| Previous changeset 3:f8113c25bc6b (2022-07-12) Next changeset 5:d7edbc9c3a07 (2024-02-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2c0e1d33bb5a462cd31bb4ad1ec4821520caccd4 |
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modified:
macros.xml merqury.xml |
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added:
test-data/output_02.assembly.only.hist test-data/output_02.assembly.spectra-cn.hist test-data/output_02.dist_only.hist test-data/output_02.spectra-asm.hist |
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| diff -r f8113c25bc6b -r 09c589057ee8 macros.xml --- a/macros.xml Tue Jul 12 15:23:31 2022 +0000 +++ b/macros.xml Thu Aug 10 22:57:52 2023 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.3</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">merqury</xref> |
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| diff -r f8113c25bc6b -r 09c589057ee8 merqury.xml --- a/merqury.xml Tue Jul 12 15:23:31 2022 +0000 +++ b/merqury.xml Thu Aug 10 22:57:52 2023 +0000 |
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| @@ -164,6 +164,7 @@ <option value="stats" selected="true">Stats file</option> <option value="bed">BED: hap-mer tracks</option> <option value="wig">WIG: hap-mer tracks</option> + <option value="hist">Histogram files</option> <option value="log">Log file</option> </param> <param name="output_add_headers" type="boolean" value="false" label="Add column header on tabular outputs" /> @@ -196,6 +197,10 @@ <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log file"> <filter>"log" in output_selector</filter> </data> + <collection name="hist_files" type="list" label="${tool.name} on ${on_string}: histograms"> + <discover_datasets pattern="(?P<name>.+)\.hist" format="tabular" directory="output_files"/> + <filter>"hist" in output_selector</filter> + </collection> </outputs> <tests> <!--Test 01: trio mode--> @@ -217,7 +222,7 @@ </output_collection> </test> <!--Test 02: standard mode with tabular headers --> - <test expect_num_outputs="6"> + <test expect_num_outputs="7"> <conditional name="mode"> <param name="options" value="default"/> <param name="meryldb_F1" value="read-db.meryldb" ftype="meryldb"/> @@ -227,7 +232,7 @@ </conditional> </conditional> <param name="label" value="output_02"/> - <param name="output_selector" value="stats,plots,bed,sizes,qv,wig"/> + <param name="output_selector" value="stats,plots,bed,sizes,qv,wig,hist"/> <output_collection name="png_files" type="list" count="6"> <element name="output_02.assembly.spectra-cn.fl"> <assert_contents> @@ -284,6 +289,12 @@ </assert_contents> </element> </output_collection> + <output_collection name="hist_files" type="list" count="4"> + <element name="output_02.spectra-asm" file="output_02.spectra-asm.hist" ftype="tabular"/> + <element name="output_02.dist_only" file="output_02.dist_only.hist" ftype="tabular"/> + <element name="output_02.assembly.spectra-cn" file="output_02.assembly.spectra-cn.hist" ftype="tabular"/> + <element name="output_02.assembly.only" file="output_02.assembly.only.hist" ftype="tabular"/> + </output_collection> </test> <!--Test 03: Standard mode two assemblies--> <test expect_num_outputs="2"> |
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| diff -r f8113c25bc6b -r 09c589057ee8 test-data/output_02.assembly.only.hist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_02.assembly.only.hist Thu Aug 10 22:57:52 2023 +0000 |
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| @@ -0,0 +1,2 @@ +1 0 0 +2 0 0 |
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| diff -r f8113c25bc6b -r 09c589057ee8 test-data/output_02.assembly.spectra-cn.hist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_02.assembly.spectra-cn.hist Thu Aug 10 22:57:52 2023 +0000 |
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| @@ -0,0 +1,210 @@ +Copies kmer_multiplicity Count +1 1 296 +2 2 381 +3 3 380 +4 4 421 +>4 5 487 +>4 6 531 +>4 7 589 +>4 8 671 +>4 9 705 +>4 10 711 +>4 11 814 +>4 12 733 +>4 13 748 +>4 14 757 +>4 15 737 +>4 16 811 +>4 17 796 +>4 18 784 +>4 19 791 +>4 20 738 +>4 21 738 +>4 22 655 +>4 23 662 +>4 24 648 +>4 25 636 +>4 26 627 +>4 27 592 +>4 28 621 +>4 29 552 +>4 30 542 +>4 31 538 +>4 32 522 +>4 33 514 +>4 34 461 +>4 35 482 +>4 36 449 +>4 37 404 +>4 38 427 +>4 39 429 +>4 40 389 +>4 41 325 +>4 42 354 +>4 43 348 +>4 44 347 +>4 45 325 +>4 46 328 +>4 47 301 +>4 48 273 +>4 49 239 +>4 50 253 +>4 51 259 +>4 52 229 +>4 53 231 +>4 54 219 +>4 55 211 +>4 56 188 +>4 57 189 +>4 58 188 +>4 59 183 +>4 60 174 +>4 61 153 +>4 62 143 +>4 63 152 +>4 64 147 +>4 65 142 +>4 66 157 +>4 67 115 +>4 68 126 +>4 69 104 +>4 70 106 +>4 71 116 +>4 72 106 +>4 73 96 +>4 74 87 +>4 75 99 +>4 76 81 +>4 77 87 +>4 78 78 +>4 79 70 +>4 80 55 +>4 81 56 +>4 82 57 +>4 83 66 +>4 84 59 +>4 85 45 +>4 86 42 +>4 87 40 +>4 88 56 +>4 89 54 +>4 90 44 +>4 91 56 +>4 92 38 +>4 93 44 +>4 94 37 +>4 95 26 +>4 96 33 +>4 97 19 +>4 98 28 +>4 99 27 +>4 100 26 +>4 101 24 +>4 102 32 +>4 103 26 +>4 104 23 +>4 105 24 +>4 106 28 +>4 107 14 +>4 108 20 +>4 109 17 +>4 110 15 +>4 111 16 +>4 112 23 +>4 113 12 +>4 114 20 +>4 115 14 +>4 116 13 +>4 117 10 +>4 118 8 +>4 119 8 +>4 120 9 +>4 121 11 +>4 122 7 +>4 123 14 +>4 124 8 +>4 125 7 +>4 126 10 +>4 127 5 +>4 128 8 +>4 129 8 +>4 130 10 +>4 131 9 +>4 132 9 +>4 133 6 +>4 134 7 +>4 135 3 +>4 136 8 +>4 137 4 +>4 138 7 +>4 139 2 +>4 140 5 +>4 141 3 +>4 142 9 +>4 143 9 +>4 144 4 +>4 145 4 +>4 146 3 +>4 147 2 +>4 148 2 +>4 149 3 +>4 150 4 +>4 151 3 +>4 152 1 +>4 153 1 +>4 154 5 +>4 155 1 +>4 156 4 +>4 157 2 +>4 158 1 +>4 159 2 +>4 160 6 +>4 161 3 +>4 164 1 +>4 165 3 +>4 166 2 +>4 167 1 +>4 168 3 +>4 169 4 +>4 170 1 +>4 171 1 +>4 172 4 +>4 173 2 +>4 174 1 +>4 175 1 +>4 176 1 +>4 177 1 +>4 178 1 +>4 179 1 +>4 182 1 +>4 184 2 +>4 186 4 +>4 187 1 +>4 188 1 +>4 190 1 +>4 192 1 +>4 196 1 +>4 197 1 +>4 198 2 +>4 199 1 +>4 200 1 +>4 201 1 +>4 202 2 +>4 205 1 +>4 206 2 +>4 210 1 +>4 213 1 +>4 218 1 +>4 219 1 +>4 224 1 +>4 225 1 +>4 227 1 +>4 231 1 +>4 242 1 +>4 262 1 +>4 268 1 +>4 271 1 +>4 276 1 +>4 298 1 +>4 304 1 +>4 321 1 |
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| diff -r f8113c25bc6b -r 09c589057ee8 test-data/output_02.dist_only.hist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_02.dist_only.hist Thu Aug 10 22:57:52 2023 +0000 |
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| @@ -0,0 +1,1 @@ +assembly 0 0 |
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| diff -r f8113c25bc6b -r 09c589057ee8 test-data/output_02.spectra-asm.hist --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_02.spectra-asm.hist Thu Aug 10 22:57:52 2023 +0000 |
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| @@ -0,0 +1,210 @@ +Assembly kmer_multiplicity Count +assembly 1 296 +assembly 2 381 +assembly 3 380 +assembly 4 421 +assembly 5 487 +assembly 6 531 +assembly 7 589 +assembly 8 671 +assembly 9 705 +assembly 10 711 +assembly 11 814 +assembly 12 733 +assembly 13 748 +assembly 14 757 +assembly 15 737 +assembly 16 811 +assembly 17 796 +assembly 18 784 +assembly 19 791 +assembly 20 738 +assembly 21 738 +assembly 22 655 +assembly 23 662 +assembly 24 648 +assembly 25 636 +assembly 26 627 +assembly 27 592 +assembly 28 621 +assembly 29 552 +assembly 30 542 +assembly 31 538 +assembly 32 522 +assembly 33 514 +assembly 34 461 +assembly 35 482 +assembly 36 449 +assembly 37 404 +assembly 38 427 +assembly 39 429 +assembly 40 389 +assembly 41 325 +assembly 42 354 +assembly 43 348 +assembly 44 347 +assembly 45 325 +assembly 46 328 +assembly 47 301 +assembly 48 273 +assembly 49 239 +assembly 50 253 +assembly 51 259 +assembly 52 229 +assembly 53 231 +assembly 54 219 +assembly 55 211 +assembly 56 188 +assembly 57 189 +assembly 58 188 +assembly 59 183 +assembly 60 174 +assembly 61 153 +assembly 62 143 +assembly 63 152 +assembly 64 147 +assembly 65 142 +assembly 66 157 +assembly 67 115 +assembly 68 126 +assembly 69 104 +assembly 70 106 +assembly 71 116 +assembly 72 106 +assembly 73 96 +assembly 74 87 +assembly 75 99 +assembly 76 81 +assembly 77 87 +assembly 78 78 +assembly 79 70 +assembly 80 55 +assembly 81 56 +assembly 82 57 +assembly 83 66 +assembly 84 59 +assembly 85 45 +assembly 86 42 +assembly 87 40 +assembly 88 56 +assembly 89 54 +assembly 90 44 +assembly 91 56 +assembly 92 38 +assembly 93 44 +assembly 94 37 +assembly 95 26 +assembly 96 33 +assembly 97 19 +assembly 98 28 +assembly 99 27 +assembly 100 26 +assembly 101 24 +assembly 102 32 +assembly 103 26 +assembly 104 23 +assembly 105 24 +assembly 106 28 +assembly 107 14 +assembly 108 20 +assembly 109 17 +assembly 110 15 +assembly 111 16 +assembly 112 23 +assembly 113 12 +assembly 114 20 +assembly 115 14 +assembly 116 13 +assembly 117 10 +assembly 118 8 +assembly 119 8 +assembly 120 9 +assembly 121 11 +assembly 122 7 +assembly 123 14 +assembly 124 8 +assembly 125 7 +assembly 126 10 +assembly 127 5 +assembly 128 8 +assembly 129 8 +assembly 130 10 +assembly 131 9 +assembly 132 9 +assembly 133 6 +assembly 134 7 +assembly 135 3 +assembly 136 8 +assembly 137 4 +assembly 138 7 +assembly 139 2 +assembly 140 5 +assembly 141 3 +assembly 142 9 +assembly 143 9 +assembly 144 4 +assembly 145 4 +assembly 146 3 +assembly 147 2 +assembly 148 2 +assembly 149 3 +assembly 150 4 +assembly 151 3 +assembly 152 1 +assembly 153 1 +assembly 154 5 +assembly 155 1 +assembly 156 4 +assembly 157 2 +assembly 158 1 +assembly 159 2 +assembly 160 6 +assembly 161 3 +assembly 164 1 +assembly 165 3 +assembly 166 2 +assembly 167 1 +assembly 168 3 +assembly 169 4 +assembly 170 1 +assembly 171 1 +assembly 172 4 +assembly 173 2 +assembly 174 1 +assembly 175 1 +assembly 176 1 +assembly 177 1 +assembly 178 1 +assembly 179 1 +assembly 182 1 +assembly 184 2 +assembly 186 4 +assembly 187 1 +assembly 188 1 +assembly 190 1 +assembly 192 1 +assembly 196 1 +assembly 197 1 +assembly 198 2 +assembly 199 1 +assembly 200 1 +assembly 201 1 +assembly 202 2 +assembly 205 1 +assembly 206 2 +assembly 210 1 +assembly 213 1 +assembly 218 1 +assembly 219 1 +assembly 224 1 +assembly 225 1 +assembly 227 1 +assembly 231 1 +assembly 242 1 +assembly 262 1 +assembly 268 1 +assembly 271 1 +assembly 276 1 +assembly 298 1 +assembly 304 1 +assembly 321 1 |