"/> 85 <param name="X" value="2"/>
86 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/> 86 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
87 <param name="arithmetic_operations" value="divide-round"/> 87 <param name="arithmetic_operations" value="divide-round"/>
88 <output name="read_db" ftype="meryldb"> 88 <output name="read_db" ftype="meryldb">
89 <assert_contents> 89 <assert_contents>
90 <has_size value="56100" delta="1000"/> 90 <has_size value="58236" delta="3000"/>
91 <expand macro="meryldb_archive_assumptions"/> 91 <expand macro="meryldb_archive_assumptions"/>
92 </assert_contents> 92 </assert_contents>
93 </output> 93 </output>
94 </test> 94 </test>
95 <test expect_num_outputs="1"> 95 <test expect_num_outputs="1">
96 <param name="X" value="3"/> 96 <param name="X" value="3"/>
97 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/> 97 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
98 <param name="arithmetic_operations" value="modulo"/> 98 <param name="arithmetic_operations" value="modulo"/>
99 <output name="read_db" ftype="meryldb"> 99 <output name="read_db" ftype="meryldb">
100 <assert_contents> 100 <assert_contents>
101 <has_size value="37501" delta="1000"/> 101 <has_size value="36971" delta="3000"/>
102 <expand macro="meryldb_archive_assumptions"/> 102 <expand macro="meryldb_archive_assumptions"/>
103 </assert_contents> 103 </assert_contents>
104 </output> 104 </output>
105 </test> 105 </test>
106 </tests> 106 </tests>