Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 7:4d82da0ca014 draft

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author greg
date Mon, 30 Jan 2017 11:03:42 -0500
parents bf355f832557
children e5110df5314b
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6:bf355f832557 7:4d82da0ca014
98 <test> 98 <test>
99 <param name="input" value="assembly.fasta" ftype="fasta" /> 99 <param name="input" value="assembly.fasta" ftype="fasta" />
100 <param name="prediction_method" value="transdecoder" /> 100 <param name="prediction_method" value="transdecoder" />
101 <param name="options_type_selector" value="basic" /> 101 <param name="options_type_selector" value="basic" />
102 <output_collection name="transcripts" type="list"> 102 <output_collection name="transcripts" type="list">
103 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" /> 103 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
104 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" /> 104 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
105 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta" /> 105 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta" compare="contains"/>
106 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" /> 106 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
107 </output_collection> 107 </output_collection>
108 </test> 108 </test>
109 <!--
110 <test> 109 <test>
111 <param name="input" value="assembly.fasta" ftype="fasta" /> 110 <param name="input" value="assembly.fasta" ftype="fasta" />
112 <param name="prediction_method" value="transdecoder" /> 111 <param name="prediction_method" value="transdecoder" />
113 <param name="options_type_selector" value="advanced" /> 112 <param name="options_type_selector" value="advanced" />
114 <param name="strand_specific" value="yes" /> 113 <param name="gap_trimming" value="0.1" />
115 <param name="dereplicate" value="yes" /> 114 <param name="dereplicate" value="yes" />
115 <param name="min_length" value="200" />
116 <output_collection name="transcripts" type="list"> 116 <output_collection name="transcripts" type="list">
117 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" /> 117 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
118 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" /> 118 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
119 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" /> 119 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
120 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" /> 120 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.pep" ftype="fasta" compare="contains"/>
121 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta" /> 121 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/>
122 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" /> 122 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
123 </output_collection> 123 </output_collection>
124 </test> 124 </test>
125 -->
126 </tests> 125 </tests>
127 <help> 126 <help>
128 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of 127 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
129 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It postprocesses de novo assembly 128 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It postprocesses de novo assembly
130 transcripts into putative coding sequences and their corresponding amino acid translations, locally assembling targeted gene families. 129 transcripts into putative coding sequences and their corresponding amino acid translations, locally assembling targeted gene families.