cnvkit_batch: batch.xml comparison

comparison batch.xml @ 5:80dc747a394d draft default tip

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

-:71f99b30a7f1
+:80dc747a394d
 ln -s '$CNV_reference.input_sample_file.metadata.bam_index' ./tumor.bam.bai &&
 #if str($CNV_reference.CNV_reference_availabel) == "yes":
 ln -s '$CNV_reference.reference' ./reference.cnn &&
 #end if
 #if str($CNV_reference.CNV_reference_availabel) == "no":
-ln -s '$CNV_reference.normal' ./normal.bam &&
+#if $CNV_reference.normal
-ln -s '$CNV_reference.normal.metadata.bam_index' ./normal.bam.bai &&
+ln -s '$CNV_reference.normal' ./normal.bam &&
+ln -s '$CNV_reference.normal.metadata.bam_index' ./normal.bam.bai &&
+#end if
 #if $CNV_reference.advanced_settings.antitargets
 ln -s '$CNV_reference.advanced_settings.antitargets' ./antitargets.bed &&
 #end if
 #if $CNV_reference.advanced_settings.annotate
 ln -s '$CNV_reference.advanced_settings.annotate' ./annotate.bed &&
 #end if
 #import os
 cnvkit.py batch
 ./tumor.bam
 #if str($CNV_reference.CNV_reference_availabel) == "no":
---normal ./normal.bam
+#if $CNV_reference.normal
+--normal ./normal.bam
+#else:
+--normal
+#end if
 --targets ./capture.bed
 --fasta ./genome.fa
 #if $CNV_reference.advanced_settings.antitargets
 --antitargets ./antitargets.bed
 #end if
 </when>
 </conditional>
 <expand macro="output_section" />
 </inputs>
 <outputs>
-<data name="out_sample_bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" />
+<data name="out_sample_bintest" format="cns" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" />
-<data name="out_sample_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" />
+<data name="out_sample_antitargetcoverage" format="cnn" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" />
-<data name="out_sample_call" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
+<data name="out_sample_call" format="cns" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
-<data name="out_sample_targetcoverage_cnn" format="tabular" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" />
+<data name="out_sample_targetcoverage_cnn" format="cnn" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" />
-<data name="out_sample_cns" format="tabular" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" />
+<data name="out_sample_cns" format="cns" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" />
-<data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" />
+<data name="out_sample_cnr" format="cnr" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" />
 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture Antitarget" from_work_dir="capture.antitarget.bed">
 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
 </data>
-<data name="out_control_targetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn">
+<data name="out_control_targetcoverage" format="cnn" label="${tool.name} on ${on_string}: Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn">
 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
 </data>
-<data name="out_control_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn">
+<data name="out_control_antitargetcoverage" format="cnn" label="${tool.name} on ${on_string}: Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn">
 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
 </data>
-<data name="out_reference_cnn" format="tabular" label="${tool.name} on ${on_string}: Copy Number Reference Profile" from_work_dir="reference.cnn">
+<data name="out_reference_cnn" format="cnn" label="${tool.name} on ${on_string}: Copy Number Reference Profile" from_work_dir="reference.cnn">
 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
 </data>
 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture Target" from_work_dir="capture.target.bed">
 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
 </data>
-<data name="out_reference_target_bed" format="tabular" label="${tool.name} on ${on_string}: Reference Target" from_work_dir="reference.target-tmp.bed">
+<data name="out_reference_target_bed" format="bed" label="${tool.name} on ${on_string}: Reference Target" from_work_dir="reference.target-tmp.bed">
 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
 </data>
 <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed">
 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
 </data>
 <assert_contents><has_text text="chromosome"/></assert_contents>
 </output>
 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
-<output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
+<output name="out_reference_cnn" file="reference.cnn" ftype="cnn" compare="sim_size">
+<assert_contents><has_size value="3000" delta="2000" /></assert_contents>
+</output>
+<output name="out_capture_target">
+<assert_contents><has_text_matching expression="chrM"/></assert_contents>
+</output>
+<output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
+<assert_contents><has_size value="13000" delta="3000" /></assert_contents>
+</output>
+<output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
+<assert_contents><has_size value="6000" delta="2000" /></assert_contents>
+</output>
+</test>
+<test expect_num_outputs="13">
+<conditional name="CNV_reference">
+<conditional name="reference_source">
+<param name="ref_selector" value="history"/>
+<param name="fasta" ftype="fasta" value="genome.fasta" />
+</conditional>
+<param name="CNV_reference_availabel" value="no" />
+<param name="input_sample_file" ftype="bam" value="tumor.bam" />
+<param name="method" value="wgs" />
+<param name="targets" ftype="bed" value="capture.bed" />
+</conditional>
+<section name="output_section">
+<param name="scatter" value="1"/>
+<param name="diagram" value="1"/>
+</section>
+<output name="out_sample_bintest">
+<assert_contents><has_text text="chromosome"/></assert_contents>
+</output>
+<output name="out_sample_antitargetcoverage">
+<assert_contents><has_text text="chromosome"/></assert_contents>
+</output>
+<output name="out_sample_call">
+<assert_contents><has_text text="chromosome"/></assert_contents>
+</output>
+<output name="out_sample_cnr">
+<assert_contents><has_text text="chromosome"/></assert_contents>
+</output>
+<output name="out_sample_targetcoverage_cnn">
+<assert_contents><has_text text="chromosome"/></assert_contents>
+</output>
+<output name="out_sample_cns">
+<assert_contents><has_text text="chromosome"/></assert_contents>
+</output>
+<output name="out_capture_antitarget" file="capture.antitarget.bed" />
+<output name="out_reference_cnn" file="reference.cnn" ftype="cnn" compare="sim_size">
 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
 </output>
 <output name="out_capture_target">
 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
 </output>
 <assert_contents><has_text text="chromosome"/></assert_contents>
 </output>
 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
-<output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
+<output name="out_reference_cnn" file="reference.cnn" ftype="cnn" compare="sim_size">
 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
 </output>
 <output name="out_capture_target">
 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
 </output>
 chromosome, Start, end, gene, log2, depth and proportional weight or reliability (weight)
 Segmented log2 ratios (.cns)
 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
+-----
+**Bin-level log2 ratios (.cnr)**
+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.
+.. csv-table::
+:header-rows: 0
+"chromosome","Genomic chromosome (e.g., chr1, chrX)"
+"start","Start position of the bin."
+"end","End position of the bin."
+"gene","Gene name(s) overlapping the bin (if applicable)."
+"log2","Normalized log2 ratio (sample coverage / reference coverage)."
+"depth","Average read depth in the bin."
+"weight","Reliability weight of the bin (higher = more reliable)."
+-----
+**Segmented log2 ratios (.cns)**
+Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
+.. csv-table::
+:header-rows: 0
+"chromosome","start, end: Genomic coordinates of the segment"
+"gene","Gene(s) overlapping the segment."
+"log2","Mean log2 ratio of the segment."
+"probes","Mean log2 ratio of the segment."
+"depth","Average read depth."
+"weight","Reliability weight."
+"p_value","Statistical confidence (lower = more significant)."
+-----
+**Copy Number Reference Profile (.cnn)**
+Tabular file defining the reference baseline built from control samples (e.g., normal samples). Used to normalize test samples.
+.. csv-table::
+:header-rows: 0
+"chromosome","Genomic chromosome (e.g., chr1, chrX)."
+"start","Start position of the bin."
+"end","End position of the bin."
+"gene","Gene name(s) (if applicable)."
+"log2","Reference log2 ratio (typically 0 for diploid regions)."
+"depth","Average read depth across control samples."
+"spread","Variability (standard deviation) of coverage in controls."
+-----
+**Target and Antitarget Bin-level Coverages (.cnn)**
+Two intermediate tabular files containing raw coverage counts for target regions (captured regions) and antitarget regions (background).
+**Target Coverage File (e.g., sample.targetcoverage.cnn):**
+- **Columns:** chromosome, start, end, gene, reads (raw read count), depth (reads normalized by bin size).
+- **Purpose:** Captures on-target sequencing depth.
+-----
+**Antitarget Coverage File (e.g., sample.antitargetcoverage.cnn):**
+- **Columns:** Same as target coverage.
+- **Purpose:** Estimates off-target background noise (corrects for whole-genome effects like tumor ploidy).
 ]]></help>
 <expand macro="citations" />
 </tool>

Mercurial > repos > iuc > cnvkit_batch

comparison batch.xml @ 5:80dc747a394d draft default tip