Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 90:7dc44a577c88 draft

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author greg
date Thu, 26 Oct 2017 07:54:33 -0400
parents 69f34ef8bfab
children a9571ff827b4
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89:69f34ef8bfab 90:7dc44a577c88
30 --dereplicate true 30 --dereplicate true
31 #end if 31 #end if
32 --min_length $options_type.min_length 32 --min_length $options_type.min_length
33 #end if 33 #end if
34 --num_threads \${GALAXY_SLOTS:-4} 34 --num_threads \${GALAXY_SLOTS:-4}
35 1>&2 35 &>proc.log
36 && mv $output_dir/transcripts.cds '$output_cds' 36 && mv $output_dir/transcripts.cds '$output_cds'
37 && mv $output_dir/transcripts.pep '$output_pep' 37 && mv $output_dir/transcripts.pep '$output_pep'
38 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds' 38 && mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
39 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep' 39 && mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
40 #if str($options_type.options_type_selector) == 'advanced': 40 #if str($options_type.options_type_selector) == 'advanced':
82 <option value="gfam" selected="true">GFam</option> 82 <option value="gfam" selected="true">GFam</option>
83 <option value="orthofinder">OrthoFinder</option> 83 <option value="orthofinder">OrthoFinder</option>
84 <option value="orthomcl">OrthoMCL</option> 84 <option value="orthomcl">OrthoMCL</option>
85 </param> 85 </param>
86 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Trim alignments"/> 86 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Trim alignments"/>
87 <param name="min_coverage" type="float" value="0.5" min="0.3" max="1.0" label="Minimum alignment coverage"/> 87 <param name="min_coverage" type="float" value="0" min="0" max="1.0" label="Minimum alignment coverage"/>
88 </when> 88 </when>
89 </conditional> 89 </conditional>
90 <param name="strand_specific" type="select" label="Strand-specific assembly?"> 90 <param name="strand_specific" type="select" label="Strand-specific assembly?">
91 <option value="no" selected="true">No</option> 91 <option value="no" selected="true">No</option>
92 <option value="yes">Yes</option> 92 <option value="yes">Yes</option>
147 <param name="target_gene_family_assembly" value="yes"/> 147 <param name="target_gene_family_assembly" value="yes"/>
148 <param name="orthogroups" value="target_orthos.ids"/> 148 <param name="orthogroups" value="target_orthos.ids"/>
149 <param name="scaffold" value="22Gv1.1"/> 149 <param name="scaffold" value="22Gv1.1"/>
150 <param name="method" value="orthomcl"/> 150 <param name="method" value="orthomcl"/>
151 <param name="dereplicate" value="yes"/> 151 <param name="dereplicate" value="yes"/>
152 <param name="min_coverage" value="0.3"/> 152 <param name="min_coverage" value="0"/>
153 <output_collection name="output_targeted_gene_families" type="list"> 153 <output_collection name="output_targeted_gene_families" type="list">
154 <element name="752.faa" file="752.faa" ftype="fasta"/> 154 <element name="752.faa" file="752.faa" ftype="fasta"/>
155 <element name="752.fasta" file="752.fasta" ftype="fasta"/> 155 <element name="752.fasta" file="752.fasta" ftype="fasta"/>
156 <element name="752.fna" file="752.fna" ftype="fasta"/> 156 <element name="752.fna" file="752.fna" ftype="fasta"/>
157 </output_collection> 157 </output_collection>
186 186
187 * **Targeted gene families** - select a history item containing a list of targeted orthogroup identifiers corresponding to the gene family classification from a specified scaffold. Gene family identifiers can be obtained from the function annotation table ("Orthogroup ID" field of .summary file) of scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and are also available in the PlantTribes "annotation" directory of the scaffold data download. 187 * **Targeted gene families** - select a history item containing a list of targeted orthogroup identifiers corresponding to the gene family classification from a specified scaffold. Gene family identifiers can be obtained from the function annotation table ("Orthogroup ID" field of .summary file) of scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and are also available in the PlantTribes "annotation" directory of the scaffold data download.
188 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds (installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool) whose orthogroup(s) are targeted for the localized assembly. 188 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds (installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool) whose orthogroup(s) are targeted for the localized assembly.
189 * **Protein clustering method** - gene family scaffold protein clustering method. Each PlantTribes scaffold data has up to three sets of clusters - GFam[8] (clusters of consensus domain architecture), OrthoFinder[9] (broadly defined clusters) or OrthoMCL[10] (narrowly defined clusters). You can also install your own data scaffold created using a different clustering method as long as it conforms to the PlantTribes scaffold data format. 189 * **Protein clustering method** - gene family scaffold protein clustering method. Each PlantTribes scaffold data has up to three sets of clusters - GFam[8] (clusters of consensus domain architecture), OrthoFinder[9] (broadly defined clusters) or OrthoMCL[10] (narrowly defined clusters). You can also install your own data scaffold created using a different clustering method as long as it conforms to the PlantTribes scaffold data format.
190 * **Trim alignments** - trim gene family multiple sequence alignments that include scaffold backbone genes and locally assembled transcripts to remove non-conserved regions (gappy sites)[11]. The trimmed alignments are used in assigning scores to locally assembled transcripts to determine how well they compare to the backbone gene models. The default setting of 0.1 removes sites that have gaps in 90% or more of the sequences in the multiple sequence alignment. This option is restricted to the range 0.0 - 1.0. 190 * **Trim alignments** - trim gene family multiple sequence alignments that include scaffold backbone genes and locally assembled transcripts to remove non-conserved regions (gappy sites)[11]. The trimmed alignments are used in assigning scores to locally assembled transcripts to determine how well they compare to the backbone gene models. The default setting of 0.1 removes sites that have gaps in 90% or more of the sequences in the multiple sequence alignment. This option is restricted to the range 0.0 - 1.0.
191 * **Minimum alignment coverage** - allowable sequence coverage in the orthogroup trimmed protein multiple sequence alignments. The default setting of 0.5 reports assembled targeted gene family transcripts with at least 50% coverage of the conserved regions in the trimmed multiple sequence alignment. 191 * **Minimum alignment coverage** - allowable sequence coverage in the orthogroup trimmed protein multiple sequence alignments. Selecting transcripts with coverage of at least the average of the backbone orthogroup gene models is recommended. Details are shown in the targeted gene family assembly statistics history item.
192 192
193 * **Strand-specific assembly?** - select 'Yes' if transcriptome library sequences were strand-specific. If 'Yes" is selected, transcripts from the minority strand (antisense) are removed. 193 * **Strand-specific assembly?** - select 'Yes' if transcriptome library sequences were strand-specific. If 'Yes" is selected, transcripts from the minority strand (antisense) are removed.
194 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12]. 194 * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12].
195 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp. 195 * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp.
196 196