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comparison phylogenomics_analysis.xml @ 61:bf5cfbf2cfbc draft

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Uploaded
author greg
date Thu, 16 Feb 2017 10:14:17 -0500
parents 29530d7a2a3d
children 785eef1c4700
comparison
equal deleted inserted replaced
60:29530d7a2a3d 61:bf5cfbf2cfbc
96 #if str($tree_inference_method) == 'raxml': 96 #if str($tree_inference_method) == 'raxml':
97 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond 97 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
98 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file 98 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
99 #if str($rooting_order_file) == 'yes': 99 #if str($rooting_order_file) == 'yes':
100 --rooting_order '$rooting_order_file_cond.rooting_order' 100 --rooting_order '$rooting_order_file_cond.rooting_order'
101 # Noe else block needed here because the default rooting_order 101 # No else block needed here because the default rooting_order
102 # configuration will be used if the --rooting_order flag is missing. 102 # configuration will be used if the --rooting_order flag is missing.
103 #end if 103 #end if
104 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates 104 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
105 #end if 105 #end if
106 --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size 106 --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size
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 && mv $src_fasta_dir/* $dest_fasta_dir || true 134 #if len($os.listdir($src_fasta_dir)) > 0:
135 && mv $src_fasta_dir/* $dest_fasta_dir
136 #end if
135 137
136 #if $generate_output_aln: 138 #if $generate_output_aln:
137 && echo -e "#Size\tName" > $output_aln 139 && echo -e "#Size\tName" > $output_aln
138 && ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln 140 #if len($os.listdir($src_aln_dir)) > 0:
139 && mv $src_aln_dir/* $dest_aln_dir || true 141 ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln
142 && mv $src_aln_dir/* $dest_aln_dir
143 #end if
140 #end if 144 #end if
141 145
142 #if $generate_output_tree: 146 #if $generate_output_tree:
143 && echo -e "#Size\tName" > $output_tree 147 && echo -e "#Size\tName" > $output_tree
144 && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree 148 #if len($os.listdir($src_tree_dir)) > 0:
145 && mv $src_tree_dir/* $dest_tree_dir || true 149 && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree
150 && mv $src_tree_dir/* $dest_tree_dir
151 #end if
146 #end if 152 #end if
147 ]]> 153 ]]>
148 </command> 154 </command>
149 <inputs> 155 <inputs>
150 <conditional name="input_format_cond"> 156 <conditional name="input_format_cond">
230 <option value="raxml" selected="true">RAxML</option> 236 <option value="raxml" selected="true">RAxML</option>
231 <option value="fasttree">FastTree</option> 237 <option value="fasttree">FastTree</option>
232 </param> 238 </param>
233 <when value="raxml"> 239 <when value="raxml">
234 <conditional name="rooting_order_file_cond"> 240 <conditional name="rooting_order_file_cond">
235 <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"> 241 <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">
236 <option value="no" selected="true">No</option> 242 <option value="no" selected="true">No</option>
237 <option value="yes">Yes</option> 243 <option value="yes">Yes</option>
238 </param> 244 </param>
239 <when value="no" /> 245 <when value="no" />
240 <when value="yes"> 246 <when value="yes">