Mercurial > repos > greg > phylogenomics_analysis
comparison phylogenomics_analysis.xml @ 62:785eef1c4700 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 16 Feb 2017 10:17:48 -0500 |
| parents | bf5cfbf2cfbc |
| children | c2d2ca6cf94b |
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| 61:bf5cfbf2cfbc | 62:785eef1c4700 |
|---|---|
| 129 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptortho | 129 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptortho |
| 130 #else: | 130 #else: |
| 131 && echo -e "#Size\tName" > $output_fasta_ptorthocs | 131 && echo -e "#Size\tName" > $output_fasta_ptorthocs |
| 132 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptorthocs | 132 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptorthocs |
| 133 #end if | 133 #end if |
| 134 #if len($os.listdir($src_fasta_dir)) > 0: | 134 && mv $src_fasta_dir/* $dest_fasta_dir |
| 135 && mv $src_fasta_dir/* $dest_fasta_dir | |
| 136 #end if | |
| 137 | 135 |
| 138 #if $generate_output_aln: | 136 #if $generate_output_aln: |
| 139 && echo -e "#Size\tName" > $output_aln | 137 && echo -e "#Size\tName" > $output_aln |
| 140 #if len($os.listdir($src_aln_dir)) > 0: | 138 && ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln |
| 141 ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln | 139 && mv $src_aln_dir/* $dest_aln_dir |
| 142 && mv $src_aln_dir/* $dest_aln_dir | |
| 143 #end if | |
| 144 #end if | 140 #end if |
| 145 | 141 |
| 146 #if $generate_output_tree: | 142 #if $generate_output_tree: |
| 147 && echo -e "#Size\tName" > $output_tree | 143 && echo -e "#Size\tName" > $output_tree |
| 148 #if len($os.listdir($src_tree_dir)) > 0: | 144 && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree |
| 149 && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree | 145 && mv $src_tree_dir/* $dest_tree_dir |
| 150 && mv $src_tree_dir/* $dest_tree_dir | |
| 151 #end if | |
| 152 #end if | 146 #end if |
| 153 ]]> | 147 ]]> |
| 154 </command> | 148 </command> |
| 155 <inputs> | 149 <inputs> |
| 156 <conditional name="input_format_cond"> | 150 <conditional name="input_format_cond"> |