cummerbund: cuffdiff_wrapper.xml annotate

annotate cuffdiff_wrapper.xml @ 2:fdf01b3c1841

Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output

author	Jim Johnson <jj@umn.edu>
date	Fri, 08 Nov 2013 14:54:01 -0600
parents	da7241f92ecf
children	f109453ecfa2

rev	line source
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	1 <tool id="cuffdiff_cummerbund" name="Cuffdiff for cummeRbund" version="0.0.7">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	2 <!-- Wrapper supports Cuffdiff versions 2.1.0-2.1.1 -->
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	3 <description>find significant changes in transcript expression, splicing, and promoter use</description>
da7241f92ecf Uploaded jjohnson parents: diff changeset	4 <requirements>
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	5 <requirement type="package" version="2.1.1">cufflinks</requirement>
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	6 </requirements>
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	7 <version_command>cuffdiff 2>&1 \| head -n 1</version_command>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	8 <command>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	9 cuffdiff
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	10 --no-update-check
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	11 --FDR=$fdr
da7241f92ecf Uploaded jjohnson parents: diff changeset	12 --num-threads="4"
da7241f92ecf Uploaded jjohnson parents: diff changeset	13 --min-alignment-count=$min_alignment_count
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	14 --library-norm-method=$library_norm_method
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	15 --dispersion-method=$dispersion_method
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	16
da7241f92ecf Uploaded jjohnson parents: diff changeset	17 ## Set advanced data parameters?
da7241f92ecf Uploaded jjohnson parents: diff changeset	18 #if $additional.sAdditional == "Yes":
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	19 #if $additional.frag_mean_len:
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	20 -m $additional.frag_mean_len
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	21 #end if
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	22 #if $additional.frag_len_std_dev:
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	23 -s $additional.frag_len_std_dev
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	24 #end if
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	25 #if $additional.max_bundle_frags:
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	26 --max-bundle-frags="$additional.max_bundle_frags"
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	27 #end if
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	28 #end if
da7241f92ecf Uploaded jjohnson parents: diff changeset	29
da7241f92ecf Uploaded jjohnson parents: diff changeset	30 ## Multi-read correct?
da7241f92ecf Uploaded jjohnson parents: diff changeset	31 #if str($multiread_correct) == "Yes":
da7241f92ecf Uploaded jjohnson parents: diff changeset	32 -u
da7241f92ecf Uploaded jjohnson parents: diff changeset	33 #end if
da7241f92ecf Uploaded jjohnson parents: diff changeset	34
da7241f92ecf Uploaded jjohnson parents: diff changeset	35 ## Bias correction?
da7241f92ecf Uploaded jjohnson parents: diff changeset	36 #if $bias_correction.do_bias_correction == "Yes":
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	37 -b
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	38 #if $bias_correction.seq_source.index_source == "history":
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	39 ## Custom genome from history.
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	40 $bias_correction.seq_source.ref_file
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	41 #else:
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	42 ## Built-in genome.
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	43 ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	44 #end if
da7241f92ecf Uploaded jjohnson parents: diff changeset	45 #end if
da7241f92ecf Uploaded jjohnson parents: diff changeset	46
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	47 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $conditions ] ) + '\''
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	48 --labels $labels
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	49
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	50 ## Inputs.
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	51 $gtf_input
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	52 #for $condition in $conditions:
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	53 #set samples = ','.join( [ str( $sample.sample ) for $sample in $condition.samples ] )
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	54 $samples
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	55 #end for
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	56
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	57 ## If build cummerbund db
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	58 #if $build_cummerbund_db:
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	59 && echo 'library(cummeRbund)' > cuffData.r
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	60 #if $bias_correction.do_bias_correction == "Yes":
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	61 #if $bias_correction.seq_source.index_source == "history":
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	62 ## Custom genome from history.
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	63 && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "$bias_correction.seq_source.ref_file", rebuild = T)' >> cuffData.r
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	64 #else:
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	65 ## Built-in genome.
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	66 ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	67 && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	68 #end if
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	69 #else
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	70 && echo 'cuff<-readCufflinks( dbFile = "cuffdata.db", rebuild = T)' >> cuffData.r
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	71 #end if
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	72 && Rscript --vanilla cuffData.r
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	73 && cp cuffdata.db $cummerbund_db
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	74 #end if
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	75 </command>
da7241f92ecf Uploaded jjohnson parents: diff changeset	76 <inputs>
da7241f92ecf Uploaded jjohnson parents: diff changeset	77 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	78
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	79 <repeat name="conditions" title="Condition" min="2">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	80 <param name="name" title="Condition name" type="text" label="Name"/>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	81 <repeat name="samples" title="Replicate" min="1">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	82 <param name="sample" label="Add replicate" type="data" format="sam,bam"/>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	83 </repeat>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	84 </repeat>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	85 <param name="time_series" type="boolean" checked="false" truevalue="--time-series" falsevalue="" optional="true" label="treat samples as a time-series">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	86 <help>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	87 Instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples.
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	88 Samples should be provided in increasing time order at the command line (e.g first time point SAM, second timepoint SAM, etc.)
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	89 </help>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	90 </param>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	91
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	92 <param name="library_norm_method" type="select" label="Library normalization method">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	93 <option value="geometric" selected="True">geometric</option>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	94 <option value="classic-fpkm">classic-fpkm</option>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	95 <option value="quartile">quartile</option>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	96 </param>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	97
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	98 <param name="dispersion_method" type="select" label="Dispersion estimation method" help="If using only one sample per condition, you must use 'blind.'">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	99 <option value="pooled" selected="True">pooled</option>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	100 <option value="per-condition">per-condition</option>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	101 <option value="blind">blind</option>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	102 </param>
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	103
da7241f92ecf Uploaded jjohnson parents: diff changeset	104 <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	105
da7241f92ecf Uploaded jjohnson parents: diff changeset	106 <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."/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	107
da7241f92ecf Uploaded jjohnson parents: diff changeset	108 <param name="multiread_correct" type="select" label="Use multi-read correct" help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.">
da7241f92ecf Uploaded jjohnson parents: diff changeset	109 <option value="No" selected="true">No</option>
da7241f92ecf Uploaded jjohnson parents: diff changeset	110 <option value="Yes">Yes</option>
da7241f92ecf Uploaded jjohnson parents: diff changeset	111 </param>
da7241f92ecf Uploaded jjohnson parents: diff changeset	112
da7241f92ecf Uploaded jjohnson parents: diff changeset	113 <conditional name="bias_correction">
da7241f92ecf Uploaded jjohnson parents: diff changeset	114 <param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates.">
da7241f92ecf Uploaded jjohnson parents: diff changeset	115 <option value="No">No</option>
da7241f92ecf Uploaded jjohnson parents: diff changeset	116 <option value="Yes">Yes</option>
da7241f92ecf Uploaded jjohnson parents: diff changeset	117 </param>
da7241f92ecf Uploaded jjohnson parents: diff changeset	118 <when value="Yes">
da7241f92ecf Uploaded jjohnson parents: diff changeset	119 <conditional name="seq_source">
da7241f92ecf Uploaded jjohnson parents: diff changeset	120 <param name="index_source" type="select" label="Reference sequence data">
da7241f92ecf Uploaded jjohnson parents: diff changeset	121 <option value="cached">Locally cached</option>
da7241f92ecf Uploaded jjohnson parents: diff changeset	122 <option value="history">History</option>
da7241f92ecf Uploaded jjohnson parents: diff changeset	123 </param>
da7241f92ecf Uploaded jjohnson parents: diff changeset	124 <when value="cached"></when>
da7241f92ecf Uploaded jjohnson parents: diff changeset	125 <when value="history">
da7241f92ecf Uploaded jjohnson parents: diff changeset	126 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
da7241f92ecf Uploaded jjohnson parents: diff changeset	127 </when>
da7241f92ecf Uploaded jjohnson parents: diff changeset	128 </conditional>
da7241f92ecf Uploaded jjohnson parents: diff changeset	129 </when>
da7241f92ecf Uploaded jjohnson parents: diff changeset	130 <when value="No"></when>
da7241f92ecf Uploaded jjohnson parents: diff changeset	131 </conditional>
da7241f92ecf Uploaded jjohnson parents: diff changeset	132
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	133 <param name="include_read_group_files" type="select" label="Include Read Group Datasets" help="Read group datasets provide information on replicates.">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	134 <option value="No" selected="true">No</option>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	135 <option value="Yes">Yes</option>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	136 </param>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	137 <param name="build_cummerbund_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Build cummeRbund database"/>
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	138 <conditional name="additional">
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	139 <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended for paired-end reads)">
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	140 <option value="No">No</option>
da7241f92ecf Uploaded jjohnson parents: diff changeset	141 <option value="Yes">Yes</option>
da7241f92ecf Uploaded jjohnson parents: diff changeset	142 </param>
da7241f92ecf Uploaded jjohnson parents: diff changeset	143 <when value="No"></when>
da7241f92ecf Uploaded jjohnson parents: diff changeset	144 <when value="Yes">
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	145 <param name="frag_mean_len" type="integer" value="" optional="true" label="Average Fragment Length Default: 200">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	146 <help>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	147 Note: Cufflinks now learns the fragment length mean for each SAM file,
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	148 so using this option is no longer recommended with paired-end reads.
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	149 </help>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	150 </param>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	151 <param name="frag_len_std_dev" type="integer" value="" optional="true" label="Fragment Length Standard Deviation Default: 80">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	152 <help>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	153 Note: Cufflinks now learns the fragment length mean for each SAM file,
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	154 so using this option is no longer recommended with paired-end reads.
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	155 </help>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	156 </param>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	157 <param name="max_bundle_frags" type="integer" value="" optional="true" label="--max-bundle-frags">
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	158 <help>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	159 Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 1000000
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	160 </help>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	161 <validator type="in_range" message="Value greater than 0" min="1"/>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	162 </param>
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	163 </when>
da7241f92ecf Uploaded jjohnson parents: diff changeset	164 </conditional>
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	165 </inputs>
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	166
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	167 <stdio>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	168 <regex match="Error" source="both" level="fatal" description="Error"/>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	169 <regex match=".*" source="both" level="log" description="tool progress"/>
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	170 </stdio>
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	171
da7241f92ecf Uploaded jjohnson parents: diff changeset	172 <outputs>
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	173 <!-- Optional read group datasets. -->
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	174 <data format="cuffdatadb" name="cummerbund_db" label="${tool.name} on ${on_string}: cummeRbund sqlite Database" >
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	175 <filter>build_cummerbund_db</filter>
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	176 </data>
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	177 <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" >
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	178 <filter>(params['include_read_group_files'] == 'Yes'</filter>
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	179 </data>
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	180 <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" >
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	181 <filter>(params['include_read_group_files'] == 'Yes'</filter>
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	182 </data>
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	183 <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" >
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	184 <filter>(params['include_read_group_files'] == 'Yes'</filter>
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	185 </data>
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	186 <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	187 <filter>(params['include_read_group_files'] == 'Yes'</filter>
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	188 </data>
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	189
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	190 <!-- Standard datasets. -->
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	191 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff" />
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	192 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff" />
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	193 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff" />
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	194 <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff" />
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	195 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking" />
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	196 <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff" />
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	197 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking" />
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	198 <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff" />
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	199 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking" />
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	200 <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff" />
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	201 <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking" />
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	202 </outputs>
da7241f92ecf Uploaded jjohnson parents: diff changeset	203
da7241f92ecf Uploaded jjohnson parents: diff changeset	204 <tests>
da7241f92ecf Uploaded jjohnson parents: diff changeset	205 <test>
da7241f92ecf Uploaded jjohnson parents: diff changeset	206 <!--
da7241f92ecf Uploaded jjohnson parents: diff changeset	207 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
da7241f92ecf Uploaded jjohnson parents: diff changeset	208 -->
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	209 <!--
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	210 NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat
fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	211 element are not supported.
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	212 <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" />
da7241f92ecf Uploaded jjohnson parents: diff changeset	213 <param name="do_groups" value="No" />
da7241f92ecf Uploaded jjohnson parents: diff changeset	214 <param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" />
da7241f92ecf Uploaded jjohnson parents: diff changeset	215 <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" />
da7241f92ecf Uploaded jjohnson parents: diff changeset	216 <param name="fdr" value="0.05" />
da7241f92ecf Uploaded jjohnson parents: diff changeset	217 <param name="min_alignment_count" value="0" />
da7241f92ecf Uploaded jjohnson parents: diff changeset	218 <param name="do_bias_correction" value="No" />
da7241f92ecf Uploaded jjohnson parents: diff changeset	219 <param name="do_normalization" value="No" />
da7241f92ecf Uploaded jjohnson parents: diff changeset	220 <param name="multiread_correct" value="No"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	221 <param name="sAdditional" value="No"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	222 <output name="splicing_diff" file="cuffdiff_out9.txt"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	223 <output name="promoters_diff" file="cuffdiff_out10.txt"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	224 <output name="cds_diff" file="cuffdiff_out11.txt"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	225 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	226 <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	227 <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	228 <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	229 <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	230 <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	231 <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/>
da7241f92ecf Uploaded jjohnson parents: diff changeset	232 <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/>
2 fdf01b3c1841 Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output Jim Johnson <jj@umn.edu> parents: 0 diff changeset	233 -->
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	234 </test>
da7241f92ecf Uploaded jjohnson parents: diff changeset	235 </tests>
da7241f92ecf Uploaded jjohnson parents: diff changeset	236
da7241f92ecf Uploaded jjohnson parents: diff changeset	237 <help>
da7241f92ecf Uploaded jjohnson parents: diff changeset	238 Cuffdiff Overview
da7241f92ecf Uploaded jjohnson parents: diff changeset	239
da7241f92ecf Uploaded jjohnson parents: diff changeset	240 Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
da7241f92ecf Uploaded jjohnson parents: diff changeset	241
da7241f92ecf Uploaded jjohnson parents: diff changeset	242 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/
da7241f92ecf Uploaded jjohnson parents: diff changeset	243
da7241f92ecf Uploaded jjohnson parents: diff changeset	244 ------
da7241f92ecf Uploaded jjohnson parents: diff changeset	245
da7241f92ecf Uploaded jjohnson parents: diff changeset	246 Know what you are doing
da7241f92ecf Uploaded jjohnson parents: diff changeset	247
da7241f92ecf Uploaded jjohnson parents: diff changeset	248 .. class:: warningmark
da7241f92ecf Uploaded jjohnson parents: diff changeset	249
da7241f92ecf Uploaded jjohnson parents: diff changeset	250 There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to understand the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
da7241f92ecf Uploaded jjohnson parents: diff changeset	251
da7241f92ecf Uploaded jjohnson parents: diff changeset	252 .. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
da7241f92ecf Uploaded jjohnson parents: diff changeset	253
da7241f92ecf Uploaded jjohnson parents: diff changeset	254 ------
da7241f92ecf Uploaded jjohnson parents: diff changeset	255
da7241f92ecf Uploaded jjohnson parents: diff changeset	256 Input format
da7241f92ecf Uploaded jjohnson parents: diff changeset	257
da7241f92ecf Uploaded jjohnson parents: diff changeset	258 Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples.
da7241f92ecf Uploaded jjohnson parents: diff changeset	259
da7241f92ecf Uploaded jjohnson parents: diff changeset	260 ------
da7241f92ecf Uploaded jjohnson parents: diff changeset	261
da7241f92ecf Uploaded jjohnson parents: diff changeset	262 Outputs
da7241f92ecf Uploaded jjohnson parents: diff changeset	263
da7241f92ecf Uploaded jjohnson parents: diff changeset	264 Cuffdiff produces many output files:
da7241f92ecf Uploaded jjohnson parents: diff changeset	265
da7241f92ecf Uploaded jjohnson parents: diff changeset	266 1. Transcript FPKM expression tracking.
da7241f92ecf Uploaded jjohnson parents: diff changeset	267 2. Gene FPKM expression tracking; tracks the summed FPKM of transcripts sharing each gene_id
da7241f92ecf Uploaded jjohnson parents: diff changeset	268 3. Primary transcript FPKM tracking; tracks the summed FPKM of transcripts sharing each tss_id
da7241f92ecf Uploaded jjohnson parents: diff changeset	269 4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, independent of tss_id
da7241f92ecf Uploaded jjohnson parents: diff changeset	270 5. Transcript differential FPKM.
da7241f92ecf Uploaded jjohnson parents: diff changeset	271 6. Gene differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each gene_id
da7241f92ecf Uploaded jjohnson parents: diff changeset	272 7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id
da7241f92ecf Uploaded jjohnson parents: diff changeset	273 8. Coding sequence differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each p_id independent of tss_id
da7241f92ecf Uploaded jjohnson parents: diff changeset	274 9. Differential splicing tests: this tab delimited file lists, for each primary transcript, the amount of overloading detected among its isoforms, i.e. how much differential splicing exists between isoforms processed from a single primary transcript. Only primary transcripts from which two or more isoforms are spliced are listed in this file.
da7241f92ecf Uploaded jjohnson parents: diff changeset	275 10. Differential promoter tests: this tab delimited file lists, for each gene, the amount of overloading detected among its primary transcripts, i.e. how much differential promoter use exists between samples. Only genes producing two or more distinct primary transcripts (i.e. multi-promoter genes) are listed here.
da7241f92ecf Uploaded jjohnson parents: diff changeset	276 11. Differential CDS tests: this tab delimited file lists, for each gene, the amount of overloading detected among its coding sequences, i.e. how much differential CDS output exists between samples. Only genes producing two or more distinct CDS (i.e. multi-protein genes) are listed here.
da7241f92ecf Uploaded jjohnson parents: diff changeset	277
da7241f92ecf Uploaded jjohnson parents: diff changeset	278 -------
da7241f92ecf Uploaded jjohnson parents: diff changeset	279
da7241f92ecf Uploaded jjohnson parents: diff changeset	280 Settings
da7241f92ecf Uploaded jjohnson parents: diff changeset	281
da7241f92ecf Uploaded jjohnson parents: diff changeset	282 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here.
da7241f92ecf Uploaded jjohnson parents: diff changeset	283
da7241f92ecf Uploaded jjohnson parents: diff changeset	284 ------
da7241f92ecf Uploaded jjohnson parents: diff changeset	285
da7241f92ecf Uploaded jjohnson parents: diff changeset	286 Cuffdiff parameter list
da7241f92ecf Uploaded jjohnson parents: diff changeset	287
da7241f92ecf Uploaded jjohnson parents: diff changeset	288 This is a list of implemented Cuffdiff options::
da7241f92ecf Uploaded jjohnson parents: diff changeset	289
da7241f92ecf Uploaded jjohnson parents: diff changeset	290 -m INT Average fragement length; default 200
da7241f92ecf Uploaded jjohnson parents: diff changeset	291 -s INT Fragment legnth standard deviation; default 80
da7241f92ecf Uploaded jjohnson parents: diff changeset	292 -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).
da7241f92ecf Uploaded jjohnson parents: diff changeset	293 --FDR FLOAT The allowed false discovery rate. The default is 0.05.
da7241f92ecf Uploaded jjohnson parents: diff changeset	294 --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000
da7241f92ecf Uploaded jjohnson parents: diff changeset	295 --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000
da7241f92ecf Uploaded jjohnson parents: diff changeset	296 -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts.
da7241f92ecf Uploaded jjohnson parents: diff changeset	297
da7241f92ecf Uploaded jjohnson parents: diff changeset	298 </help>
da7241f92ecf Uploaded jjohnson parents: diff changeset	299 </tool>

Mercurial > repos > jjohnson > cummerbund

annotate cuffdiff_wrapper.xml @ 2:fdf01b3c1841