Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 65:774c1ad296e7 draft

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Uploaded
author greg
date Thu, 09 Feb 2017 13:04:32 -0500
parents c96583b389a7
children 7525307aa1d7
comparison
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64:c96583b389a7 65:774c1ad296e7
104 #end if 104 #end if
105 #end if 105 #end if
106 106
107 #if $create_ortho_sequences: 107 #if $create_ortho_sequences:
108 #if $create_corresponding_coding_sequences: 108 #if $create_corresponding_coding_sequences:
109 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptorthocs 109 && echo "#Size\tName" > $output_ptorthocs
110 #else: 110 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptorthocs
111 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptortho 111 #else:
112 && echo "#Size\tName" > $output_ptortho
113 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptortho
112 #end if 114 #end if
113 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir 115 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
114 #end if 116 #end if
115 117
116 #if $single_copy_orthogroup: 118 #if $single_copy_orthogroup:
117 #if $create_ortho_sequences: 119 #if $create_ortho_sequences:
118 && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco 120 && echo "#Size\tName" > $output_ptsco
121 && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptsco
119 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir 122 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir
120 #end if 123 #end if
121 #end if 124 #end if
122 ]]> 125 ]]>
123 </command> 126 </command>
186 ~/config/*.singleCopy.config files are not easy to manage by a suer 189 ~/config/*.singleCopy.config files are not easy to manage by a suer
187 and the GeneFamilyClassifier pipeline must be enhanced to provide an 190 and the GeneFamilyClassifier pipeline must be enhanced to provide an
188 optional parameter for the hard-coded path to the config. 191 optional parameter for the hard-coded path to the config.
189 <option value="custom" selected="true">Single copy orthogroup custom</option> 192 <option value="custom" selected="true">Single copy orthogroup custom</option>
190 --> 193 -->
191 <option value="taxa">Minumum single copy taxa required in orthogroup</option> 194 <option value="taxa">Minimum single copy taxa required in orthogroup</option>
192 </param> 195 </param>
193 <when value="custom" /> 196 <when value="custom" />
194 <when value="taxa"> 197 <when value="taxa">
195 <param name="single_copy_taxa" type="integer" value="20" label="Minumum single copy taxa required in orthogroup"/> 198 <param name="single_copy_taxa" type="integer" value="20" label="Minimum single copy taxa required in orthogroup"/>
196 <param name="taxa_present" type="integer" value="21" label="Minumum taxa required in single copy orthogroup"/> 199 <param name="taxa_present" type="integer" value="21" label="Minimum taxa required in single copy orthogroup"/>
197 </when> 200 </when>
198 </conditional> 201 </conditional>
199 </when> 202 </when>
200 </conditional> 203 </conditional>
201 <conditional name="create_orthogroup_cond"> 204 <conditional name="create_orthogroup_cond">
277 280
278 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. 281 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
279 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). 282 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
280 * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive). 283 * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive).
281 * **Super Orthogroups** - Secondary MCL clusters of orthogroups. 284 * **Super Orthogroups** - Secondary MCL clusters of orthogroups.
282 * **Specify single copy orthogroup selection?** - Select 'Yes' to specify one of 'Single copy orthogroup custom' (not yet supported) or 'Minumum single copy taxa required in orthogroup'. 285 * **Specify single copy orthogroup selection?** - Select 'Yes' to specify 'Minimum single copy taxa required in orthogroup'.
283 * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only. 286 * **Minimum single copy taxa required in orthogroup** - Used with "Minimum single copy taxa required in orthogroup" configuration only.
284 * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only. 287 * **Minimum taxa required in single copy orthogroup** - Used with "Minimum single copy taxa required in orthogroup" configuration only.
285 * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?". 288 * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".
286 289
287 </help> 290 </help>
288 <citations> 291 <citations>
289 <citation type="bibtex"> 292 <citation type="bibtex">