Mercurial > repos > greg > plant_tribes_assembly_post_processor
changeset 30:6dd02ba54da1 draft default tip
Deleted selected files
| author | greg |
|---|---|
| date | Fri, 09 Dec 2016 08:28:56 -0500 |
| parents | 7af9033b21a2 |
| children | |
| files | plant_tribes_assembly_post_processor.xml |
| diffstat | 1 files changed, 0 insertions(+), 144 deletions(-) [+] |
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--- a/plant_tribes_assembly_post_processor.xml Fri Dec 09 08:28:49 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,144 +0,0 @@ -<tool id="plant_tribes_assembly_post_processor" name="PlantTribes AssemblyPostProcessor" version="1.0.0"> - <description>pipeline</description> - <requirements> - <requirement type="package" version="0.2">plant_tribes_assembly_post_processor</requirement> - </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <!-- In case the return code has not been set properly check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - <command> - <![CDATA[ - AssemblyPostProcesser - --transcripts "$input" - --prediction_method $prediction_method_cond.prediction_method - #if str($prediction_method_cond.prediction_method) == 'estscan': - --score_matrices "$score_matrices" - #end if - #if str($options_type.options_type_selector) == 'advanced': - #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == "yes": - --gene_family_search "$options_type.target_gene_family_assembly_cond.orthogroups" - --scaffold "$options_type.target_gene_family_assembly_cond.scaffold" - --method "$options_type.target_gene_family_assembly_cond.method" - #end if - --gap_trimming $options_type.gap_trimming - #if str($options_type.strand_specific) == 'yes': - --strand_specific - #end if - #if str($options_type.dereplicate) == 'yes': - --dereplicate - #end if - --min_length $options_type.min_length - --num_threads \${GALAXY_SLOTS:-4} - #end if - ]]> - </command> - <inputs> - <param name="input" format="fasta" type="data" label="De novo transcriptome assembly fasta file"/> - <conditional name="prediction_method_cond"> - <param name="prediction_method" type="select" label="Prediction method for coding regions"> - <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> - <option value="advanced">Advanced</option> - </param> - <when value="basic" /> - <when value="advanced"> - <conditional name="target_gene_family_assembly_cond"> - <param name="target_gene_family_assembly" type="select" label="Target gene family assembly?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="orthogroups" format="tabular" type="data" label="List of orthogroup identifiers for target gene families to assemble"/> - <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> - <options from_data_table="plant_tribes_scaffolds" /> - <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/> - </param> - <param name="method" type="select" label="Protein clustering method"> - <option value="gfam" selected="true">GFam</option> - <option value="orthofinder">OrthoFinder</option> - <option value="orthomcl">OrthoMCL</option> - </param> - </when> - </conditional> - <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove gappy sites in alignments" help="0.1 removes sites with 90% gaps"/> - <param name="strand_specific" type="select" label="De novo transcriptome assembly was performed with strand-specific library?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <param name="dereplicate" type="select" label="Remove repeated sequences in predicted coding regions?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <param name="min_length" type="integer" value="200" label="Minimum sequence length of predicted coding regions"/> - </when> - </conditional> - </inputs> - <outputs> - <collection name="transcripts" type="list"> - <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="false" ext="fasta" /> - </collection> - </outputs> - <tests> - <test> - <param name="input" value="assembly.fasta" ftype="fasta" /> - <param name="prediction_method" value="transdecoder"/> - <param name="target_gene_family_assembly" value="no"/> - <param name="strand_specific" value="yes"/> - <param name="dereplicate" value="yes"/> - <param name="min_length" value="200"/> - <output_collection name="transcripts" type="list"> - <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" /> - <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" /> - <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" /> - <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" /> - <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta" /> - <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" /> - </output_collection> - </test> - </tests> - <help> -This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of -complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It post-processes de novo assembly -transcripts into putative coding sequences and their corresponding amino acid translations. - ------ - -**Options** - - * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder. - * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms. - * **Target gene family assembly?** - Select yes to target gene families to assemble. - * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble. The next version of this tool will use a dynamic select list for this feature. - * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. - * **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL. - * **Remove gappy sites in alignments** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0] - * **De novo transcriptome assembly was performed with strand-specific library?** - Select yes if de novo transcriptome assembly was performed with strand-specific library. - * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions. - * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions. - - </help> - <citations> - <citation type="bibtex"> - @unpublished{None, - author = {None}, - title = {None}, - year = {None}, - eprint = {None}, - url = {None} - }</citation> - </citations> -</tool>