| Previous changeset 10:4d73965d99a2 (2021-06-09) |
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Commit message:
planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/assembly_post_processor commit 5b19bd262023af92bc9aaa65f75b5ec81814e90f-dirty |
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modified:
assembly_post_processor.xml macros.xml |
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removed:
utils.py |
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| diff -r 4d73965d99a2 -r 2c2ad8af0a4e assembly_post_processor.xml --- a/assembly_post_processor.xml Wed Jun 09 20:26:55 2021 +0000 +++ b/assembly_post_processor.xml Wed Jun 12 19:29:25 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="@WRAPPER_VERSION@.4.0" profile="18.09"> +<tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="@TOOL_VERSION@.4.0+galaxy0" profile="18.09"> <description>post-processes de novo transcriptome assembly</description> <macros> <import>macros.xml</import> @@ -118,21 +118,21 @@ <data name="output_cds" format="fasta" label="transcripts.cds: ${tool.name} on ${on_string}"/> </outputs> <tests> - <test> + <test expect_num_outputs="4"> <param name="input" value="assembly.fasta" ftype="fasta"/> <output name="output_cds" file="transcripts.cds" ftype="fasta"/> <output name="output_cleaned_cds" file="transcripts.cleaned.cds" ftype="fasta"/> <output name="output_cleaned_pep" file="transcripts.cleaned.pep" ftype="fasta"/> <output name="output_pep" file="transcripts.pep" ftype="fasta"/> </test> - <test> + <test expect_num_outputs="8"> <param name="input" value="assembly_tgf.fasta" ftype="fasta"/> <param name="options_type_selector" value="advanced"/> <param name="target_gene_family_assembly" value="yes"/> <param name="orthogroups" value="target_orthos.ids"/> <param name="method" value="orthomcl"/> <param name="dereplicate" value="yes"/> - <output_collection name="output_targeted_gene_families" type="list"> + <output_collection name="output_targeted_gene_families" type="list" count="0"> </output_collection> <output name="output_targeted_gene_families_stats" file="output_targeted_gene_families_stats.tabular" ftype="tabular"/> <output name="output_cds" file="transcripts_tgf.cds" ftype="fasta"/> @@ -174,105 +174,16 @@ </help> <citations> - <expand macro="citation1" /> - <citation type="bibtex"> - @article{Honaas2016, - journal = {PloS one}, - author = {2. Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH}, - title = {Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome}, - year = {2016}, - volume = {11}, - number = {1}, - pages = {e0146062},} - </citation> - <citation type="bibtex"> - @article{Haas2013, - journal = {Nature Protocols}, - author = {3. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD}, - title = {De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis}, - year = {2013}, - volume = {8}, - number = {8}, - pages = {1494-1512},} - </citation> - <citation type="bibtex"> - @article{Huang1999, - journal = {Genome Research}, - author = {5. Huang X, Madan A}, - title = {CAP3: A DNA sequence assembly program}, - year = {1999}, - volume = {9}, - number = {9}, - pages = {868-877}, - url = {http://seq.cs.iastate.edu/cap3.html},} - </citation> - <citation type="bibtex"> - @article{Eddy2009, - journal = {Genome Inform}, - author = {6. Eddy SR}, - title = {A new generation of homology search tools based on probabilistic inference}, - year = {2009}, - volume = {23}, - number = {1}, - pages = {205-211},} - </citation> - <citation type="bibtex"> - @article{Katoh2013, - journal = {Molecular biology and evolution}, - author = {7. Katoh K, Standley DM}, - title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability}, - year = {2013}, - volume = {30}, - number = {4}, - pages = {772-780},} - </citation> - <citation type="bibtex"> - @article{Sasidharan2012, - journal = {Nucleic Acids Research}, - author = {8. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A}, - title = {GFam: a platform for automatic annotation of gene families}, - year = {2012}, - pages = {gks631},} - </citation> - <citation type="bibtex"> - @article{Li2003, - journal = {Genome Research} - author = {9. Li L, Stoeckert CJ, Roos DS}, - title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes}, - year = {2003}, - volume = {13}, - number = {9}, - pages = {2178-2189},} - </citation> - <citation type="bibtex"> - @article{Emms2015, - journal = {Genome Biology} - author = {10. Emms DM, Kelly S}, - title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy}, - year = {2015}, - volume = {16}, - number = {1}, - pages = {157},} - </citation> - <citation type="bibtex"> - @article{Capella-Gutierrez2009, - journal = {Bioinformatics,}, - author = {11. Capella-Gutierrez S, Silla-MartÃnez JM, Gabaldón T}, - title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses}, - year = {2009}, - volume = {25}, - number = {15}, - pages = {1972-1973},} - </citation> - <citation type="bibtex"> - @article{Gremme2013, - journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, - author = {12. Gremme G, Steinbiss S, Kurtz S}, - title = {GenomeTools: a comprehensive software library for efficient processing of structured genome annotations}, - year = {2013}, - volume = {10}, - number = {3}, - pages = {645-656},} - </citation> + <citation type="doi">10.3389/fpls.2022.1011199</citation> + <citation type="doi">10.1371/journal.pone.0146062</citation> + <citation type="doi">10.1038/nprot.2013.084</citation> + <citation type="doi">10.1101/gr.9.9.868</citation> + <citation type="doi">10.1142/9781848165632_0019</citation> + <citation type="doi">10.1093/molbev/mst010</citation> + <citation type="doi">10.1093/nar/gks631</citation> + <citation type="doi">10.1101/gr.1224503</citation> + <citation type="doi">10.1186/s13059-015-0721-2</citation> + <citation type="doi">10.1093/bioinformatics/btp348</citation> + <citation type="doi">10.1109/TCBB.2013.68</citation> </citations> </tool> |
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| diff -r 4d73965d99a2 -r 2c2ad8af0a4e macros.xml --- a/macros.xml Wed Jun 09 20:26:55 2021 +0000 +++ b/macros.xml Wed Jun 12 19:29:25 2024 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version='1.0' encoding='UTF-8'?> <macros> - <token name="@WRAPPER_VERSION@">1.0</token> + <token name="@TOOL_VERSION@">1.0</token> <xml name="param_method"> <param name="method" type="select" label="Protein clustering method" dynamic_options="get_clustering_method_options(scaffold)"/> </xml> @@ -15,14 +15,4 @@ </options> </param> </xml> - <xml name="citation1"> - <citation type="bibtex"> - @misc{None, - journal = {None}, - author = {1. Wafula EK}, - title = {Manuscript in preparation}, - year = {None}, - url = {https://github.com/dePamphilis/PlantTribes},} - </citation> - </xml> </macros> |
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| diff -r 4d73965d99a2 -r 2c2ad8af0a4e utils.py --- a/utils.py Wed Jun 09 20:26:55 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,56 +0,0 @@ -import os -import shutil -import subprocess -import sys - -FSTDERR = 'stderr.txt' -FSTDOUT = 'stdout.txt' - - -def check_execution_errors(rc, fstderr, fstdout): - if rc != 0: - fh = open(fstdout, 'rb') - out_msg = fh.read() - fh.close() - fh = open(fstderr, 'rb') - err_msg = fh.read() - fh.close() - msg = '%s\n%s\n' % (str(out_msg), str(err_msg)) - stop_err(msg) - - -def get_response_buffers(): - fstderr = os.path.join(os.getcwd(), FSTDERR) - fherr = open(fstderr, 'wb') - fstdout = os.path.join(os.getcwd(), FSTDOUT) - fhout = open(fstdout, 'wb') - return fstderr, fherr, fstdout, fhout - - -def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False): - source_directory = os.path.abspath(source_dir) - destination_directory = os.path.abspath(destination_dir) - if not os.path.isdir(destination_directory): - os.makedirs(destination_directory) - for dir_entry in os.listdir(source_directory): - source_entry = os.path.join(source_directory, dir_entry) - if copy: - shutil.copy(source_entry, destination_directory) - else: - shutil.move(source_entry, destination_directory) - if remove_source_dir: - os.rmdir(source_directory) - - -def run_command(cmd): - fstderr, fherr, fstdout, fhout = get_response_buffers() - proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True) - rc = proc.wait() - # Check results. - fherr.close() - fhout.close() - check_execution_errors(rc, fstderr, fstdout) - - -def stop_err(msg): - sys.exit(msg) |