Mercurial > repos > greg > gene_family_classifier
changeset 151:0864e87fbcd1 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 08 Jun 2017 09:39:26 -0400 |
| parents | 8f2cd8053f78 |
| children | 3ba64b663526 |
| files | gene_family_classifier.xml macros.xml test-data/tool-data/plant_tribes/scaffolds/README.txt |
| diffstat | 3 files changed, 103 insertions(+), 102 deletions(-) [+] |
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--- a/gene_family_classifier.xml Tue Jun 06 08:39:14 2017 -0400 +++ b/gene_family_classifier.xml Thu Jun 08 09:39:26 2017 -0400 @@ -4,105 +4,103 @@ <import>macros.xml</import> </macros> <expand macro="requirements_gene_family_classifier" /> - <command detect_errors="exit_code"> - <![CDATA[ - #if str($options_type.options_type_selector) == 'advanced': - #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond - #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups - #set create_orthogroup_cond = $options_type.create_orthogroup_cond - #set create_orthogroup = $create_orthogroup_cond.create_orthogroup - #set specify_single_copy_cond = $options_type.specify_single_copy_cond - #set specify_single_copy = $specify_single_copy_cond.specify_single_copy - #if str($specify_super_orthogroups) == 'yes': - #set specify_super_orthos = True - #set super_orthogroups = $specify_super_orthogroups_cond.super_orthogroups - #else: - #set specify_super_orthos = False - #end if - #if str($create_orthogroup) == 'yes': - #set create_ortho_sequences = True - #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond - #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes': - #set create_corresponding_coding_sequences = True - #else: - #set create_corresponding_coding_sequences = False - #end if - #else: - #set create_ortho_sequences = False - #set create_corresponding_coding_sequences = False - #end if - #if str($specify_single_copy) == 'yes': - #set single_copy_orthogroup = True - #set single_copy_cond = $specify_single_copy_cond.single_copy_cond - #set single_copy = $single_copy_cond.single_copy - #else: - #set single_copy_orthogroup = False - #end if - #else: - #set single_copy_orthogroup = False - #set create_ortho_sequences = False - #set create_corresponding_coding_sequences = False - #end if + <command detect_errors="exit_code"><![CDATA[ +#if str($options_type.options_type_selector) == 'advanced': + #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond + #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups + #set create_orthogroup_cond = $options_type.create_orthogroup_cond + #set create_orthogroup = $create_orthogroup_cond.create_orthogroup + #set specify_single_copy_cond = $options_type.specify_single_copy_cond + #set specify_single_copy = $specify_single_copy_cond.specify_single_copy + #if str($specify_super_orthogroups) == 'yes': + #set specify_super_orthos = True + #set super_orthogroups = $specify_super_orthogroups_cond.super_orthogroups + #else: + #set specify_super_orthos = False + #end if + #if str($create_orthogroup) == 'yes': + #set create_ortho_sequences = True + #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond + #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes': + #set create_corresponding_coding_sequences = True + #else: + #set create_corresponding_coding_sequences = False + #end if + #else: + #set create_ortho_sequences = False + #set create_corresponding_coding_sequences = False + #end if + #if str($specify_single_copy) == 'yes': + #set single_copy_orthogroup = True + #set single_copy_cond = $specify_single_copy_cond.single_copy_cond + #set single_copy = $single_copy_cond.single_copy + #else: + #set single_copy_orthogroup = False + #end if +#else: + #set single_copy_orthogroup = False + #set create_ortho_sequences = False + #set create_corresponding_coding_sequences = False +#end if - python $__tool_directory__/gene_family_classifier.py - --input '$input' - --scaffold '$scaffold.fields.path' - --method $method - --classifier $save_hmmscan_log_cond.classifier - --config_dir '$scaffold.fields.path' - --num_threads \${GALAXY_SLOTS:-4} +python $__tool_directory__/gene_family_classifier.py +--input '$input' +--scaffold '$scaffold.fields.path' +--method $method +--classifier $save_hmmscan_log_cond.classifier +--config_dir '$scaffold.fields.path' +--num_threads \${GALAXY_SLOTS:-4} - #if str($options_type.options_type_selector) == 'advanced': - #if specify_super_orthos: - --super_orthogroups $super_orthogroups - #end if - #if $single_copy_orthogroup: - #if str($single_copy) == 'custom': - #set single_copy_custom_cond = $single_copy_cond.single_copy_custom_cond - #set single_copy_custom = $single_copy_custom_cond.single_copy_custom - #if str($single_copy_custom) == 'no': - --single_copy_custom 'default' - #else: - --single_copy_custom '$single_copy_custom_cond.single_copy_custom_config' - #end if - #else: - #if str($single_copy_cond.single_copy_taxa): - --single_copy_taxa $single_copy_cond.single_copy_taxa - #end if - #if str($single_copy_cond.taxa_present): - --taxa_present $single_copy_cond.taxa_present - #end if - #end if - #end if - #if $create_ortho_sequences: - --orthogroup_fasta "true" - #if $create_corresponding_coding_sequences: - --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences' - #end if - #end if +#if str($options_type.options_type_selector) == 'advanced': + #if specify_super_orthos: + --super_orthogroups $super_orthogroups + #end if + #if $single_copy_orthogroup: + #if str($single_copy) == 'custom': + #set single_copy_custom_cond = $single_copy_cond.single_copy_custom_cond + #set single_copy_custom = $single_copy_custom_cond.single_copy_custom + #if str($single_copy_custom) == 'no': + --single_copy_custom 'default' + #else: + --single_copy_custom '$single_copy_custom_cond.single_copy_custom_config' + #end if + #else: + #if str($single_copy_cond.single_copy_taxa): + --single_copy_taxa $single_copy_cond.single_copy_taxa + #end if + #if str($single_copy_cond.taxa_present): + --taxa_present $single_copy_cond.taxa_present #end if + #end if + #end if + #if $create_ortho_sequences: + --orthogroup_fasta "true" + #if $create_corresponding_coding_sequences: + --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences' + #end if + #end if +#end if - #if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes': - --save_hmmscan_log 'true' - --hmmscan_log '$hmmscan_log' - #end if - #if $create_ortho_sequences: - #if $create_corresponding_coding_sequences: - --output_ptorthocs '$output_ptorthocs' - --output_ptorthocs_dir '$output_ptorthocs.files_path' - #else: - --output_ptortho '$output_ptortho' - --output_ptortho_dir '$output_ptortho.files_path' - #end if - #end if - #if $single_copy_orthogroup: - #if $create_ortho_sequences: - --output_ptsco '$output_ptsco' - --output_ptsco_dir '$output_ptsco.files_path' - #end if - #end if - ]]> - </command> +#if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes': + --save_hmmscan_log 'true' + --hmmscan_log '$hmmscan_log' +#end if +#if $create_ortho_sequences: + #if $create_corresponding_coding_sequences: + --output_ptorthocs '$output_ptorthocs' + --output_ptorthocs_dir '$output_ptorthocs.files_path' + #else: + --output_ptortho '$output_ptortho' + --output_ptortho_dir '$output_ptortho.files_path' + #end if +#end if +#if $single_copy_orthogroup: + #if $create_ortho_sequences: + --output_ptsco '$output_ptsco' + --output_ptsco_dir '$output_ptsco.files_path' + #end if +#end if + ]]></command> <inputs> <param name="input" format="fasta" type="data" label="Proteins fasta file"/> <param name="scaffold" type="select" label="Gene family scaffold">
--- a/macros.xml Tue Jun 06 08:39:14 2017 -0400 +++ b/macros.xml Thu Jun 08 09:39:26 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">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tool-data/plant_tribes/scaffolds/README.txt Thu Jun 08 09:39:26 2017 -0400 @@ -0,0 +1,3 @@ +For functional tests to work, this directory must contain symlinks to the scaffolds data +installed into the Galaxy instance to which planemo points via the --galaxy_root parameter. +This would typically be something like ~/galaxy/tool-data/plant_tribes/scaffolds/22Gv1.1.