# HG changeset patch # User brinkmanlab # Date 1643081188 0 # Node ID de3a45e9ccce74e5aa74f56fd24dbc9a5a452ef0 "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99" diff -r 000000000000 -r de3a45e9ccce emboss_format_corrector.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/emboss_format_corrector.py Tue Jan 25 03:26:28 2022 +0000 @@ -0,0 +1,47 @@ +# EMBOSS format corrector +import operator + + +# Properly set file formats before job run +def exec_before_job(app, inp_data=None, out_data=None, tool=None, param_dict=None): + # why isn't items an ordered list? + items = out_data.items() + items = sorted(items, key=operator.itemgetter(0)) + + # normal filetype correction + data_count = 1 + for name, data in items: + outputType = param_dict.get('out_format' + str(data_count), None) + if outputType is not None: + if outputType == 'ncbi': + outputType = "fasta" + elif outputType == 'excel': + outputType = "tabular" + elif outputType == 'text': + outputType = "txt" + data = app.datatypes_registry.change_datatype(data, outputType) + app.model.context.add(data) + app.model.context.flush() + data_count += 1 + + # html filetype correction + data_count = 1 + for name, data in items: + wants_plot = param_dict.get('html_out' + str(data_count), None) + ext = "html" + if wants_plot == "yes": + data = app.datatypes_registry.change_datatype(data, ext) + app.model.context.add(data) + app.model.context.flush() + data_count += 1 + + # png file correction + data_count = 1 + for name, data in items: + wants_plot = param_dict.get('plot' + str(data_count), None) + ext = "png" + if wants_plot == "yes": + data = app.datatypes_registry.change_datatype(data, ext) + app.model.context.add(data) + app.model.context.flush() + data_count += 1 diff -r 000000000000 -r de3a45e9ccce emboss_fuzznuc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/emboss_fuzznuc.xml Tue Jan 25 03:26:28 2022 +0000 @@ -0,0 +1,133 @@ + + Nucleic acid pattern search + + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + +
+ +
+ + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: warningmark + +The input dataset needs to be sequences. + +----- + + You can view the original documentation here_. + + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzznuc.html + + + diff -r 000000000000 -r de3a45e9ccce macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jan 25 03:26:28 2022 +0000 @@ -0,0 +1,50 @@ + + 6.6.0 + + + emboss + perl + + + + + + + + + + + emboss + + + + + 10.1016/S0168-9525(00)02024-2 + 10.1101/gr.5578007 + + + + + + + + + + + + + + + + + + + + + + + + + .*[^\\]$ + + diff -r 000000000000 -r de3a45e9ccce test-data/2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.fasta Tue Jan 25 03:26:28 2022 +0000 @@ -0,0 +1,11 @@ +>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; +gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt +tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac +cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg +aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg +gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt +tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac +ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt +ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt +tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa +aacaattcta atggtcaaaa a \ No newline at end of file diff -r 000000000000 -r de3a45e9ccce test-data/emboss_fuzznuc_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_fuzznuc_out.tabular Tue Jan 25 03:26:28 2022 +0000 @@ -0,0 +1,41 @@ +SeqName Start End Score Strand Pattern_name Mismatch +Sequence 12 13 2 + pattern1 . +Sequence 13 14 2 + pattern1 . +Sequence 14 15 2 + pattern1 . +Sequence 53 54 2 + pattern1 . +Sequence 73 74 2 + pattern1 . +Sequence 74 75 2 + pattern1 . +Sequence 85 86 2 + pattern1 . +Sequence 92 93 2 + pattern1 . +Sequence 97 98 2 + pattern1 . +Sequence 98 99 2 + pattern1 . +Sequence 157 158 2 + pattern1 . +Sequence 158 159 2 + pattern1 . +Sequence 181 182 2 + pattern1 . +Sequence 193 194 2 + pattern1 . +Sequence 196 197 2 + pattern1 . +Sequence 201 202 2 + pattern1 . +Sequence 204 205 2 + pattern1 . +Sequence 252 253 2 + pattern1 . +Sequence 264 265 2 + pattern1 . +Sequence 274 275 2 + pattern1 . +Sequence 287 288 2 + pattern1 . +Sequence 326 327 2 + pattern1 . +Sequence 340 341 2 + pattern1 . +Sequence 364 365 2 + pattern1 . +Sequence 393 394 2 + pattern1 . +Sequence 409 410 2 + pattern1 . +Sequence 429 430 2 + pattern1 . +Sequence 430 431 2 + pattern1 . +Sequence 431 432 2 + pattern1 . +Sequence 449 450 2 + pattern1 . +Sequence 534 535 2 + pattern1 . +Sequence 539 540 2 + pattern1 . +Sequence 540 541 2 + pattern1 . +Sequence 541 542 2 + pattern1 . +Sequence 544 545 2 + pattern1 . +Sequence 550 551 2 + pattern1 . +Sequence 557 558 2 + pattern1 . +Sequence 558 559 2 + pattern1 . +Sequence 559 560 2 + pattern1 . +Sequence 560 561 2 + pattern1 . diff -r 000000000000 -r de3a45e9ccce test-data/emboss_fuzznuc_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_fuzznuc_out2.tabular Tue Jan 25 03:26:28 2022 +0000 @@ -0,0 +1,6 @@ +SeqName Start End Score Strand Pattern_name Mismatch +Sequence 157 158 2 + pattern1 . +Sequence 158 159 2 + pattern1 . +Sequence 181 182 2 + pattern1 . +Sequence 193 194 2 + pattern1 . +Sequence 196 197 2 + pattern1 .