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comparison assembly_post_processor.xml @ 14:b468a86f87d9 draft

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author greg
date Wed, 08 Feb 2017 09:04:01 -0500
parents 521d09ac701a
children ff5c714e01d1
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13:521d09ac701a 14:b468a86f87d9
1 <tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.3"> 1 <tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.3">
2 <description>into putative coding sequences</description> 2 <description>into putative coding sequences</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.3">plant_tribes_assembly_post_processor</requirement> 4 <requirement type="package" version="0.4">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 <exit_code range=":-1" /> 9 <exit_code range=":-1" />
11 <regex match="Error:" /> 11 <regex match="Error:" />
12 <regex match="Exception:" /> 12 <regex match="Exception:" />
13 </stdio> 13 </stdio>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 #import os
17 AssemblyPostProcesser 16 AssemblyPostProcesser
18 --transcripts '$input' 17 --transcripts "$input"
19 --prediction_method $prediction_method_cond.prediction_method 18 --prediction_method $prediction_method_cond.prediction_method
20 #if str($prediction_method_cond.prediction_method) == 'estscan': 19 #if str($prediction_method_cond.prediction_method) == 'estscan':
21 --score_matrices '$score_matrices' 20 --score_matrices "$score_matrices"
22 #end if 21 #end if
23 #if str($options_type.options_type_selector) == 'advanced': 22 #if str($options_type.options_type_selector) == 'advanced':
24 #if str($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':
25 #set scaffold_path = $options_type.target_gene_family_assembly_cond.scaffold.fields.path 24 --gene_family_search "$options_type.target_gene_family_assembly_cond.orthogroups"
26 #set scaffold_dir = $os.path.split($scaffold_path)[0] 25 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
27 #set scaffold = $os.path.split($scaffold_path)[1] 26 --scaffold "$options_type.target_gene_family_assembly_cond.scaffold"
28 --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups' 27 --method "$options_type.target_gene_family_assembly_cond.method"
29 --scaffold_dir $scaffold_dir
30 --scaffold $scaffold
31 --method '$options_type.target_gene_family_assembly_cond.method'
32 #end if 28 #end if
33 --gap_trimming $options_type.gap_trimming 29 --gap_trimming $options_type.gap_trimming
34 #if str($options_type.strand_specific) == 'yes': 30 #if str($options_type.strand_specific) == 'yes':
35 --strand_specific 31 --strand_specific
36 #end if 32 #end if
100 </outputs> 96 </outputs>
101 <tests> 97 <tests>
102 <test> 98 <test>
103 <param name="input" value="assembly.fasta" ftype="fasta" /> 99 <param name="input" value="assembly.fasta" ftype="fasta" />
104 <param name="prediction_method" value="transdecoder" /> 100 <param name="prediction_method" value="transdecoder" />
101 <param name="options_type_selector" value="basic" />
105 <output_collection name="transcripts" type="list"> 102 <output_collection name="transcripts" type="list">
106 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/> 103 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
107 <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"/>
108 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta"/> 105 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta" compare="contains"/>
109 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/> 106 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
110 </output_collection> 107 </output_collection>
111 </test> 108 </test>
112 <test> 109 <test>
113 <param name="input" value="assembly.fasta" ftype="fasta" /> 110 <param name="input" value="assembly.fasta" ftype="fasta" />
114 <param name="prediction_method" value="transdecoder" /> 111 <param name="prediction_method" value="transdecoder" />
118 <param name="min_length" value="200" /> 115 <param name="min_length" value="200" />
119 <output_collection name="transcripts" type="list"> 116 <output_collection name="transcripts" type="list">
120 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/> 117 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
121 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/> 118 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
122 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" compare="contains"/> 119 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" compare="contains"/>
123 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" compare="contains"/> 120 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.pep" ftype="fasta" compare="contains"/>
124 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/> 121 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/>
125 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/> 122 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
126 </output_collection> 123 </output_collection>
127 </test> 124 </test>
128 </tests> 125 </tests>
151 <citation type="bibtex"> 148 <citation type="bibtex">
152 @unpublished{None, 149 @unpublished{None,
153 author = {Eric Wafula}, 150 author = {Eric Wafula},
154 title = {None}, 151 title = {None},
155 year = {None}, 152 year = {None},
156 url = {https://github.com/dePamphilis/PlantTribes} 153 eprint = {None},
154 url = {None}
157 }</citation> 155 }</citation>
158 <citation type="bibtex">
159 @published{Proc Int Conf Intell Syst Mol Biol,
160 author = {Iseli C, Jongeneel CV, Bucher P.},
161 title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.},
162 year = {1999},
163 url = {http://estscan.sourceforge.net/}
164 }</citation>
165 <citation type="doi">10.1038/nprot.2013.084</citation>
166 <citation type="doi">10.1109/tcbb.2013.68</citation>
167 </citations> 156 </citations>
168 </tool> 157 </tool>