Mercurial > repos > greg > phylogenomics_analysis
changeset 10:b3712c598290 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 05 Jan 2017 14:56:53 -0500 |
| parents | 0ca4bba49038 |
| children | cac8a85418c2 |
| files | phylogenomics_analysis.xml |
| diffstat | 1 files changed, 15 insertions(+), 3 deletions(-) [+] |
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--- a/phylogenomics_analysis.xml Thu Jan 05 14:38:49 2017 -0500 +++ b/phylogenomics_analysis.xml Thu Jan 05 14:56:53 2017 -0500 @@ -14,10 +14,18 @@ <![CDATA[ #import os #import sys - #if not os.exists($orthogroup_faa.extra_files_path): - print > sys.stderr("The select input is not a valid list of sequences classified into gene family clusters, select another input.") + #set invalid_input = "The selected input is not a valid list of sequences classified into gene family clusters, select another input." + #if not $os.path.exists($orthogroup_faa.extra_files_path): + print > $sys.stderr($invalid_input) + $sys.exit(1) #end if #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta') + #set num_orthogroup_faa = `ls $src_dir/*.faa | wc -l` + #if $num_orthogroup_faa == 0: + print > $sys.stderr($invalid_input) + $sys.exit(1) + #end if + #set num_orthogroup_fna = `ls $src_dir/*.fna | wc -l` #set dest_dir = $output.extra_files_path mkdir -p $dest_dir && PhylogenomicsAnalysis @@ -43,6 +51,10 @@ #if str($multiple_codon_alignments) == 'yes': --codon_alignments #if str($use_corresponding_coding_sequences) == 'yes': + #if $num_orthogroup_fna == 0: + print > $sys.stderr("No corresponding coding sequences were generated for the selected input. You must not have selected 'Yes' for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool for the selected input.") + $sys.exit(1) + #end if --orthogroup_fna #end if --sequence_type $multiple_codon_alignments_cond.sequence_type @@ -128,7 +140,7 @@ <option value="dna">Nucleotide based</option> </param> <conditional name="use_corresponding_coding_sequences_cond"> - <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences if available?" help="Ignored if 'No' was selected for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool for the selected 'sequences classified into gene family clusters' input above"> + <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences if available?" help="Must have selected 'Yes' for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool for the selected input above"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param>