Mercurial > repos > greg > phylogenomics_analysis
comparison phylogenomics_analysis.xml @ 37:79c8d886e43b draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 12 Jan 2017 10:49:47 -0500 |
| parents | c42769258e0d |
| children | 5423ad5c4f00 |
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| 36:c42769258e0d | 37:79c8d886e43b |
|---|---|
| 144 #end if | 144 #end if |
| 145 #end if | 145 #end if |
| 146 | 146 |
| 147 && echo "Sequence alignments and corresponding phylogenies: `ls $src_fasta_dir | grep f | wc -l` files" > $output_fasta | 147 && echo "Sequence alignments and corresponding phylogenies: `ls $src_fasta_dir | grep f | wc -l` files" > $output_fasta |
| 148 && ls -al $src_fasta_dir | grep f >> $output_fasta | 148 && ls -al $src_fasta_dir | grep f >> $output_fasta |
| 149 && mv $src_fasta_dir/* $dest_fasta_dir | 149 && mv $src_fasta_dir/* $dest_fasta_dir || true |
| 150 | 150 |
| 151 #if $generate_output_aln: | 151 #if $generate_output_aln: |
| 152 && echo "Multiple sequence alignments using method '$multiple_sequence_alignments_option' (note that some files may be empty): `ls $src_aln_dir | grep f | wc -l` files" > $output_aln | 152 && echo "Multiple sequence alignments using method '$multiple_sequence_alignments_option' (note that some files may be empty): `ls $src_aln_dir | grep f | wc -l` files" > $output_aln |
| 153 && ls -al $src_aln_dir | grep f >> $output_aln | 153 && ls -al $src_aln_dir | grep f >> $output_aln |
| 154 && mv $src_aln_dir/* $dest_aln_dir | 154 && mv $src_aln_dir/* $dest_aln_dir || true |
| 155 #end if | 155 #end if |
| 156 | 156 |
| 157 #if $generate_output_tree: | 157 #if $generate_output_tree: |
| 158 && echo "Phylogenetic trees (note that some files may be empty): `ls $src_tree_dir | grep f | wc -l` files" > $output_tree | 158 && echo "Phylogenetic trees (note that some files may be empty): `ls $src_tree_dir | grep f | wc -l` files" > $output_tree |
| 159 && ls -al $src_tree_dir | grep f >> $output_tree | 159 && ls -al $src_tree_dir | grep f >> $output_tree |
| 160 && mv $src_tree_dir/* $dest_tree_dir | 160 && mv $src_tree_dir/* $dest_tree_dir || true |
| 161 #end if | 161 #end if |
| 162 ]]> | 162 ]]> |
| 163 </command> | 163 </command> |
| 164 <inputs> | 164 <inputs> |
| 165 <param name="orthogroup_faa" format="txt" type="data" label="Select sequences classified into gene family clusters"/> | 165 <param name="orthogroup_faa" format="txt" type="data" label="Select sequences classified into gene family clusters"/> |