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comparison cuffdiff_wrapper.xml @ 16:af3e173cad7f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
author iuc
date Fri, 03 Jul 2020 11:43:55 -0400
parents 43b36b3d4333
children 43221aef70e2
comparison
equal deleted inserted replaced
15:43b36b3d4333 16:af3e173cad7f
1 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.5"> 1 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.6">
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 <macros> 3 <macros>
4 <import>cuff_macros.xml</import> 4 <import>cuff_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
66 '$gtf_input' 66 '$gtf_input'
67 67
68 @CONDITION_SAMPLES@ 68 @CONDITION_SAMPLES@
69 #if $generate_sqlite: 69 #if $generate_sqlite:
70 && 70 &&
71 Rscript '$__tool_directory__/cummeRbund.R' && mv cummeRbund.sqlite '${output_cummerbund}' 71 Rscript '$__tool_directory__/cummeRbund.R'
72 #end if 72 #end if
73 ]]> 73 ]]>
74 </command> 74 </command>
75 <inputs> 75 <inputs>
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."/> 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."/>
102 <option value="No">No</option> 102 <option value="No">No</option>
103 <option value="Yes">Yes</option> 103 <option value="Yes">Yes</option>
104 </param> 104 </param>
105 <when value="Yes"> 105 <when value="Yes">
106 <conditional name="seq_source"> 106 <conditional name="seq_source">
107 <param name="index_source" type="select" label="Reference sequence data"> 107 <param name="index_source" type="select" label="Reference sequence data">
108 <option value="cached">Locally cached</option> 108 <option value="cached">Locally cached</option>
109 <option value="history">History</option> 109 <option value="history">History</option>
110 </param>
111 <when value="cached">
112 <param name="index" type="select" label="Using reference genome">
113 <options from_data_table="fasta_indexes">
114 <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />
115 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
116 </options>
117 </param> 110 </param>
118 </when> 111 <when value="cached">
119 <when value="history"> 112 <param name="index" type="select" label="Using reference genome">
120 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> 113 <options from_data_table="fasta_indexes">
121 </when> 114 <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />
115 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
116 </options>
117 </param>
118 </when>
119 <when value="history">
120 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
121 </when>
122 </conditional> 122 </conditional>
123 </when> 123 </when>
124 <when value="No"></when> 124 <when value="No"></when>
125 </conditional> 125 </conditional>
126 126
207 <data format="txt" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" > 207 <data format="txt" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" >
208 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter> 208 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
209 </data> 209 </data>
210 <!-- Standard datasets. --> 210 <!-- Standard datasets. -->
211 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff"> 211 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff">
212 <filter>not omit_tabular_output</filter> 212 <filter>not omit_tabular_output</filter>
213 </data> 213 </data>
214 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff"> 214 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff">
215 <filter>not omit_tabular_output</filter> 215 <filter>not omit_tabular_output</filter>
216 </data> 216 </data>
217 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff"> 217 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff">
218 <filter>not omit_tabular_output</filter> 218 <filter>not omit_tabular_output</filter>
219 </data> 219 </data>
220 <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff"> 220 <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff">
221 <filter>not omit_tabular_output</filter> 221 <filter>not omit_tabular_output</filter>
222 </data> 222 </data>
223 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking"> 223 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking">
224 <filter>not omit_tabular_output</filter> 224 <filter>not omit_tabular_output</filter>
225 </data> 225 </data>
226 <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" > 226 <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" >
227 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter> 227 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
228 </data> 228 </data>
229 229
230 <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff"> 230 <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff">
231 <filter>not omit_tabular_output</filter> 231 <filter>not omit_tabular_output</filter>
232 </data> 232 </data>
233 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking"> 233 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking">
234 <filter>not omit_tabular_output</filter> 234 <filter>not omit_tabular_output</filter>
235 </data> 235 </data>
236 <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" > 236 <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" >
237 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter> 237 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
238 </data> 238 </data>
239 239
240 <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff"> 240 <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff">
241 <filter>not omit_tabular_output</filter> 241 <filter>not omit_tabular_output</filter>
242 </data> 242 </data>
243 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking"> 243 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking">
244 <filter>not omit_tabular_output</filter> 244 <filter>not omit_tabular_output</filter>
245 </data> 245 </data>
246 <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene count tracking" from_work_dir="genes.count_tracking" > 246 <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene count tracking" from_work_dir="genes.count_tracking" >
254 <filter>not omit_tabular_output</filter> 254 <filter>not omit_tabular_output</filter>
255 </data> 255 </data>
256 <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking"> 256 <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking">
257 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter> 257 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
258 </data> 258 </data>
259 <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database"> 259 <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database" from_work_dir="cummeRbund.sqlite">
260 <filter>generate_sqlite</filter> 260 <filter>generate_sqlite</filter>
261 </data> 261 </data>
262 </outputs> 262 </outputs>
263 263
264 <tests> 264 <tests>
265 <test> 265 <test>
266 <!-- 266 <!--
267 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 267 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
268 --> 268 -->
269 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" /> 269 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
270 <param name="generate_sqlite" value="yes" /> 270 <param name="generate_sqlite" value="yes" />
271 <param name="omit_tabular_output" value="yes" /> 271 <param name="omit_tabular_output" value="yes" />
272 <conditional name="in_type"> 272 <conditional name="in_type">
273 <param name="set_in_type" value="BAM" /> 273 <param name="set_in_type" value="BAM" />
274 <repeat name="conditions"> 274 <repeat name="conditions">
275 <param name="name" value="q1" /> 275 <param name="name" value="q1" />
276 <param name="samples" value="cuffdiff_in1.sam" ftype="sam" /> 276 <param name="samples" value="cuffdiff_in1.sam" ftype="sam" />
277 </repeat> 277 </repeat>
278 <repeat name="conditions"> 278 <repeat name="conditions">
279 <param name="name" value="q2" /> 279 <param name="name" value="q2" />
280 <param name="samples" value="cuffdiff_in2.sam" ftype="sam" /> 280 <param name="samples" value="cuffdiff_in2.sam" ftype="sam" />
281 </repeat> 281 </repeat>
282 </conditional> 282 </conditional>
283 <param name="fdr" value="0.05" /> 283 <param name="fdr" value="0.05" />
284 <param name="min_alignment_count" value="0" /> 284 <param name="min_alignment_count" value="0" />
285 <param name="do_bias_correction" value="No" /> 285 <param name="do_bias_correction" value="No" />
286 <param name="do_normalization" value="No" /> 286 <param name="do_normalization" value="No" />
287 <param name="multiread_correct" value="No"/> 287 <param name="multiread_correct" value="No"/>
288 <param name="sAdditional" value="No"/> 288 <param name="sAdditional" value="No"/>
289 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" /> 289 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
290 </test> 290 </test>
291 <test> 291 <test>
292 <!-- 292 <!--
293 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 293 Use a list collection as conditions input
294 --> 294 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
295 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" /> 295 -->
296 <param name="omit_tabular_output" value="no" /> 296 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
297 <conditional name="in_type"> 297 <param name="generate_sqlite" value="yes" />
298 <param name="set_in_type" value="BAM" /> 298 <param name="omit_tabular_output" value="yes" />
299 <repeat name="conditions"> 299 <conditional name="in_type">
300 <param name="name" value="q1" /> 300 <param name="set_in_type" value="CONDITION_LIST" />
301 <param name="samples" value="cuffdiff_in1.sam" ftype="sam" /> 301 <param name="conditions">
302 </repeat> 302 <collection type="list">
303 <repeat name="conditions"> 303 <element name="q1" value="cuffdiff_in1.sam" />
304 <param name="name" value="q2" /> 304 <element name="q2" value="cuffdiff_in2.sam" />
305 <param name="samples" value="cuffdiff_in2.sam" ftype="sam" /> 305 </collection>
306 </repeat> 306 </param>
307 </conditional> 307 </conditional>
308 <param name="fdr" value="0.05" /> 308 <param name="fdr" value="0.05" />
309 <param name="min_alignment_count" value="0" /> 309 <param name="min_alignment_count" value="0" />
310 <param name="do_bias_correction" value="No" /> 310 <param name="do_bias_correction" value="No" />
311 <param name="do_normalization" value="No" /> 311 <param name="do_normalization" value="No" />
312 <param name="multiread_correct" value="No"/> 312 <param name="multiread_correct" value="No"/>
313 <param name="sAdditional" value="No"/> 313 <param name="sAdditional" value="No"/>
314 <output name="splicing_diff" file="splicing.diff"/> 314 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
315 <output name="promoters_diff" file="promoters.diff"/> 315 </test>
316 <output name="cds_diff" file="cds.diff"/> 316 <test>
317 <output name="cds_exp_fpkm_tracking" file="cds.exp_fpkm_tracking"/> 317 <!--
318 <output name="cds_fpkm_tracking" file="cds.fpkm_tracking"/> 318 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
319 <output name="tss_groups_exp" file="tss.groups_exp" lines_diff="200"/> 319 -->
320 <output name="tss_groups_fpkm_tracking" file="tss.groups_fpkm_tracking"/> 320 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
321 <output name="genes_exp" file="genes.exp" lines_diff="200"/> 321 <param name="omit_tabular_output" value="no" />
322 <output name="genes_fpkm_tracking" file="genes.fpkm_tracking" lines_diff="200"/> 322 <conditional name="in_type">
323 <output name="isoforms_exp" file="isoforms.exp" lines_diff="200"/> 323 <param name="set_in_type" value="BAM" />
324 <output name="isoforms_fpkm_tracking" file="isoforms.fpkm_tracking" lines_diff="200"/> 324 <repeat name="conditions">
325 <param name="name" value="q1" />
326 <param name="samples" value="cuffdiff_in1.sam" ftype="sam" />
327 </repeat>
328 <repeat name="conditions">
329 <param name="name" value="q2" />
330 <param name="samples" value="cuffdiff_in2.sam" ftype="sam" />
331 </repeat>
332 </conditional>
333 <param name="fdr" value="0.05" />
334 <param name="min_alignment_count" value="0" />
335 <param name="do_bias_correction" value="No" />
336 <param name="do_normalization" value="No" />
337 <param name="multiread_correct" value="No"/>
338 <param name="sAdditional" value="No"/>
339 <output name="splicing_diff" file="splicing.diff"/>
340 <output name="promoters_diff" file="promoters.diff"/>
341 <output name="cds_diff" file="cds.diff"/>
342 <output name="cds_exp_fpkm_tracking" file="cds.exp_fpkm_tracking"/>
343 <output name="cds_fpkm_tracking" file="cds.fpkm_tracking"/>
344 <output name="tss_groups_exp" file="tss.groups_exp" lines_diff="200"/>
345 <output name="tss_groups_fpkm_tracking" file="tss.groups_fpkm_tracking"/>
346 <output name="genes_exp" file="genes.exp" lines_diff="200"/>
347 <output name="genes_fpkm_tracking" file="genes.fpkm_tracking" lines_diff="200"/>
348 <output name="isoforms_exp" file="isoforms.exp" lines_diff="200"/>
349 <output name="isoforms_fpkm_tracking" file="isoforms.fpkm_tracking" lines_diff="200"/>
325 </test> 350 </test>
326 </tests> 351 </tests>
327 <help> 352 <help>
328 **Cuffdiff Overview** 353 **Cuffdiff Overview**
329 354