Mercurial > repos > devteam > cuffdiff

comparison cuffdiff_wrapper.xml @ 8:88fcac97c2a0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded updated cuffdiff.
author devteam
date Tue, 23 Dec 2014 15:55:31 -0500
parents 8da0eade1f59
children 4e6f043995ff
comparison
equal deleted inserted replaced
7:8da0eade1f59 8:88fcac97c2a0
1 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.0"> 1 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.1">
2 <description>find significant changes in transcript expression, splicing, and promoter use</description> 2 <description>find significant changes in transcript expression, splicing, and promoter use</description>
3 <expand macro="requirements" /> 3 <requirements>
4 <requirement type="set_environment">CUFFDIFF_SCRIPT_PATH</requirement>
5 <requirement type="package" version="2.2.1">cufflinks</requirement>
6 <requirement type="package" version="2.8.2">cummeRbund</requirement>
7 </requirements>
4 <expand macro="stdio" /> 8 <expand macro="stdio" />
5 <macros> 9 <macros>
6 <import>cuff_macros.xml</import> 10 <import>cuff_macros.xml</import>
7 </macros> 11 </macros>
8 <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command> 12 <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
9 <command> 13 <command><![CDATA[
10 cuffdiff 14 cuffdiff
11 --no-update-check 15 --no-update-check
12 --FDR=$fdr 16 --FDR=$fdr
13 --num-threads="\${GALAXY_SLOTS:-4}" 17 --num-threads="\${GALAXY_SLOTS:-4}"
14 --min-alignment-count=$min_alignment_count 18 --min-alignment-count=$min_alignment_count
62 #end if 66 #end if
63 ## Inputs. 67 ## Inputs.
64 $gtf_input 68 $gtf_input
65 69
66 @CONDITION_SAMPLES@ 70 @CONDITION_SAMPLES@
71 &&
72 R --vanilla --no-save -f \$CUFFDIFF_SCRIPT_PATH/cummeRbund.R && mv cummeRbund.sqlite "${output_cummerbund}"
73 ]]>
67 </command> 74 </command>
68 <inputs> 75 <inputs>
69 <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."/> 76 <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."/>
70 <expand macro="condition_inputs" /> 77 <expand macro="condition_inputs" />
71 <param name="library_norm_method" type="select" label="Library normalization method"> 78 <param name="library_norm_method" type="select" label="Library normalization method">
177 <param name="min_reps_for_js_test" type="integer" value="3" label="Minimal Replicates for isoform shift testing" help="Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates. Default: 3." /> 184 <param name="min_reps_for_js_test" type="integer" value="3" label="Minimal Replicates for isoform shift testing" help="Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates. Default: 3." />
178 </when> 185 </when>
179 </conditional> 186 </conditional>
180 </inputs> 187 </inputs>
181 <outputs> 188 <outputs>
182 <!-- Optional read group datasets. --> 189 <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database" />
183 <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" >
184 <filter>(include_read_group_files == 'Yes')</filter>
185 </data>
186 <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" >
187 <filter>(include_read_group_files == 'Yes')</filter>
188 </data>
189 <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" >
190 <filter>(include_read_group_files == 'Yes')</filter>
191 </data>
192 <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
193 <filter>(include_read_group_files == 'Yes')</filter>
194 </data>
195 <data format="text" name="read_group_info" label="${tool.name} on ${on_string}: read group info" from_work_dir="read_groups.info" >
196 <filter>(include_read_group_files == 'Yes')</filter>
197 </data>
198 <data format="text" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" >
199 <filter>(include_read_group_files == 'Yes')</filter>
200 </data>
201 <!-- Standard datasets. -->
202 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff" />
203 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff" />
204 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff" />
205 <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff" />
206 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking" />
207 <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" >
208 <filter>(include_count_files == 'Yes')</filter>
209 </data>
210
211 <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff" />
212 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking" />
213 <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" >
214 <filter>(include_count_files == 'Yes')</filter>
215 </data>
216
217 <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff" />
218 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking" />
219 <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene count tracking" from_work_dir="genes.count_tracking" >
220 <filter>(include_count_files == 'Yes')</filter>
221 </data>
222
223 <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff" />
224 <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking" />
225 <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking" >
226 <filter>(include_count_files == 'Yes')</filter>
227 </data>
228 </outputs> 190 </outputs>
229 191
230 <tests> 192 <tests>
231 <test> 193 <test>
232 <!-- 194 <!--
252 <param name="min_alignment_count" value="0" /> 214 <param name="min_alignment_count" value="0" />
253 <param name="do_bias_correction" value="No" /> 215 <param name="do_bias_correction" value="No" />
254 <param name="do_normalization" value="No" /> 216 <param name="do_normalization" value="No" />
255 <param name="multiread_correct" value="No"/> 217 <param name="multiread_correct" value="No"/>
256 <param name="sAdditional" value="No"/> 218 <param name="sAdditional" value="No"/>
257 <output name="splicing_diff" file="cuffdiff_out9.txt"/> 219 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite"/>
258 <output name="promoters_diff" file="cuffdiff_out10.txt"/>
259 <output name="cds_diff" file="cuffdiff_out11.txt"/>
260 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
261 <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>
262 <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/>
263 <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
264 <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
265 <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>
266 <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/>
267 <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/>
268 </test> 220 </test>
269 </tests> 221 </tests>
270 <help> 222 <help>
271 **Cuffdiff Overview** 223 **Cuffdiff Overview**
272 224