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comparison phylogenomics_analysis.xml @ 37:79c8d886e43b draft

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author greg
date Thu, 12 Jan 2017 10:49:47 -0500
parents c42769258e0d
children 5423ad5c4f00
comparison
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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"/>