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comparison cuffdiff_wrapper.xml @ 15:2d7eee38ab5b

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Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
author Jim Johnson <jj@umn.edu>
date Fri, 08 Nov 2013 13:28:44 -0600
parents d10befb0867a
children
comparison
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14:d10befb0867a 15:2d7eee38ab5b
1 <tool id="cuffdiff_cummerbund" name="Cuffdiff" version="0.0.6"> 1 <tool id="cuffdiff_cummerbund" name="Cuffdiff for cummeRbund" version="0.0.7">
2 <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 --> 2 <!-- Wrapper supports Cuffdiff versions 2.1.0-2.1.1 -->
3 <description>find significant changes in transcript expression, splicing, and promoter use</description> 3 <description>find significant changes in transcript expression, splicing, and promoter use</description>
4 <requirements> 4 <requirements>
5 <requirement type="package">cufflinks</requirement> 5 <requirement type="package" version="2.1.1">cufflinks</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="python"> 7 <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
8 #set sel_outputs = $output_sel.__str__.split(',') 8 <command>
9 cuffdiff_wrapper.py 9 cuffdiff
10 --no-update-check
10 --FDR=$fdr 11 --FDR=$fdr
11 --num-threads="4" 12 --num-threads="4"
12 --min-alignment-count=$min_alignment_count 13 --min-alignment-count=$min_alignment_count
13 --library-norm-method=$library_norm_method 14 --library-norm-method=$library_norm_method
14 --dispersion-method=$dispersion_method 15 --dispersion-method=$dispersion_method
15 16
16 #if 'cuffdata' in $sel_outputs or not $output_sel:
17 --cuffdatadir=$cuffdata.extra_files_path
18 #end if
19 #if 'cummeRbund_db' in $sel_outputs:
20 --cummeRbund_db=$cummeRbund_db
21 #end if
22
23 #if 'isoforms_fpkm_tracking' in $sel_outputs:
24 --isoforms_fpkm_tracking_output=$isoforms_fpkm_tracking
25 #end if
26 #if 'genes_fpkm_tracking' in $sel_outputs:
27 --genes_fpkm_tracking_output=$genes_fpkm_tracking
28 #end if
29 #if 'cds_fpkm_tracking' in $sel_outputs:
30 --cds_fpkm_tracking_output=$cds_fpkm_tracking
31 #end if
32 #if 'tss_groups_fpkm_tracking' in $sel_outputs:
33 --tss_groups_fpkm_tracking_output=$tss_groups_fpkm_tracking
34 #end if
35 #if 'isoforms_exp_diff' in $sel_outputs:
36 --isoforms_exp_output=$isoforms_exp_diff
37 #end if
38 #if 'genes_exp_diff' in $sel_outputs:
39 --genes_exp_output=$genes_exp_diff
40 #end if
41 #if 'tss_groups_exp_diff' in $sel_outputs:
42 --tss_groups_exp_output=$tss_groups_exp_diff
43 #end if
44 #if 'cds_exp_fpkm_tracking' in $sel_outputs:
45 --cds_exp_fpkm_tracking_output=$cds_exp_fpkm_tracking
46 #end if
47 #if 'splicing_diff' in $sel_outputs:
48 --splicing_diff_output=$splicing_diff
49 #end if
50 #if 'cds_diff' in $sel_outputs:
51 --cds_diff_output=$cds_diff
52 #end if
53 #if 'promoters_diff' in $sel_outputs:
54 --promoters_diff_output=$promoters_diff
55 #end if
56 #if 'cds_read_group_tracking' in $sel_outputs:
57 --cds_read_group_tracking=$cds_read_group_tracking
58 #end if
59 #if 'tss_groups_read_group_tracking' in $sel_outputs:
60 --tss_groups_read_group_tracking=$tss_groups_read_group_tracking
61 #end if
62 #if 'genes_read_group_tracking' in $sel_outputs:
63 --genes_read_group_tracking=$genes_read_group_tracking
64 #end if
65 #if 'isoforms_read_group_tracking' in $sel_outputs:
66 --isoforms_read_group_tracking=$isoforms_read_group_tracking
67 #end if
68
69 ## Set advanced data parameters? 17 ## Set advanced data parameters?
70 #if $additional.sAdditional == "Yes": 18 #if $additional.sAdditional == "Yes":
71 -m $additional.frag_mean_len 19 #if $additional.frag_mean_len:
72 -s $additional.frag_len_std_dev 20 -m $additional.frag_mean_len
73 #end if 21 #end if
74 22 #if $additional.frag_len_std_dev:
75 ## Normalization? 23 -s $additional.frag_len_std_dev
76 #if str($do_normalization) == "Yes": 24 #end if
77 -N 25 #if $additional.max_bundle_frags:
26 --max-bundle-frags="$additional.max_bundle_frags"
27 #end if
78 #end if 28 #end if
79 29
80 ## Multi-read correct? 30 ## Multi-read correct?
81 #if str($multiread_correct) == "Yes": 31 #if str($multiread_correct) == "Yes":
82 -u 32 -u
83 #end if 33 #end if
84 34
85 ## Bias correction? 35 ## Bias correction?
86 #if $bias_correction.do_bias_correction == "Yes": 36 #if $bias_correction.do_bias_correction == "Yes":
87 -b 37 -b
88 #if $bias_correction.seq_source.index_source == "history": 38 #if $bias_correction.seq_source.index_source == "history":
89 --ref_file=$bias_correction.seq_source.ref_file 39 ## Custom genome from history.
40 $bias_correction.seq_source.ref_file
90 #else: 41 #else:
91 --ref_file="None" 42 ## Built-in genome.
92 #end if 43 ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
93 --dbkey=${gtf_input.metadata.dbkey} 44 #end if
94 --index_dir=${GALAXY_DATA_INDEX_DIR} 45 #end if
95 #end if 46
96 47 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $conditions ] ) + '\''
48 --labels $labels
49
97 ## Inputs. 50 ## Inputs.
98 --inputA=$gtf_input 51 $gtf_input
99 #if $group_analysis.do_groups == "No": 52 #for $condition in $conditions:
100 --input1=$aligned_reads1 53 #set samples = ','.join( [ str( $sample.sample ) for $sample in $condition.samples ] )
101 --input2=$aligned_reads2 54 $samples
102 #else: 55 #end for
103 ## Replicates. 56
104 --labels 57 ## If build cummerbund db
105 #for $group in $group_analysis.groups 58 #if $build_cummerbund_db:
106 ${group.group} 59 &amp;&amp; echo 'library(cummeRbund)' > cuffData.r
107 #end for 60 #if $bias_correction.do_bias_correction == "Yes":
108 --files 61 #if $bias_correction.seq_source.index_source == "history":
109 #for $group in $group_analysis.groups 62 ## Custom genome from history.
110 #for $file in $group.files: 63 &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "$bias_correction.seq_source.ref_file", rebuild = T)' >> cuffData.r
111 ${file.file} 64 #else:
112 #end for 65 ## Built-in genome.
113 , 66 ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
114 #end for 67 &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r
115 #end if 68 #end if
116 69 #else
70 &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", rebuild = T)' >> cuffData.r
71 #end if
72 &amp;&amp; Rscript --vanilla cuffData.r
73 &amp;&amp; cp cuffdata.db $cummerbund_db
74 #end if
117 </command> 75 </command>
118 <inputs> 76 <inputs>
119 <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."/> 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."/>
120 <conditional name="group_analysis"> 78
121 <param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group."> 79 <repeat name="conditions" title="Condition" min="2">
122 <option value="No">No</option> 80 <param name="name" title="Condition name" type="text" label="Name"/>
123 <option value="Yes">Yes</option> 81 <repeat name="samples" title="Replicate" min="1">
124 </param> 82 <param name="sample" label="Add replicate" type="data" format="sam,bam"/>
125 <when value="Yes"> 83 </repeat>
126 <repeat name="groups" title="Group"> 84 </repeat>
127 <param name="group" title="Group name" type="text" label="Group name (no spaces or commas)"/> 85 <param name="time_series" type="boolean" checked="false" truevalue="--time-series" falsevalue="" optional="true" label="treat samples as a time-series">
128 <repeat name="files" title="Replicate"> 86 <help>
129 <param name="file" label="Add file" type="data" format="sam,bam"/> 87 Instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples.
130 </repeat> 88 Samples should be provided in increasing time order at the command line (e.g first time point SAM, second timepoint SAM, etc.)
131 </repeat> 89 </help>
132 </when> 90 </param>
133 <when value="No">
134 <param format="sam,bam" name="aligned_reads1" 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=""/>
136 </when>
137 </conditional>
138 91
139 <param name="library_norm_method" type="select" label="Library normalization method"> 92 <param name="library_norm_method" type="select" label="Library normalization method">
140 <option value="geometric" selected="True">geometric</option> 93 <option value="geometric" selected="True">geometric</option>
141 <option value="classic-fpkm">classic-fpkm</option> 94 <option value="classic-fpkm">classic-fpkm</option>
142 <option value="quartile">quartile</option> 95 <option value="quartile">quartile</option>
149 </param> 102 </param>
150 103
151 <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/> 104 <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
152 105
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."/> 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."/>
154
155 <param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts.">
156 <option value="No">No</option>
157 <option value="Yes">Yes</option>
158 </param>
159 107
160 <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."> 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.">
161 <option value="No" selected="true">No</option> 109 <option value="No" selected="true">No</option>
162 <option value="Yes">Yes</option> 110 <option value="Yes">Yes</option>
163 </param> 111 </param>
180 </conditional> 128 </conditional>
181 </when> 129 </when>
182 <when value="No"></when> 130 <when value="No"></when>
183 </conditional> 131 </conditional>
184 132
133 <param name="include_read_group_files" type="select" label="Include Read Group Datasets" help="Read group datasets provide information on replicates.">
134 <option value="No" selected="true">No</option>
135 <option value="Yes">Yes</option>
136 </param>
137 <param name="build_cummerbund_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Build cummeRbund database"/>
185 <conditional name="additional"> 138 <conditional name="additional">
186 <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended)"> 139 <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended for paired-end reads)">
187 <option value="No">No</option> 140 <option value="No">No</option>
188 <option value="Yes">Yes</option> 141 <option value="Yes">Yes</option>
189 </param> 142 </param>
190 <when value="No"></when> 143 <when value="No"></when>
191 <when value="Yes"> 144 <when value="Yes">
192 <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/> 145 <param name="frag_mean_len" type="integer" value="" optional="true" label="Average Fragment Length Default: 200">
193 <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/> 146 <help>
147 Note: Cufflinks now learns the fragment length mean for each SAM file,
148 so using this option is no longer recommended with paired-end reads.
149 </help>
150 </param>
151 <param name="frag_len_std_dev" type="integer" value="" optional="true" label="Fragment Length Standard Deviation Default: 80">
152 <help>
153 Note: Cufflinks now learns the fragment length mean for each SAM file,
154 so using this option is no longer recommended with paired-end reads.
155 </help>
156 </param>
157 <param name="max_bundle_frags" type="integer" value="" optional="true" label="--max-bundle-frags">
158 <help>
159 Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 1000000
160 </help>
161 <validator type="in_range" message="Value greater than 0" min="1"/>
162 </param>
194 </when> 163 </when>
195 </conditional> 164 </conditional>
196
197 <param name="output_sel" type="select" multiple="true" display="checkboxes" force_select="true" label="Select outputs for history datasets">
198 <option value="cuffdata">cuffdata - html page with links to cuffdiff outputs</option>
199 <option value="cummeRbund_db">cummeRbund database</option>
200 <option value="run_info">run.info</option>
201 <option value="read_groups_info">read_groups.info</option>
202 <option value="splicing_diff">splicing.diff</option>
203 <option value="promoters_diff">promoters.diff</option>
204 <option value="genes_exp_diff">genes_exp.diff</option>
205 <option value="genes_fpkm_tracking">genes.fpkm_tracking</option>
206 <option value="genes_count_tracking">genes.count_tracking</option>
207 <option value="genes_read_group_tracking">genes.read_group_tracking</option>
208 <option value="isoforms_exp_diff">isoforms.exp_diff</option>
209 <option value="isoforms_fpkm_tracking">isoforms.fpkm_tracking</option>
210 <option value="isoforms_count_tracking">isoforms.count_tracking</option>
211 <option value="isoforms_read_group_tracking">isoforms.read_group_tracking</option>
212 <option value="cds_diff">cds.diff</option>
213 <option value="cds_exp_diff">cds_exp.diff</option>
214 <option value="cds_fpkm_tracking">cds.fpkm_tracking</option>
215 <option value="cds_count_tracking">cds.count_tracking</option>
216 <option value="cds_read_group_tracking">cds.read_group_tracking</option>
217 <option value="tss_groups_exp_diff">tss_groups_exp.diff</option>
218 <option value="tss_groups_fpkm_tracking">tss_groups.fpkm_tracking</option>
219 <option value="tss_groups_count_tracking">tss_groups.count_tracking</option>
220 <option value="tss_groups_read_group_tracking">tss_groups.read_group_tracking</option>
221 </param>
222
223 </inputs> 165 </inputs>
224 166
167 <stdio>
168 <regex match="Error" source="both" level="fatal" description="Error"/>
169 <regex match=".*" source="both" level="log" description="tool progress"/>
170 </stdio>
171
225 <outputs> 172 <outputs>
226 <data format="text" name="run_info" label="${tool.name} on ${on_string}: run.info"> 173 <!-- Optional read group datasets. -->
227 <filter>output_sel and 'run_info' in output_sel</filter> 174 <data format="cuffdatadb" name="cummerbund_db" label="${tool.name} on ${on_string}: cummeRbund sqlite Database" >
228 </data> 175 <filter>build_cummerbund_db</filter>
229 <data format="tabular" name="read_groups_info" label="${tool.name} on ${on_string}: read_groups.info"> 176 </data>
230 <filter>output_sel and 'read_groups_info' in output_sel</filter> 177 <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" >
231 </data> 178 <filter>(params['include_read_group_files'] == 'Yes'</filter>
232 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing"> 179 </data>
233 <filter>output_sel and 'splicing_diff' in output_sel</filter> 180 <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" >
234 </data> 181 <filter>(params['include_read_group_files'] == 'Yes'</filter>
235 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing"> 182 </data>
236 <filter>output_sel and 'promoters_diff' in output_sel</filter> 183 <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" >
237 </data> 184 <filter>(params['include_read_group_files'] == 'Yes'</filter>
238 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing"> 185 </data>
239 <filter>output_sel and 'cds_diff' in output_sel</filter> 186 <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
240 </data> 187 <filter>(params['include_read_group_files'] == 'Yes'</filter>
241 <data format="tabular" name="cds_exp_diff" label="${tool.name} on ${on_string}: CDS differential expression testing"> 188 </data>
242 <filter>output_sel and 'cds_exp_diff' in output_sel</filter> 189
243 </data> 190 <!-- Standard datasets. -->
244 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking"> 191 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff" />
245 <filter>output_sel and 'cds_fpkm_tracking' in output_sel</filter> 192 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff" />
246 </data> 193 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff" />
247 <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS counts"> 194 <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff" />
248 <filter>output_sel and 'cds_count_tracking' in output_sel</filter> 195 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking" />
249 </data> 196 <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff" />
250 <data format="tabular" name="cds_read_group_tracking" label="${tool.name} on ${on_string}: CDS Read Group tracking"> 197 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking" />
251 <filter>output_sel and 'cds_read_group_tracking' in output_sel</filter> 198 <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff" />
252 </data> 199 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking" />
253 <data format="tabular" name="tss_groups_exp_diff" label="${tool.name} on ${on_string}: TSS groups differential expression testing"> 200 <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff" />
254 <filter>output_sel and 'tss_groups_exp_diff' in output_sel</filter> 201 <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking" />
255 </data>
256 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
257 <filter>output_sel and 'tss_groups_fpkm_tracking' in output_sel</filter>
258 </data>
259 <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS groups counts">
260 <filter>output_sel and 'tss_groups_count_tracking' in output_sel</filter>
261 </data>
262 <data format="tabular" name="tss_groups_read_group_tracking" label="${tool.name} on ${on_string}: TSS groups Read Group tracking">
263 <filter>output_sel and 'tss_groups_read_group_tracking' in output_sel</filter>
264 </data>
265 <data format="tabular" name="isoforms_exp_diff" label="${tool.name} on ${on_string}: transcript differential expression testing">
266 <filter>output_sel and 'isoforms_exp_diff' in output_sel</filter>
267 </data>
268 <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking">
269 <filter>output_sel and 'isoforms_fpkm_tracking' in output_sel</filter>
270 </data>
271 <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript counts">
272 <filter>output_sel and 'isoforms_count_tracking' in output_sel</filter>
273 </data>
274 <data format="tabular" name="isoforms_read_group_tracking" label="${tool.name} on ${on_string}: transcript Read Group tracking">
275 <filter>output_sel and 'isoforms_read_group_tracking' in output_sel</filter>
276 </data>
277 <data format="tabular" name="genes_exp_diff" label="${tool.name} on ${on_string}: gene differential expression testing">
278 <filter>output_sel and 'genes_exp_diff' in output_sel</filter>
279 </data>
280 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking">
281 <filter>output_sel and 'genes_fpkm_tracking' in output_sel</filter>
282 </data>
283 <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene counts">
284 <filter>output_sel and 'genes_count_tracking' in output_sel</filter>
285 </data>
286 <data format="tabular" name="genes_read_group_tracking" label="${tool.name} on ${on_string}: gene Read Group tracking">
287 <filter>output_sel and 'genes_read_group_tracking' in output_sel</filter>
288 </data>
289 <data format="cuffdata" name="cuffdata" label="${tool.name} on ${on_string}: cuffdata" >
290 <filter>not output_sel or output_sel and 'cuffdata' in output_sel</filter>
291 </data>
292 <data format="cuffdatadb" name="cummeRbund_db" label="${tool.name} on ${on_string}: cummeRbund sqlite Database" >
293 <filter>output_sel and 'cummeRbund_db' in output_sel</filter>
294 </data>
295 </outputs> 202 </outputs>
296 <stdio>
297 <exit_code range="1:" level="fatal" description="Cufflinks Err" />
298 </stdio>
299
300 203
301 <tests> 204 <tests>
302 <test> 205 <test>
303 <!-- 206 <!--
304 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 207 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
305 --> 208 -->
209 <!--
210 NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat
211 element are not supported.
306 <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" /> 212 <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" />
307 <param name="do_groups" value="No" /> 213 <param name="do_groups" value="No" />
308 <param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" /> 214 <param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" />
309 <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" /> 215 <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" />
310 <!-- Defaults. -->
311 <param name="fdr" value="0.05" /> 216 <param name="fdr" value="0.05" />
312 <param name="min_alignment_count" value="0" /> 217 <param name="min_alignment_count" value="0" />
313 <param name="do_bias_correction" value="No" /> 218 <param name="do_bias_correction" value="No" />
314 <param name="do_normalization" value="No" /> 219 <param name="do_normalization" value="No" />
315 <param name="multiread_correct" value="No"/> 220 <param name="multiread_correct" value="No"/>
316 <param name="sAdditional" value="No"/> 221 <param name="sAdditional" value="No"/>
317 <!--
318 Line diffs are needed because cuffdiff does not produce deterministic output.
319 TODO: can we find datasets that lead to deterministic behavior?
320 -->
321 <output name="splicing_diff" file="cuffdiff_out9.txt"/> 222 <output name="splicing_diff" file="cuffdiff_out9.txt"/>
322 <output name="promoters_diff" file="cuffdiff_out10.txt"/> 223 <output name="promoters_diff" file="cuffdiff_out10.txt"/>
323 <output name="cds_diff" file="cuffdiff_out11.txt"/> 224 <output name="cds_diff" file="cuffdiff_out11.txt"/>
324 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> 225 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
325 <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/> 226 <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>
327 <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/> 228 <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
328 <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/> 229 <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
329 <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/> 230 <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>
330 <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/> 231 <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/>
331 <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/> 232 <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/>
233 -->
332 </test> 234 </test>
333 </tests> 235 </tests>
334 236
335 <help> 237 <help>
336 **Cuffdiff Overview** 238 **Cuffdiff Overview**