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comparison phylogenomics_analysis.xml @ 53:c24ca7fed70c draft

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Uploaded
author greg
date Fri, 10 Feb 2017 10:22:18 -0500
parents ebc846754dcb
children 77c1b345bc95
comparison
equal deleted inserted replaced
52:ebc846754dcb 53:c24ca7fed70c
120 --gap_trimming $trim_type_cond.gap_trimming 120 --gap_trimming $trim_type_cond.gap_trimming
121 #end if 121 #end if
122 #end if 122 #end if
123 #end if 123 #end if
124 #end if 124 #end if
125 >/dev/null
125 126
126 && echo "Sequence alignments and corresponding phylogenies" 127 && echo "Sequence alignments and corresponding phylogenies"
127 #if str($input_format) == 'ptortho': 128 #if str($input_format) == 'ptortho':
128 && echo -e "#Size\tName" > $output_fasta_ptortho 129 && echo -e "#Size\tName" > $output_fasta_ptortho
129 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptortho 130 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptortho
147 ]]> 148 ]]>
148 </command> 149 </command>
149 <inputs> 150 <inputs>
150 <conditional name="input_format_cond"> 151 <conditional name="input_format_cond">
151 <param name="input_format" type="select" label="Select type of data to sub sample"> 152 <param name="input_format" type="select" label="Select type of data to sub sample">
152 <option value="ptortho">Gene family clusters</option> 153 <option value="ptortho">Precomputed orthologous gene family clusters</option>
153 <option value="ptorthocs">Gene family clusters and corresponding coding sequences</option> 154 <option value="ptorthocs">Precomputed orthologous gene family clusters with corresponding coding sequences</option>
154 </param> 155 </param>
155 <when value="ptortho"> 156 <when value="ptortho">
156 <param name="input_ptortho" format="ptortho" type="data" label="Precomputed orthologous gene family clusters" /> 157 <param name="input_ptortho" format="ptortho" type="data" label="Precomputed orthologous gene family clusters" />
157 </when> 158 </when>
158 <when value="ptorthocs"> 159 <when value="ptorthocs">
289 <filter>input_format_cond['input_format'] == 'ptorthocs'</filter> 290 <filter>input_format_cond['input_format'] == 'ptorthocs'</filter>
290 </data> 291 </data>
291 <data name="output_aln" format="txt" label="Multiple alignments using method ${options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']} on ${on_string}"> 292 <data name="output_aln" format="txt" label="Multiple alignments using method ${options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']} on ${on_string}">
292 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter> 293 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
293 </data> 294 </data>
294 <data name="output_tree" format="ptpt" label="Phylogenetic trees on ${on_string}"> 295 <data name="output_tree" format="pttree" label="Phylogenetic trees on ${on_string}">
295 <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter> 296 <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
296 </data> 297 </data>
297 </outputs> 298 </outputs>
298 <tests> 299 <tests>
299 <test> 300 <test>