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comparison assembly_post_processor.xml @ 8:e5110df5314b draft

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author greg
date Tue, 31 Jan 2017 11:10:35 -0500
parents 4d82da0ca014
children 5a0a049d11aa
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7:4d82da0ca014 8:e5110df5314b
12 <regex match="Exception:" /> 12 <regex match="Exception:" />
13 </stdio> 13 </stdio>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 AssemblyPostProcesser 16 AssemblyPostProcesser
17 --transcripts "$input" 17 --transcripts '$input'
18 --prediction_method $prediction_method_cond.prediction_method 18 --prediction_method $prediction_method_cond.prediction_method
19 #if str($prediction_method_cond.prediction_method) == 'estscan': 19 #if str($prediction_method_cond.prediction_method) == 'estscan':
20 --score_matrices "$score_matrices" 20 --score_matrices '$score_matrices'
21 #end if 21 #end if
22 #if str($options_type.options_type_selector) == 'advanced': 22 #if str($options_type.options_type_selector) == 'advanced':
23 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 23 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
24 --gene_family_search "$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" 25 --scaffold_dir '${GALAXY_DATA_MANAGER_DATA_PATH}/plant_tribes/scaffolds'
26 --scaffold "$options_type.target_gene_family_assembly_cond.scaffold" 26 --scaffold '$options_type.target_gene_family_assembly_cond.scaffold'
27 --method "$options_type.target_gene_family_assembly_cond.method" 27 --method '$options_type.target_gene_family_assembly_cond.method'
28 #end if 28 #end if
29 --gap_trimming $options_type.gap_trimming 29 --gap_trimming $options_type.gap_trimming
30 #if str($options_type.strand_specific) == 'yes': 30 #if str($options_type.strand_specific) == 'yes':
31 --strand_specific 31 --strand_specific
32 #end if 32 #end if
96 </outputs> 96 </outputs>
97 <tests> 97 <tests>
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" />
102 <output_collection name="transcripts" type="list"> 101 <output_collection name="transcripts" type="list">
103 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/> 102 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
104 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/> 103 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
105 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta" compare="contains"/> 104 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta"/>
106 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/> 105 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
107 </output_collection> 106 </output_collection>
108 </test> 107 </test>
109 <test> 108 <test>
110 <param name="input" value="assembly.fasta" ftype="fasta" /> 109 <param name="input" value="assembly.fasta" ftype="fasta" />
111 <param name="prediction_method" value="transdecoder" /> 110 <param name="prediction_method" value="transdecoder" />
114 <param name="dereplicate" value="yes" /> 113 <param name="dereplicate" value="yes" />
115 <param name="min_length" value="200" /> 114 <param name="min_length" value="200" />
116 <output_collection name="transcripts" type="list"> 115 <output_collection name="transcripts" type="list">
117 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/> 116 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
118 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/> 117 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
119 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/> 118 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" compare="contains"/>
120 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.pep" ftype="fasta" compare="contains"/> 119 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" compare="contains"/>
121 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/> 120 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/>
122 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/> 121 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
123 </output_collection> 122 </output_collection>
124 </test> 123 </test>
125 </tests> 124 </tests>
148 <citation type="bibtex"> 147 <citation type="bibtex">
149 @unpublished{None, 148 @unpublished{None,
150 author = {Eric Wafula}, 149 author = {Eric Wafula},
151 title = {None}, 150 title = {None},
152 year = {None}, 151 year = {None},
153 eprint = {None}, 152 url = {https://github.com/dePamphilis/PlantTribes}
154 url = {None}
155 }</citation> 153 }</citation>
154 <citation type="bibtex">
155 @published{Proc Int Conf Intell Syst Mol Biol,
156 author = {Iseli C, Jongeneel CV, Bucher P.},
157 title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.},
158 year = {1999},
159 url = {http://estscan.sourceforge.net/}
160 }</citation>
161 <citation type="doi">10.1038/nprot.2013.084</citation>
162 <citation type="doi">10.1109/tcbb.2013.68</citation>
156 </citations> 163 </citations>
157 </tool> 164 </tool>