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comparison assembly_post_processor.xml @ 3:d651432961fb draft

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author greg
date Wed, 11 Jan 2017 13:32:42 -0500
parents 4eb05d406410
children 842c77ce5fd8
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2:4eb05d406410 3:d651432961fb
33 #end if 33 #end if
34 --min_length $options_type.min_length 34 --min_length $options_type.min_length
35 #end if 35 #end if
36 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 36 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
37 --num_threads \${GALAXY_SLOTS:-4} 37 --num_threads \${GALAXY_SLOTS:-4}
38 --no_config_override
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"/>
42 <conditional name="prediction_method_cond"> 43 <conditional name="prediction_method_cond">
73 <option value="orthofinder">OrthoFinder</option> 74 <option value="orthofinder">OrthoFinder</option>
74 <option value="orthomcl">OrthoMCL</option> 75 <option value="orthomcl">OrthoMCL</option>
75 </param> 76 </param>
76 </when> 77 </when>
77 </conditional> 78 </conditional>
78 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove gappy sites in alignments" help="0.1 removes sites with 90% gaps"/> 79 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps"/>
79 <param name="strand_specific" type="select" label="De novo transcriptome assembly was performed with strand-specific library?"> 80 <param name="strand_specific" type="select" label="De novo transcriptome assembly was performed with strand-specific library?">
80 <option value="no" selected="true">No</option> 81 <option value="no" selected="true">No</option>
81 <option value="yes">Yes</option> 82 <option value="yes">Yes</option>
82 </param> 83 </param>
83 <param name="dereplicate" type="select" label="Remove repeated sequences in predicted coding regions?"> 84 <param name="dereplicate" type="select" label="Remove repeated sequences in predicted coding regions?">