Mercurial > repos > greg > plant_tribes_gene_family_integrator
diff macros.xml @ 3:276f0f31ddb0 draft
Uploaded
author | greg |
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date | Mon, 30 Oct 2017 09:53:09 -0400 |
parents | a322e5e668a3 |
children | 00f14e3bbe9f |
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--- a/macros.xml Thu Aug 24 13:32:01 2017 -0400 +++ b/macros.xml Mon Oct 30 09:53:09 2017 -0400 @@ -1,47 +1,6 @@ <?xml version='1.0' encoding='UTF-8'?> <macros> <token name="@WRAPPER_VERSION@">1.0</token> - <xml name="requirements_assembly_post_processor"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_assembly_post_processor</requirement> - </requirements> - </xml> - <xml name="requirements_gene_family_aligner"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_gene_family_aligner</requirement> - </requirements> - </xml> - <xml name="requirements_gene_family_classifier"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_gene_family_classifier</requirement> - </requirements> - </xml> - <xml name="requirements_gene_family_integrator"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_gene_family_integrator</requirement> - </requirements> - </xml> - <xml name="requirements_kaks_analysis"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_kaks_analysis</requirement> - </requirements> - </xml> - <xml name="requirements_ks_distribution"> - <requirements> - <requirement type="package" version="1.3.2">r-optparse</requirement> - </requirements> - </xml> - <xml name="requirements_gene_family_phylogeny_builder"> - <requirements> - <requirement type="package" version="1.0.2">plant_tribes_gene_family_phylogeny_builder</requirement> - </requirements> - </xml> - <xml name="param_codon_alignments"> - <param name="codon_alignments" type="select" label="Codon alignments"> - <option value="yes" selected="true">Yes</option> - <option value="no">No</option> - </param> - </xml> <xml name="param_method"> <param name="method" type="select" label="Protein clustering method"> <option value="gfam" selected="true">GFam</option> @@ -49,74 +8,12 @@ <option value="orthomcl">OrthoMCL</option> </param> </xml> - <xml name="param_options_type"> - <param name="options_type" type="select" label="Options Configuration"> - <option value="basic" selected="true">Basic</option> - <option value="advanced">Advanced</option> - </param> - </xml> - <xml name="param_orthogroup_fna"> - <param name="orthogroup_fna" type="select" label="Orthogroups coding sequences"> - <option value="yes" selected="true">Yes</option> - <option value="no">No</option> - </param> - </xml> <xml name="param_scaffold"> <param name="scaffold" type="select" label="Gene family 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 in Galaxy to install and populate the PlantTribes scaffolds data table." /> </param> </xml> - <xml name="param_sequence_type"> - <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)"> - <option value="protein" selected="true">Amino acid based</option> - <option value="dna">Nucleotide based</option> - </param> - </xml> - <xml name="cond_alignment_method"> - <conditional name="alignment_method_cond"> - <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method"> - <option value="mafft" selected="true">MAFFT</option> - <option value="pasta">PASTA</option> - </param> - <when value="mafft" /> - <when value="pasta"> - <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" /> - </when> - </conditional> - </xml> - <xml name="cond_remove_gappy_sequences"> - <conditional name="remove_gappy_sequences_cond"> - <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <when value="no" /> - <when value="yes"> - <conditional name="trim_type_cond"> - <param name="trim_type" type="select" label="Trimming method"> - <option value="gap_trimming" selected="true">Gap score based trimming</option> - <option value="automated_trimming">Automated heuristic trimming</option> - </param> - <when value="gap_trimming"> - <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" /> - </when> - <when value="automated_trimming" /> - </conditional> - <conditional name="remove_sequences_with_gaps_cond"> - <param name="remove_sequences_with_gaps" type="select" label="Remove sequences"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" /> - <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" /> - </when> - </conditional> - </when> - </conditional> - </xml> <xml name="citation1"> <citation type="bibtex"> @misc{None,