Mercurial > repos > greg > phylogenomics_analysis
changeset 61:bf5cfbf2cfbc draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 16 Feb 2017 10:14:17 -0500 |
| parents | 29530d7a2a3d |
| children | 785eef1c4700 |
| files | phylogenomics_analysis.xml |
| diffstat | 1 files changed, 13 insertions(+), 7 deletions(-) [+] |
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--- a/phylogenomics_analysis.xml Thu Feb 16 09:26:48 2017 -0500 +++ b/phylogenomics_analysis.xml Thu Feb 16 10:14:17 2017 -0500 @@ -98,7 +98,7 @@ #set rooting_order_file = $rooting_order_file_cond.rooting_order_file #if str($rooting_order_file) == 'yes': --rooting_order '$rooting_order_file_cond.rooting_order' - # Noe else block needed here because the default rooting_order + # No else block needed here because the default rooting_order # configuration will be used if the --rooting_order flag is missing. #end if --bootstrap_replicates $tree_inference_cond.bootstrap_replicates @@ -131,18 +131,24 @@ && echo -e "#Size\tName" > $output_fasta_ptorthocs && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptorthocs #end if - && mv $src_fasta_dir/* $dest_fasta_dir || true + #if len($os.listdir($src_fasta_dir)) > 0: + && mv $src_fasta_dir/* $dest_fasta_dir + #end if #if $generate_output_aln: && echo -e "#Size\tName" > $output_aln - && ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln - && mv $src_aln_dir/* $dest_aln_dir || true + #if len($os.listdir($src_aln_dir)) > 0: + ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln + && mv $src_aln_dir/* $dest_aln_dir + #end if #end if #if $generate_output_tree: && echo -e "#Size\tName" > $output_tree - && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree - && mv $src_tree_dir/* $dest_tree_dir || true + #if len($os.listdir($src_tree_dir)) > 0: + && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree + && mv $src_tree_dir/* $dest_tree_dir + #end if #end if ]]> </command> @@ -232,7 +238,7 @@ </param> <when value="raxml"> <conditional name="rooting_order_file_cond"> - <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select no for the default rooting order configuration which uses the most distant taxon present in the orthogroup"> + <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param>