Mercurial > repos > greg > assembly_post_processor
changeset 70:cf4bf94e87d2 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 07 Jun 2017 10:01:51 -0400 |
| parents | 61f9552be416 |
| children | 7a488497e6c6 |
| files | assembly_post_processor.xml macros.xml |
| diffstat | 2 files changed, 40 insertions(+), 42 deletions(-) [+] |
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--- a/assembly_post_processor.xml Tue Jun 06 08:31:58 2017 -0400 +++ b/assembly_post_processor.xml Wed Jun 07 10:01:51 2017 -0400 @@ -4,41 +4,39 @@ <import>macros.xml</import> </macros> <expand macro="requirements_assembly_post_processor" /> - <command detect_errors="exit_code"> - <![CDATA[ - python $__tool_directory__/assembly_post_processor.py - --transcripts '$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': - #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': - --gene_family_search '$target_gene_family_assembly_cond.orthogroups' - --output_pttgf $output_pttgf - --output_pttgf_dir $output_pttgf.files_path - --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' - --method '$target_gene_family_assembly_cond.method' - --gap_trimming $target_gene_family_assembly_cond.gap_trimming - #end if - #if str($options_type.strand_specific) == 'yes': - --strand_specific 'true' - #end if - #if str($options_type.dereplicate) == 'yes': - --dereplicate 'true' - --output_cleaned_nr_cds '$output_cleaned_nr_cds' - --output_cleaned_nr_pep '$output_cleaned_nr_pep' - #end if - --min_length $options_type.min_length - #end if - --num_threads \${GALAXY_SLOTS:-4} - --output_cds '$output_cds' - --output_cleaned_cds '$output_cleaned_cds' - --output_cleaned_pep '$output_cleaned_pep' - --output_pep '$output_pep' - ]]> - </command> + <command detect_errors="exit_code"><![CDATA[ +python $__tool_directory__/assembly_post_processor.py +--transcripts '$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': + #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': + --gene_family_search '$target_gene_family_assembly_cond.orthogroups' + --output_pttgf $output_pttgf + --output_pttgf_dir $output_pttgf.files_path + --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' + --method '$target_gene_family_assembly_cond.method' + --gap_trimming $target_gene_family_assembly_cond.gap_trimming + #end if + #if str($options_type.strand_specific) == 'yes': + --strand_specific 'true' + #end if + #if str($options_type.dereplicate) == 'yes': + --dereplicate 'true' + --output_cleaned_nr_cds '$output_cleaned_nr_cds' + --output_cleaned_nr_pep '$output_cleaned_nr_pep' + #end if + --min_length $options_type.min_length +#end if +--num_threads \${GALAXY_SLOTS:-4} +--output_cds '$output_cds' +--output_cleaned_cds '$output_cleaned_cds' +--output_cleaned_pep '$output_cleaned_pep' +--output_pep '$output_pep' + ]]></command> <inputs> <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> <conditional name="prediction_method_cond">
--- a/macros.xml Tue Jun 06 08:31:58 2017 -0400 +++ b/macros.xml Wed Jun 07 10:01:51 2017 -0400 @@ -1,29 +1,29 @@ <?xml version='1.0' encoding='UTF-8'?> <macros> - <token name="@WRAPPER_VERSION@">0.8</token> + <token name="@WRAPPER_VERSION@">1.0</token> <xml name="requirements_assembly_post_processor"> <requirements> - <requirement type="package" version="0.8">plant_tribes_assembly_post_processor</requirement> + <requirement type="package" version="1.0.0">plant_tribes_assembly_post_processor</requirement> </requirements> </xml> <xml name="requirements_gene_family_aligner"> <requirements> - <requirement type="package" version="0.8">plant_tribes_gene_family_aligner</requirement> + <requirement type="package" version="1.0.0">plant_tribes_gene_family_aligner</requirement> </requirements> </xml> <xml name="requirements_gene_family_classifier"> <requirements> - <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement> + <requirement type="package" version="1.0.0">plant_tribes_gene_family_classifier</requirement> </requirements> </xml> <xml name="requirements_gene_family_integrator"> <requirements> - <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement> + <requirement type="package" version="1.0.0">plant_tribes_gene_family_integrator</requirement> </requirements> </xml> <xml name="requirements_kaks_analysis"> <requirements> - <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement> + <requirement type="package" version="1.0.0">plant_tribes_kaks_analysis</requirement> </requirements> </xml> <xml name="requirements_ks_distribution"> @@ -33,7 +33,7 @@ </xml> <xml name="requirements_gene_family_phylogeny_builder"> <requirements> - <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement> + <requirement type="package" version="1.0.0">plant_tribes_gene_family_phylogeny_builder</requirement> </requirements> </xml> <xml name="param_codon_alignments">