Mercurial > repos > jjohnson > cummerbund
comparison cuffdiff_wrapper.xml @ 14:d10befb0867a
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 |
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| 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 |