Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 66:09ae3a0d7273 draft

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author greg
date Wed, 24 May 2017 13:22:35 -0400
parents 9eabe9e58fb5
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65:baf10f7f3d4a 66:09ae3a0d7273
25 #if str($options_type.strand_specific) == 'yes': 25 #if str($options_type.strand_specific) == 'yes':
26 --strand_specific 'true' 26 --strand_specific 'true'
27 #end if 27 #end if
28 #if str($options_type.dereplicate) == 'yes': 28 #if str($options_type.dereplicate) == 'yes':
29 --dereplicate 'true' 29 --dereplicate 'true'
30 --output_cleaned_nr_cds '$output_cleaned_nr_cds'
31 --output_cleaned_nr_pep '$output_cleaned_nr_pep'
30 #end if 32 #end if
31 --min_length $options_type.min_length 33 --min_length $options_type.min_length
32 #end if 34 #end if
33 --num_threads \${GALAXY_SLOTS:-4} 35 --num_threads \${GALAXY_SLOTS:-4}
36 --output_cds '$output_cds'
37 --output_cleaned_cds '$output_cleaned_cds'
38 --output_cleaned_pep '$output_cleaned_pep'
39 --output_pep '$output_pep'
34 ]]> 40 ]]>
35 </command> 41 </command>
36 <inputs> 42 <inputs>
37 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> 43 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
38 <conditional name="prediction_method_cond"> 44 <conditional name="prediction_method_cond">
86 </inputs> 92 </inputs>
87 <outputs> 93 <outputs>
88 <data name="output_pttgf" format="pttgf" label="${tool.name} (targeted gene families) on ${on_string}"> 94 <data name="output_pttgf" format="pttgf" label="${tool.name} (targeted gene families) on ${on_string}">
89 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter> 95 <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
90 </data> 96 </data>
91 <collection name="transcripts" type="list"> 97 <data name="output_cds" format="fasta" label="${tool.name} on ${on_string} (transcripts.cds)"/>
92 <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="true" ext="fasta" /> 98 <data name="output_cleaned_cds" format="fasta" label="${tool.name} on ${on_string} (transcripts.cleaned.cds)"/>
93 </collection> 99 <data name="output_cleaned_nr_cds" format="fasta" label="${tool.name} on ${on_string} (transcripts.cleaned.nr.cds)">
100 <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter>
101 </data>
102 <data name="output_cleaned_nr_pep" format="fasta" label="${tool.name} on ${on_string} (transcripts.cleaned.nr.pep)">
103 <filter>options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes'</filter>
104 </data>
105 <data name="output_cleaned_pep" format="fasta" label="${tool.name} on ${on_string} (transcripts.cleaned.pep)"/>
106 <data name="output_pep" format="fasta" label="${tool.name} on ${on_string} (transcripts.pep)"/>
94 </outputs> 107 </outputs>
95 <tests> 108 <tests>
96 <test> 109 <test>
97 <param name="input" value="assembly.fasta" ftype="fasta" /> 110 <param name="input" value="assembly.fasta" ftype="fasta"/>
98 <param name="prediction_method" value="transdecoder" /> 111 <param name="prediction_method" value="transdecoder"/>
99 <output_collection name="transcripts" type="list"> 112 <output name="output_cds" file="transcripts.cds" ftype="fasta"/>
100 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/> 113 <output name="output_cleaned_cds" file="transcripts.cleaned.cds" ftype="fasta"/>
101 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/> 114 <output name="output_cleaned._ep" file="transcripts.cleaned.pep" ftype="fasta"/>
102 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep" ftype="fasta"/> 115 <output name="output_pep" file="transcripts.pep" ftype="fasta"/>
103 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
104 </output_collection>
105 </test> 116 </test>
106 <test> 117 <test>
107 <param name="input" value="assembly.fasta" ftype="fasta" /> 118 <param name="input" value="assembly.fasta" ftype="fasta"/>
108 <param name="prediction_method" value="estscan" /> 119 <param name="prediction_method" value="estscan"/>
109 <param name="score_matrices" value="arabidopsis_thaliana.smat" ftype="smat"/> 120 <param name="score_matrices" value="arabidopsis_thaliana.smat" ftype="smat"/>
110 <param name="options_type_selector" value="advanced" /> 121 <param name="options_type_selector" value="advanced"/>
111 <param name="dereplicate" value="yes" /> 122 <param name="dereplicate" value="yes"/>
112 <output_collection name="transcripts" type="list"> 123 <output name="output_cds" file="transcripts2.cds" ftype="fasta"/>
113 <element name="transcripts.cds" file="transcripts2.cds" ftype="fasta"/> 124 <output name="output_cleaned_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
114 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/> 125 <output name="output_cleaned_nr_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/>
115 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/> 126 <output name="output_cleaned_nr_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
116 <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/> 127 <output name="output_cleaned_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/>
117 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/> 128 <output name="output_pep" file="transcripts2.pep" ftype="fasta"/>
118 <element name="transcripts.pep" file="transcripts2.pep" ftype="fasta"/> 129 </test>
119 </output_collection> 130 <test>
131 <param name="input" value="assembly_tgf.fasta" ftype="fasta"/>
132 <param name="prediction_method" value="transdecoder"/>
133 <param name="options_type_selector" value="advanced"/>
134 <param name="target_gene_family_assembly" value="yes"/>
135 <param name="orthogroups" value="target_orthos.ids"/>
136 <param name="scaffold" value="22Gv1.1"/>
137 <param name="method" value="orthomcl"/>
138 <param name="dereplicate" value="yes"/>
139 <output name="output_pttgf" file="output.pttgf" ftype="pttgf"/>
140 <output name="output_cds" file="transcripts_tgf.cds" ftype="fasta"/>
141 <output name="output_cleaned_cds" file="transcripts.cleaned_tgf.cds" ftype="fasta"/>
142 <output name="output_cleaned_nr_cds" file="transcripts_tgf.cleaned.nr.cds" ftype="fasta"/>
143 <output name="output_cleaned_nr_pep" file="transcripts_tgf.cleaned.nr.pep" ftype="fasta"/>
144 <output name="output_cleaned_pep" file="transcripts.cleaned_tgf.pep" ftype="fasta"/>
145 <output name="output_pep" file="transcripts_tgf.pep" ftype="fasta"/>
120 </test> 146 </test>
121 </tests> 147 </tests>
122 <help> 148 <help>
123 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and 149 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and
124 evolutionary analyses of genome-scale gene families and transcriptomes. This tool post-processes de novo 150 evolutionary analyses of genome-scale gene families and transcriptomes. This tool post-processes de novo