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comparison groups-kmers.xml @ 1:c4758f3bf36e 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 16:44:04 +0000
parents 9f9d2625f6c3
children
comparison
equal deleted inserted replaced
0:9f9d2625f6c3 1:c4758f3bf36e
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 #for $i,$mdb in enumerate($input_meryldb_02) 14 #for $i,$mdb in enumerate($input_meryldb_02)
15 mkdir -p ./tmp_folder_$i/ && 15 mkdir -p ./tmp_folder_$i/ &&
16 tar -zxf $mdb -C ./tmp_folder_$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 && 17 mv ./tmp_folder_$i/* db_'${i}'.meryl &&
18 #end for 18 #end for
19 meryl $groups_operations output read-db.meryl db_* && 19 meryl $groups_operations output read-db.meryl db_* &&
20 tar -zcf read-db.meryldb read-db.meryl 20 tar -cf read-db.meryldb --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" read-db.meryl
21 ]]></command> 21 ]]></command>
22 <inputs> 22 <inputs>
23 <param name="groups_operations" type="select" label="Operations on sets of k-mers" help="Select an operation to be executed"> 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> 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> 25 <option value="union-min">Union-min: return k-mers that occur in any input, set the count to the minimum count</option>
42 <test expect_num_outputs="1"> 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"/> 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"/> 44 <param name="groups_operations" value="union"/>
45 <output name="read_db" ftype="meryldb"> 45 <output name="read_db" ftype="meryldb">
46 <assert_contents> 46 <assert_contents>
47 <has_size value="36100" delta="1000"/> 47 <has_size value="34918" delta="3000"/>
48 <expand macro="meryldb_archive_assumptions"/> 48 <expand macro="meryldb_archive_assumptions"/>
49 </assert_contents> 49 </assert_contents>
50 </output> 50 </output>
51 </test> 51 </test>
52 <test expect_num_outputs="1"> 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"/> 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"/> 54 <param name="groups_operations" value="union-min"/>
55 <output name="read_db" ftype="meryldb"> 55 <output name="read_db" ftype="meryldb">
56 <assert_contents> 56 <assert_contents>
57 <has_size value="58925" delta="1000"/> 57 <has_size value="59637" 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="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb"/> 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"/> 64 <param name="groups_operations" value="union-max"/>
65 <output name="read_db" ftype="meryldb"> 65 <output name="read_db" ftype="meryldb">
66 <assert_contents> 66 <assert_contents>
67 <has_size value="58930" delta="1000"/> 67 <has_size value="60705" delta="3000"/>
68 <expand macro="meryldb_archive_assumptions"/> 68 <expand macro="meryldb_archive_assumptions"/>
69 </assert_contents> 69 </assert_contents>
70 </output> 70 </output>
71 </test> 71 </test>
72 <test expect_num_outputs="1"> 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"/> 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"/> 74 <param name="groups_operations" value="union-sum"/>
75 <output name="read_db" ftype="meryldb"> 75 <output name="read_db" ftype="meryldb">
76 <assert_contents> 76 <assert_contents>
77 <has_size value="58600" delta="1000"/> 77 <has_size value="61311" delta="3000"/>
78 <expand macro="meryldb_archive_assumptions"/> 78 <expand macro="meryldb_archive_assumptions"/>
79 </assert_contents> 79 </assert_contents>
80 </output> 80 </output>
81 </test> 81 </test>
82 <test expect_num_outputs="1"> 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"/> 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"/> 84 <param name="groups_operations" value="intersect"/>
85 <output name="read_db" ftype="meryldb"> 85 <output name="read_db" ftype="meryldb">
86 <assert_contents> 86 <assert_contents>
87 <has_size value="14951" delta="1000"/> 87 <has_size value="16003" delta="3000"/>
88 <expand macro="meryldb_archive_assumptions"/> 88 <expand macro="meryldb_archive_assumptions"/>
89 </assert_contents> 89 </assert_contents>
90 </output> 90 </output>
91 </test> 91 </test>
92 <test expect_num_outputs="1"> 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"/> 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"/> 94 <param name="groups_operations" value="intersect-min"/>
95 <output name="read_db" ftype="meryldb"> 95 <output name="read_db" ftype="meryldb">
96 <assert_contents> 96 <assert_contents>
97 <has_size value="14957" delta="1000"/> 97 <has_size value="15413" delta="3000"/>
98 <expand macro="meryldb_archive_assumptions"/> 98 <expand macro="meryldb_archive_assumptions"/>
99 </assert_contents> 99 </assert_contents>
100 </output> 100 </output>
101 </test> 101 </test>
102 <test expect_num_outputs="1"> 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"/> 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"/> 104 <param name="groups_operations" value="intersect-max"/>
105 <output name="read_db" ftype="meryldb"> 105 <output name="read_db" ftype="meryldb">
106 <assert_contents> 106 <assert_contents>
107 <has_size value="14956" delta="1000"/> 107 <has_size value="15424" delta="3000"/>
108 <expand macro="meryldb_archive_assumptions"/> 108 <expand macro="meryldb_archive_assumptions"/>
109 </assert_contents> 109 </assert_contents>
110 </output> 110 </output>
111 </test> 111 </test>
112 <test expect_num_outputs="1"> 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"/> 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"/> 114 <param name="groups_operations" value="intersect-sum"/>
115 <output name="read_db" ftype="meryldb"> 115 <output name="read_db" ftype="meryldb">
116 <assert_contents> 116 <assert_contents>
117 <has_size value="14953" delta="1000"/> 117 <has_size value="15965" delta="3000"/>
118 <expand macro="meryldb_archive_assumptions"/> 118 <expand macro="meryldb_archive_assumptions"/>
119 </assert_contents> 119 </assert_contents>
120 </output> 120 </output>
121 </test> 121 </test>
122 <test expect_num_outputs="1"> 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"/> 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"/> 124 <param name="groups_operations" value="subtract"/>
125 <output name="read_db" ftype="meryldb"> 125 <output name="read_db" ftype="meryldb">
126 <assert_contents> 126 <assert_contents>
127 <has_size value="23999" delta="1000"/> 127 <has_size value="25728" delta="3000"/>
128 <expand macro="meryldb_archive_assumptions"/> 128 <expand macro="meryldb_archive_assumptions"/>
129 </assert_contents> 129 </assert_contents>
130 </output> 130 </output>
131 </test> 131 </test>
132 <test expect_num_outputs="1"> 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"/> 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"/> 134 <param name="groups_operations" value="difference"/>
135 <output name="read_db" ftype="meryldb"> 135 <output name="read_db" ftype="meryldb">
136 <assert_contents> 136 <assert_contents>
137 <has_size value="24016" delta="1000"/> 137 <has_size value="24666" delta="3000"/>
138 <expand macro="meryldb_archive_assumptions"/> 138 <expand macro="meryldb_archive_assumptions"/>
139 </assert_contents> 139 </assert_contents>
140 </output> 140 </output>
141 </test> 141 </test>
142 <test expect_num_outputs="1"> 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"/> 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"/> 144 <param name="groups_operations" value="symmetric-difference"/>
145 <output name="read_db" ftype="meryldb"> 145 <output name="read_db" ftype="meryldb">
146 <assert_contents> 146 <assert_contents>
147 <has_size value="57455" delta="1000"/> 147 <has_size value="60385" delta="3000"/>
148 <expand macro="meryldb_archive_assumptions"/> 148 <expand macro="meryldb_archive_assumptions"/>
149 </assert_contents> 149 </assert_contents>
150 </output> 150 </output>
151 </test> 151 </test>
152 </tests> 152 </tests>