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comparison gene_family_classifier.xml @ 28:a63b610ec5bd draft

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author greg
date Fri, 27 Jan 2017 15:03:15 -0500
parents f041f7778540
children 59d1ec149c64
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27:f041f7778540 28:a63b610ec5bd
1 <tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="1.0.0"> 1 <tool id="plant_tribes_gene_family_classifier" name="Classify gene sequences" version="0.3">
2 <description>pipeline</description> 2 <description>into precomputed orthologous gene family clusters</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2">plant_tribes_gene_family_classifier</requirement> 4 <requirement type="package" version="0.3">plant_tribes_gene_family_classifier</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <!-- Anything other than zero is an error --> 7 <!-- Anything other than zero is an error -->
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 <!-- In case the return code has not been set properly check stderr too --> 9 <!-- In case the return code has not been set properly check stderr too -->
69 #end if 69 #end if
70 #end if 70 #end if
71 71
72 #if $create_ortho_sequences: 72 #if $create_ortho_sequences:
73 #if $create_corresponding_coding_sequences: 73 #if $create_corresponding_coding_sequences:
74 && echo "Sequences classified into pre-computed orthologous plant gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output 74 && echo "Sequences classified into precomputed orthologous plant gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output
75 #else: 75 #else:
76 && echo "Sequences classified into pre-computed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output 76 && echo "Sequences classified into precomputed orthologous plant gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output
77 #end if 77 #end if
78 && ls -al $orthogroups_fasta_src_dir | grep f >> $output 78 && ls -al $orthogroups_fasta_src_dir | grep f >> $output
79 && mv $orthogroups_fasta_src_dir/* $dest_dir || true 79 && mv $orthogroups_fasta_src_dir/* $dest_dir || true
80 #end if 80 #end if
81 81
117 <option value="basic" selected="true">Basic</option> 117 <option value="basic" selected="true">Basic</option>
118 <option value="advanced">Advanced</option> 118 <option value="advanced">Advanced</option>
119 </param> 119 </param>
120 <when value="basic" /> 120 <when value="basic" />
121 <when value="advanced"> 121 <when value="advanced">
122 <param name="super_orthogroups" type="select" label="SuperOrthogroups MCL clustering" help="blastp e-value matrix between all pairs of orthogroups"> 122 <param name="super_orthogroups" type="select" label="Super Orthogroups" help="Secondary MCL clusters of orthogroups">
123 <option value="min_evalue" selected="true">Minimum e-value</option> 123 <option value="min_evalue" selected="true">Minimum e-value</option>
124 <option value="avg_evalue">Average e-value</option> 124 <option value="avg_evalue">Average e-value</option>
125 </param> 125 </param>
126 <conditional name="single_copy_cond"> 126 <conditional name="single_copy_cond">
127 <param name="single_copy" type="select" label="Select single copy configuration"> 127 <param name="single_copy" type="select" label="Select single copy configuration">
180 </output_collection> 180 </output_collection>
181 </test> 181 </test>
182 </tests> 182 </tests>
183 <help> 183 <help>
184 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of 184 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
185 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs gene family 185 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. This tool classifies gene
186 classification of the post processed de novo transcripts using either blastp (faster), HMMScan (slower but more sensitive to remote 186 sequences into precomputed orthologous gene family clusters using either blastp (faster), HMMScan (slower but more sensitive
187 homologs) or both (more exhaustive). 187 to remote homologs) or both (more exhaustive).
188
189 This tool accepts any of the following as input.
190
191 * the postprocessed assemblies produced by the **Postprocess de novo assembly transcripts into putative coding sequences** tool
192 * externally predicted coding sequences and their corresponding amino acid translations derived from a transcriptome assembly
193 * gene predictions from a sequenced genome
188 194
189 ----- 195 -----
190 196
191 **Options** 197 **Options**
192 198
193 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. 199 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
194 * **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL. 200 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
195 * **Protein classification method** - One of blastp, HMMScan or both. 201 * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive).
196 * **SuperOrthogroups MCL clustering** - blastp e-value matrix between all pairs of orthogroups. 202 * **Super Orthogroups** - Secondary MCL clusters of orthogroups.
197 * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only. 203 * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
198 * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only. 204 * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
199 * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?". 205 * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".
200 206
201 </help> 207 </help>
202 <citations> 208 <citations>
203 <citation type="bibtex"> 209 <citation type="bibtex">
204 @unpublished{None, 210 @unpublished{None,
205 author = {None}, 211 author = {Eric Wafula},
206 title = {None}, 212 title = {None},
207 year = {None}, 213 year = {None},
208 eprint = {None}, 214 eprint = {None},
209 url = {None} 215 url = {None}
210 }</citation> 216 }</citation>