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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 12:02:49 +0000
parents 97d2b6742760
children
comparison
equal deleted inserted replaced
4:71f99b30a7f1 5:80dc747a394d
11 ln -s '$CNV_reference.input_sample_file.metadata.bam_index' ./tumor.bam.bai && 11 ln -s '$CNV_reference.input_sample_file.metadata.bam_index' ./tumor.bam.bai &&
12 #if str($CNV_reference.CNV_reference_availabel) == "yes": 12 #if str($CNV_reference.CNV_reference_availabel) == "yes":
13 ln -s '$CNV_reference.reference' ./reference.cnn && 13 ln -s '$CNV_reference.reference' ./reference.cnn &&
14 #end if 14 #end if
15 #if str($CNV_reference.CNV_reference_availabel) == "no": 15 #if str($CNV_reference.CNV_reference_availabel) == "no":
16 ln -s '$CNV_reference.normal' ./normal.bam && 16 #if $CNV_reference.normal
17 ln -s '$CNV_reference.normal.metadata.bam_index' ./normal.bam.bai && 17 ln -s '$CNV_reference.normal' ./normal.bam &&
18 ln -s '$CNV_reference.normal.metadata.bam_index' ./normal.bam.bai &&
19 #end if
18 #if $CNV_reference.advanced_settings.antitargets 20 #if $CNV_reference.advanced_settings.antitargets
19 ln -s '$CNV_reference.advanced_settings.antitargets' ./antitargets.bed && 21 ln -s '$CNV_reference.advanced_settings.antitargets' ./antitargets.bed &&
20 #end if 22 #end if
21 #if $CNV_reference.advanced_settings.annotate 23 #if $CNV_reference.advanced_settings.annotate
22 ln -s '$CNV_reference.advanced_settings.annotate' ./annotate.bed && 24 ln -s '$CNV_reference.advanced_settings.annotate' ./annotate.bed &&
35 #end if 37 #end if
36 #import os 38 #import os
37 cnvkit.py batch 39 cnvkit.py batch
38 ./tumor.bam 40 ./tumor.bam
39 #if str($CNV_reference.CNV_reference_availabel) == "no": 41 #if str($CNV_reference.CNV_reference_availabel) == "no":
40 --normal ./normal.bam 42 #if $CNV_reference.normal
43 --normal ./normal.bam
44 #else:
45 --normal
46 #end if
41 --targets ./capture.bed 47 --targets ./capture.bed
42 --fasta ./genome.fa 48 --fasta ./genome.fa
43 #if $CNV_reference.advanced_settings.antitargets 49 #if $CNV_reference.advanced_settings.antitargets
44 --antitargets ./antitargets.bed 50 --antitargets ./antitargets.bed
45 #end if 51 #end if
109 </when> 115 </when>
110 </conditional> 116 </conditional>
111 <expand macro="output_section" /> 117 <expand macro="output_section" />
112 </inputs> 118 </inputs>
113 <outputs> 119 <outputs>
114 <data name="out_sample_bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" /> 120 <data name="out_sample_bintest" format="cns" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" />
115 <data name="out_sample_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" /> 121 <data name="out_sample_antitargetcoverage" format="cnn" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" />
116 <data name="out_sample_call" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" /> 122 <data name="out_sample_call" format="cns" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
117 <data name="out_sample_targetcoverage_cnn" format="tabular" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" /> 123 <data name="out_sample_targetcoverage_cnn" format="cnn" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" />
118 <data name="out_sample_cns" format="tabular" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" /> 124 <data name="out_sample_cns" format="cns" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" />
119 <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" /> 125 <data name="out_sample_cnr" format="cnr" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" />
120 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture Antitarget" from_work_dir="capture.antitarget.bed"> 126 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture Antitarget" from_work_dir="capture.antitarget.bed">
121 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> 127 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
122 </data> 128 </data>
123 <data name="out_control_targetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn"> 129 <data name="out_control_targetcoverage" format="cnn" label="${tool.name} on ${on_string}: Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn">
124 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> 130 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
125 </data> 131 </data>
126 <data name="out_control_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn"> 132 <data name="out_control_antitargetcoverage" format="cnn" label="${tool.name} on ${on_string}: Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn">
127 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> 133 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
128 </data> 134 </data>
129 <data name="out_reference_cnn" format="tabular" label="${tool.name} on ${on_string}: Copy Number Reference Profile" from_work_dir="reference.cnn"> 135 <data name="out_reference_cnn" format="cnn" label="${tool.name} on ${on_string}: Copy Number Reference Profile" from_work_dir="reference.cnn">
130 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> 136 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
131 </data> 137 </data>
132 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture Target" from_work_dir="capture.target.bed"> 138 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture Target" from_work_dir="capture.target.bed">
133 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter> 139 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
134 </data> 140 </data>
135 <data name="out_reference_target_bed" format="tabular" label="${tool.name} on ${on_string}: Reference Target" from_work_dir="reference.target-tmp.bed"> 141 <data name="out_reference_target_bed" format="bed" label="${tool.name} on ${on_string}: Reference Target" from_work_dir="reference.target-tmp.bed">
136 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter> 142 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
137 </data> 143 </data>
138 <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed"> 144 <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed">
139 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter> 145 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
140 </data> 146 </data>
178 <assert_contents><has_text text="chromosome"/></assert_contents> 184 <assert_contents><has_text text="chromosome"/></assert_contents>
179 </output> 185 </output>
180 <output name="out_capture_antitarget" file="capture.antitarget.bed" /> 186 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
181 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" /> 187 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
182 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" /> 188 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
183 <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size"> 189 <output name="out_reference_cnn" file="reference.cnn" ftype="cnn" compare="sim_size">
190 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
191 </output>
192 <output name="out_capture_target">
193 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
194 </output>
195 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
196 <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
197 </output>
198 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
199 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
200 </output>
201 </test>
202 <test expect_num_outputs="13">
203 <conditional name="CNV_reference">
204 <conditional name="reference_source">
205 <param name="ref_selector" value="history"/>
206 <param name="fasta" ftype="fasta" value="genome.fasta" />
207 </conditional>
208 <param name="CNV_reference_availabel" value="no" />
209 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
210 <param name="method" value="wgs" />
211 <param name="targets" ftype="bed" value="capture.bed" />
212 </conditional>
213 <section name="output_section">
214 <param name="scatter" value="1"/>
215 <param name="diagram" value="1"/>
216 </section>
217 <output name="out_sample_bintest">
218 <assert_contents><has_text text="chromosome"/></assert_contents>
219 </output>
220 <output name="out_sample_antitargetcoverage">
221 <assert_contents><has_text text="chromosome"/></assert_contents>
222 </output>
223 <output name="out_sample_call">
224 <assert_contents><has_text text="chromosome"/></assert_contents>
225 </output>
226 <output name="out_sample_cnr">
227 <assert_contents><has_text text="chromosome"/></assert_contents>
228 </output>
229 <output name="out_sample_targetcoverage_cnn">
230 <assert_contents><has_text text="chromosome"/></assert_contents>
231 </output>
232 <output name="out_sample_cns">
233 <assert_contents><has_text text="chromosome"/></assert_contents>
234 </output>
235 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
236
237 <output name="out_reference_cnn" file="reference.cnn" ftype="cnn" compare="sim_size">
184 <assert_contents><has_size value="3000" delta="2000" /></assert_contents> 238 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
185 </output> 239 </output>
186 <output name="out_capture_target"> 240 <output name="out_capture_target">
187 <assert_contents><has_text_matching expression="chrM"/></assert_contents> 241 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
188 </output> 242 </output>
225 <assert_contents><has_text text="chromosome"/></assert_contents> 279 <assert_contents><has_text text="chromosome"/></assert_contents>
226 </output> 280 </output>
227 <output name="out_capture_antitarget" file="capture.antitarget.bed" /> 281 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
228 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" /> 282 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
229 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" /> 283 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
230 <output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size"> 284 <output name="out_reference_cnn" file="reference.cnn" ftype="cnn" compare="sim_size">
231 <assert_contents><has_size value="3000" delta="2000" /></assert_contents> 285 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
232 </output> 286 </output>
233 <output name="out_capture_target"> 287 <output name="out_capture_target">
234 <assert_contents><has_text_matching expression="chrM"/></assert_contents> 288 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
235 </output> 289 </output>
292 chromosome, Start, end, gene, log2, depth and proportional weight or reliability (weight) 346 chromosome, Start, end, gene, log2, depth and proportional weight or reliability (weight)
293 347
294 Segmented log2 ratios (.cns) 348 Segmented log2 ratios (.cns)
295 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes) 349 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
296 350
297 351 -----
352
353 **Bin-level log2 ratios (.cnr)**
354
355 Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
356
357 .. csv-table::
358 :header-rows: 0
359
360 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
361 "start","Start position of the bin."
362 "end","End position of the bin."
363 "gene","Gene name(s) overlapping the bin (if applicable)."
364 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
365 "depth","Average read depth in the bin."
366 "weight","Reliability weight of the bin (higher = more reliable)."
367
368 -----
369
370 **Segmented log2 ratios (.cns)**
371
372 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
373
374 .. csv-table::
375 :header-rows: 0
376
377 "chromosome","start, end: Genomic coordinates of the segment"
378 "gene","Gene(s) overlapping the segment."
379 "log2","Mean log2 ratio of the segment."
380 "probes","Mean log2 ratio of the segment."
381 "depth","Average read depth."
382 "weight","Reliability weight."
383 "p_value","Statistical confidence (lower = more significant)."
384
385 -----
386
387 **Copy Number Reference Profile (.cnn)**
388
389 Tabular file defining the reference baseline built from control samples (e.g., normal samples). Used to normalize test samples.
390
391 .. csv-table::
392 :header-rows: 0
393
394 "chromosome","Genomic chromosome (e.g., chr1, chrX)."
395 "start","Start position of the bin."
396 "end","End position of the bin."
397 "gene","Gene name(s) (if applicable)."
398 "log2","Reference log2 ratio (typically 0 for diploid regions)."
399 "depth","Average read depth across control samples."
400 "spread","Variability (standard deviation) of coverage in controls."
401
402 -----
403
404
405 **Target and Antitarget Bin-level Coverages (.cnn)**
406
407 Two intermediate tabular files containing raw coverage counts for target regions (captured regions) and antitarget regions (background).
408
409 **Target Coverage File (e.g., sample.targetcoverage.cnn):**
410
411 - **Columns:** chromosome, start, end, gene, reads (raw read count), depth (reads normalized by bin size).
412
413 - **Purpose:** Captures on-target sequencing depth.
414
415 -----
416
417 **Antitarget Coverage File (e.g., sample.antitargetcoverage.cnn):**
418
419 - **Columns:** Same as target coverage.
420
421 - **Purpose:** Estimates off-target background noise (corrects for whole-genome effects like tumor ploidy).
298 ]]></help> 422 ]]></help>
299 <expand macro="citations" /> 423 <expand macro="citations" />
300 </tool> 424 </tool>