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comparison assembly_post_processor.xml @ 5:31673ee3734f draft

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author greg
date Fri, 27 Jan 2017 15:03:00 -0500
parents 842c77ce5fd8
children bf355f832557
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4:842c77ce5fd8 5:31673ee3734f
1 <tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="1.0.0"> 1 <tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.3">
2 <description>pipeline</description> 2 <description>into putative coding sequences</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2">plant_tribes_assembly_post_processor</requirement> 4 <requirement type="package" version="0.3">plant_tribes_assembly_post_processor</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 -->
110 </output_collection> 110 </output_collection>
111 </test> 111 </test>
112 </tests> 112 </tests>
113 <help> 113 <help>
114 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of 114 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
115 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It post-processes de novo assembly 115 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It postprocesses de novo assembly
116 transcripts into putative coding sequences and their corresponding amino acid translations. 116 transcripts into putative coding sequences and their corresponding amino acid translations, locally assembling targeted gene families.
117 117
118 ----- 118 -----
119 119
120 **Options** 120 **Options**
121 121
122 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder. 122 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder.
123 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms. 123 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
124 * **Target gene family assembly?** - Select yes to target gene families to assemble. 124 * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble.
125 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble. The next version of this tool will use a dynamic select list for this feature. 125 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.
126 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. 126 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
127 * **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL. 127 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
128 * **Remove gappy sites in alignments** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0] 128 * **Remove sites in alignments with gaps of** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
129 * **De novo transcriptome assembly was performed with strand-specific library?** - Select yes if de novo transcriptome assembly was performed with strand-specific library. 129 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.
130 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions. 130 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
131 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions. 131 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.
132 132
133 </help> 133 </help>
134 <citations> 134 <citations>
135 <citation type="bibtex"> 135 <citation type="bibtex">
136 @unpublished{None, 136 @unpublished{None,
137 author = {None}, 137 author = {Eric Wafula},
138 title = {None}, 138 title = {None},
139 year = {None}, 139 year = {None},
140 eprint = {None}, 140 eprint = {None},
141 url = {None} 141 url = {None}
142 }</citation> 142 }</citation>