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comparison assembly_post_processor.xml @ 6:bf355f832557 draft

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author greg
date Mon, 30 Jan 2017 09:23:36 -0500
parents 31673ee3734f
children 4d82da0ca014
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5:31673ee3734f 6:bf355f832557
4 <requirement type="package" version="0.3">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 <exit_code range=":-1" />
10 <!-- In case the return code has not been set propery check stderr too -->
10 <regex match="Error:" /> 11 <regex match="Error:" />
11 <regex match="Exception:" /> 12 <regex match="Exception:" />
12 </stdio> 13 </stdio>
13 <command> 14 <command>
14 <![CDATA[ 15 <![CDATA[
19 --score_matrices "$score_matrices" 20 --score_matrices "$score_matrices"
20 #end if 21 #end if
21 #if str($options_type.options_type_selector) == 'advanced': 22 #if str($options_type.options_type_selector) == 'advanced':
22 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 23 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
23 --gene_family_search "$options_type.target_gene_family_assembly_cond.orthogroups" 24 --gene_family_search "$options_type.target_gene_family_assembly_cond.orthogroups"
25 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
24 --scaffold "$options_type.target_gene_family_assembly_cond.scaffold" 26 --scaffold "$options_type.target_gene_family_assembly_cond.scaffold"
25 --method "$options_type.target_gene_family_assembly_cond.method" 27 --method "$options_type.target_gene_family_assembly_cond.method"
26 #end if 28 #end if
27 --gap_trimming $options_type.gap_trimming 29 --gap_trimming $options_type.gap_trimming
28 #if str($options_type.strand_specific) == 'yes': 30 #if str($options_type.strand_specific) == 'yes':
31 #if str($options_type.dereplicate) == 'yes': 33 #if str($options_type.dereplicate) == 'yes':
32 --dereplicate 34 --dereplicate
33 #end if 35 #end if
34 --min_length $options_type.min_length 36 --min_length $options_type.min_length
35 #end if 37 #end if
36 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
37 --num_threads \${GALAXY_SLOTS:-4} 38 --num_threads \${GALAXY_SLOTS:-4}
38 ]]> 39 ]]>
39 </command> 40 </command>
40 <inputs> 41 <inputs>
41 <param name="input" format="fasta" type="data" label="De novo transcriptome assembly fasta file"/> 42 <param name="input" format="fasta" type="data" label="De novo transcriptome assembly fasta file"/>
95 </outputs> 96 </outputs>
96 <tests> 97 <tests>
97 <test> 98 <test>
98 <param name="input" value="assembly.fasta" ftype="fasta" /> 99 <param name="input" value="assembly.fasta" ftype="fasta" />
99 <param name="prediction_method" value="transdecoder" /> 100 <param name="prediction_method" value="transdecoder" />
101 <param name="options_type_selector" value="basic" />
102 <output_collection name="transcripts" type="list">
103 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" />
104 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" />
105 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta" />
106 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" />
107 </output_collection>
108 </test>
109 <!--
110 <test>
111 <param name="input" value="assembly.fasta" ftype="fasta" />
112 <param name="prediction_method" value="transdecoder" />
100 <param name="options_type_selector" value="advanced" /> 113 <param name="options_type_selector" value="advanced" />
101 <param name="strand_specific" value="yes" /> 114 <param name="strand_specific" value="yes" />
102 <param name="dereplicate" value="yes" /> 115 <param name="dereplicate" value="yes" />
103 <output_collection name="transcripts" type="list"> 116 <output_collection name="transcripts" type="list">
104 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" /> 117 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" />
107 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" /> 120 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" />
108 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta" /> 121 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta" />
109 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" /> 122 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" />
110 </output_collection> 123 </output_collection>
111 </test> 124 </test>
125 -->
112 </tests> 126 </tests>
113 <help> 127 <help>
114 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of 128 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 postprocesses de novo assembly 129 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, locally assembling targeted gene families. 130 transcripts into putative coding sequences and their corresponding amino acid translations, locally assembling targeted gene families.