Mercurial > repos > greg > assembly_post_processor
changeset 15:ff5c714e01d1 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 08 Feb 2017 09:13:53 -0500 |
| parents | b468a86f87d9 |
| children | 1e639e679f61 |
| files | assembly_post_processor.xml |
| diffstat | 1 files changed, 26 insertions(+), 15 deletions(-) [+] |
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--- a/assembly_post_processor.xml Wed Feb 08 09:04:01 2017 -0500 +++ b/assembly_post_processor.xml Wed Feb 08 09:13:53 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.3"> +<tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.4"> <description>into putative coding sequences</description> <requirements> <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement> @@ -13,18 +13,22 @@ </stdio> <command> <![CDATA[ + #import os AssemblyPostProcesser - --transcripts "$input" + --transcripts '$input' --prediction_method $prediction_method_cond.prediction_method #if str($prediction_method_cond.prediction_method) == 'estscan': - --score_matrices "$score_matrices" + --score_matrices '$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 "$options_type.target_gene_family_assembly_cond.orthogroups" - --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" - --scaffold "$options_type.target_gene_family_assembly_cond.scaffold" - --method "$options_type.target_gene_family_assembly_cond.method" + #set scaffold_path = $options_type.target_gene_family_assembly_cond.scaffold.fields.path + #set scaffold_dir = $os.path.split($scaffold_path)[0] + #set scaffold = $os.path.split($scaffold_path)[1] + --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups' + --scaffold_dir '$scaffold_dir' + --scaffold '$scaffold' + --method '$options_type.target_gene_family_assembly_cond.method' #end if --gap_trimming $options_type.gap_trimming #if str($options_type.strand_specific) == 'yes': @@ -98,12 +102,11 @@ <test> <param name="input" value="assembly.fasta" ftype="fasta" /> <param name="prediction_method" value="transdecoder" /> - <param name="options_type_selector" value="basic" /> <output_collection name="transcripts" type="list"> - <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/> - <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/> - <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta" compare="contains"/> - <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/> + <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/> + <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/> + <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta"/> + <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/> </output_collection> </test> <test> @@ -117,7 +120,7 @@ <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/> <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/> <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" compare="contains"/> - <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.pep" ftype="fasta" compare="contains"/> + <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" compare="contains"/> <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/> <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/> </output_collection> @@ -150,8 +153,16 @@ author = {Eric Wafula}, title = {None}, year = {None}, - eprint = {None}, - url = {None} + url = {https://github.com/dePamphilis/PlantTribes} }</citation> + <citation type="bibtex"> + @published{Proc Int Conf Intell Syst Mol Biol, + author = {Iseli C, Jongeneel CV, Bucher P.}, + title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.}, + year = {1999}, + url = {http://estscan.sourceforge.net/} + }</citation> + <citation type="doi">10.1038/nprot.2013.084</citation> + <citation type="doi">10.1109/tcbb.2013.68</citation> </citations> </tool>