Mercurial > repos > greg > plant_tribes_assembly_post_processor
diff assembly_post_processor.xml @ 10:4d73965d99a2 draft
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/assembly_post_processor commit 71ba0e157346927bf42b788f552b95a71556b28a"
author | greg |
---|---|
date | Wed, 09 Jun 2021 20:26:55 +0000 |
parents | 9c72c91d291f |
children | 2c2ad8af0a4e |
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--- a/assembly_post_processor.xml Thu Jan 10 10:45:23 2019 -0500 +++ b/assembly_post_processor.xml Wed Jun 09 20:26:55 2021 +0000 @@ -11,10 +11,7 @@ #set output_dir = 'assemblyPostProcessing_dir' AssemblyPostProcessor --transcripts '$input' ---prediction_method $prediction_method_cond.prediction_method -#if str($prediction_method_cond.prediction_method) == 'estscan': - --score_matrices '$score_matrices' -#end if +--prediction_method 'transdecoder' #if str($options_type.options_type_selector) == 'advanced': #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': @@ -68,16 +65,6 @@ fi]]></command> <inputs> <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> - <conditional name="prediction_method_cond"> - <param name="prediction_method" type="select" label="Coding regions prediction method"> - <option value="transdecoder" selected="true">TransDecoder</option> - <option value="estscan">ESTScan</option> - </param> - <when value="transdecoder" /> - <when value="estscan"> - <param name="score_matrices" format="smat" type="data" label="Scores matrices"/> - </when> - </conditional> <conditional name="options_type"> <param name="options_type_selector" type="select" label="Options configuration"> <option value="basic" selected="true">Basic</option> @@ -133,32 +120,16 @@ <tests> <test> <param name="input" value="assembly.fasta" ftype="fasta"/> - <param name="prediction_method" value="transdecoder"/> <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> - <param name="input" value="assembly.fasta" ftype="fasta"/> - <param name="prediction_method" value="estscan"/> - <param name="score_matrices" value="arabidopsis_thaliana.smat" ftype="smat"/> - <param name="options_type_selector" value="advanced"/> - <param name="dereplicate" value="yes"/> - <output name="output_cds" file="transcripts2.cds" ftype="fasta"/> - <output name="output_cleaned_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/> - <output name="output_cleaned_nr_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/> - <output name="output_cleaned_nr_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/> - <output name="output_cleaned_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/> - <output name="output_pep" file="transcripts2.pep" ftype="fasta"/> - </test> - <test> <param name="input" value="assembly_tgf.fasta" ftype="fasta"/> - <param name="prediction_method" value="transdecoder"/> <param name="options_type_selector" value="advanced"/> <param name="target_gene_family_assembly" value="yes"/> <param name="orthogroups" value="target_orthos.ids"/> - <param name="scaffold" value="22Gv1.1"/> <param name="method" value="orthomcl"/> <param name="dereplicate" value="yes"/> <output_collection name="output_targeted_gene_families" type="list"> @@ -186,7 +157,6 @@ * **Transcriptome assembly fasta file** - either de novo or reference-guided transcriptome assembly fasta file selected from your history. * **Coding regions prediction method** - method for finding coding regions within transcripts. Available methods are TransDecoder[3] and ESTScan[4]. - * **Scores matrices** - scores matrices, based on a related species, are required when ESTScan is used to find coding regions. Details of how to create species-specific scores matrices can be found on the ESTScan website (http://estscan.sourceforge.net). Matrices of some organisms are also available to download. **Other options** @@ -226,16 +196,6 @@ pages = {1494-1512},} </citation> <citation type="bibtex"> - @article{Iseli1999, - journal = {ISMB}, - author = {4. Iseli C, Jongeneel CV, Bucher P}, - title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences}, - year = {1999}, - volume = {99}, - pages = {138-148}, - url = {http://estscan.sourceforge.net},} - </citation> - <citation type="bibtex"> @article{Huang1999, journal = {Genome Research}, author = {5. Huang X, Madan A},