Mercurial > repos > greg > gene_family_classifier
changeset 73:6e859426c873 draft
Uploaded
author | greg |
---|---|
date | Fri, 17 Feb 2017 14:00:43 -0500 |
parents | e8a8650c7165 |
children | 9969b17ae656 |
files | gene_family_classifier.xml |
diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/gene_family_classifier.xml Fri Feb 17 13:05:55 2017 -0500 +++ b/gene_family_classifier.xml Fri Feb 17 14:00:43 2017 -0500 @@ -189,19 +189,19 @@ <when value="no"/> <when value="yes"> <conditional name="single_copy_cond"> - <param name="single_copy" type="select" label="Select single copy configuration"> + <param name="single_copy" type="select" label="Select single copy orthogroup configuration option"> <option value="custom" selected="true">Single copy orthogroup custom configuration</option> <option value="taxa">Minimum single copy taxa required in orthogroup</option> </param> <when value="custom"> <conditional name="single_copy_custom_cond"> - <param name="single_copy_custom" type="select" label="Select single copy orthogroup custom configuration?" help="Select No to use the default configuration"> + <param name="single_copy_custom" type="select" label="Select single copy orthogroup custom configuration from the current history?" help="Select No to use the default configuration"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> - <param name="single_copy_custom_config" format="txt" type="data" label="Select single copy custom configuration file"/> + <param name="single_copy_custom_config" format="txt" type="data" label="Single copy orthogroup custom configuration file"/> </when> </conditional> </when> @@ -293,7 +293,8 @@ * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive). * **Super Orthogroups** - Secondary MCL clusters of orthogroups. - * **Specify single copy orthogroup selection?** - Select 'Yes' to specify 'Minimum single copy taxa required in orthogroup'. + * **Specify single copy orthogroup selection?** - Specify a single copy orthogroup custom configuration or the minimum single copy taxa required in the orthogroup. + * **Select single copy orthogroup custom configuration from the current history?** - If a custom configuration is chosen, the configuration can be selected from the current history or the default configuration can be used. * **Minimum single copy taxa required in orthogroup** - Used with "Minimum single copy taxa required in orthogroup" configuration only. * **Minimum taxa required in single copy orthogroup** - Used with "Minimum single copy taxa required in orthogroup" configuration only. * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".