Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 47:3227f0f39800 draft

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author greg
date Wed, 03 May 2017 10:14:11 -0400
parents 61977f3f19ea
children 564163c7afd8
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46:b7858b1f64f1 47:3227f0f39800
5 </macros> 5 </macros>
6 <expand macro="requirements_assembly_post_processor" /> 6 <expand macro="requirements_assembly_post_processor" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 AssemblyPostProcessor 10 python $__tool_directory__/assembly_post_processor.py
11 --transcripts '$input' 11 --transcripts '$input'
12 --prediction_method $prediction_method_cond.prediction_method 12 --prediction_method $prediction_method_cond.prediction_method
13 #if str($prediction_method_cond.prediction_method) == 'estscan': 13 #if str($prediction_method_cond.prediction_method) == 'estscan':
14 --score_matrices '$score_matrices' 14 --score_matrices '$score_matrices'
15 #end if 15 #end if
20 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path' 20 --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
21 --method '$target_gene_family_assembly_cond.method' 21 --method '$target_gene_family_assembly_cond.method'
22 --gap_trimming $target_gene_family_assembly_cond.gap_trimming 22 --gap_trimming $target_gene_family_assembly_cond.gap_trimming
23 #end if 23 #end if
24 #if str($options_type.strand_specific) == 'yes': 24 #if str($options_type.strand_specific) == 'yes':
25 --strand_specific 25 --strand_specific 'true'
26 #end if 26 #end if
27 #if str($options_type.dereplicate) == 'yes': 27 #if str($options_type.dereplicate) == 'yes':
28 --dereplicate 28 --dereplicate 'true'
29 #end if 29 #end if
30 --min_length $options_type.min_length 30 --min_length $options_type.min_length
31 #end if 31 #end if
32 --num_threads \${GALAXY_SLOTS:-4} 32 --num_threads \${GALAXY_SLOTS:-4}
33 >/dev/null
34 ]]> 33 ]]>
35 </command> 34 </command>
36 <inputs> 35 <inputs>
37 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> 36 <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
38 <conditional name="prediction_method_cond"> 37 <conditional name="prediction_method_cond">