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comparison cuffdiff_wrapper.xml @ 14:d10befb0867a

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Add library_norm_method and dispersion_method params to cuffdiff tool.
author Jim Johnson <jj@umn.edu>
date Wed, 17 Jul 2013 08:25:52 -0500
parents 4597c429b6fb
children 2d7eee38ab5b
comparison
equal deleted inserted replaced
13:4597c429b6fb 14:d10befb0867a
8 #set sel_outputs = $output_sel.__str__.split(',') 8 #set sel_outputs = $output_sel.__str__.split(',')
9 cuffdiff_wrapper.py 9 cuffdiff_wrapper.py
10 --FDR=$fdr 10 --FDR=$fdr
11 --num-threads="4" 11 --num-threads="4"
12 --min-alignment-count=$min_alignment_count 12 --min-alignment-count=$min_alignment_count
13 --library-norm-method=$library_norm_method
14 --dispersion-method=$dispersion_method
13 15
14 #if 'cuffdata' in $sel_outputs or not $output_sel: 16 #if 'cuffdata' in $sel_outputs or not $output_sel:
15 --cuffdatadir=$cuffdata.extra_files_path 17 --cuffdatadir=$cuffdata.extra_files_path
16 #end if 18 #end if
17 #if 'cummeRbund_db' in $sel_outputs: 19 #if 'cummeRbund_db' in $sel_outputs:
131 <when value="No"> 133 <when value="No">
132 <param format="sam,bam" name="aligned_reads1" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> 134 <param format="sam,bam" name="aligned_reads1" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
133 <param format="sam,bam" name="aligned_reads2" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> 135 <param format="sam,bam" name="aligned_reads2" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
134 </when> 136 </when>
135 </conditional> 137 </conditional>
138
139 <param name="library_norm_method" type="select" label="Library normalization method">
140 <option value="geometric" selected="True">geometric</option>
141 <option value="classic-fpkm">classic-fpkm</option>
142 <option value="quartile">quartile</option>
143 </param>
144
145 <param name="dispersion_method" type="select" label="Dispersion estimation method" help="If using only one sample per condition, you must use 'blind.'">
146 <option value="pooled" selected="True">pooled</option>
147 <option value="per-condition">per-condition</option>
148 <option value="blind">blind</option>
149 </param>
136 150
137 <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/> 151 <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
138 152
139 <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/> 153 <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
140 154