| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_batch/cnvkit_batch/0.9.12+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_batch/cnvkit_batch/0.9.11+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_batch/cnvkit_batch/0.9.11+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_batch/cnvkit_batch/0.9.10+galaxy0.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_batch/cnvkit_batch/0.9.10+galaxy0 |
| cnvkit_batch |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| cnvkit | 0.9.12 | package |
| samtools | 1.21 | package |
| Additional information about this tool |
ln -s '$CNV_reference.input_sample_file' ./tumor.bam &&
ln -s '$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":
#if $CNV_reference.normal
ln -s '$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
#if $CNV_reference.advanced_settings.access
ln -s '$CNV_reference.advanced_settings.access' ./access.bed &&
#end if
ln -s '$CNV_reference.targets' ./capture.bed &&
#if str($CNV_reference.reference_source.ref_selector) == 'history':
ln -s '$CNV_reference.reference_source.fasta' ./genome.fa &&
samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
#else
ln -s '$CNV_reference.reference_source.fasta.fields.path' ./genome.fa &&
ln -s '${CNV_reference.reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
#end if
#end if
#import os
cnvkit.py batch
./tumor.bam
#if str($CNV_reference.CNV_reference_availabel) == "no":
#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
#if $CNV_reference.advanced_settings.annotate
--annotate ./annotate.bed
#end if
#if $CNV_reference.advanced_settings.access
--access ./access.bed
#end if
#end if
#if str($CNV_reference.CNV_reference_availabel) == "yes":
--reference ./reference.cnn
#end if
$output_section.scatter
$output_section.diagram
--processes \${GALAXY_SLOTS:-4}
#if $CNV_reference.advanced_settings.method == "hybrid"
#set $method_val = "hybrid"
--method '$method_val'
#else
--method '$CNV_reference.advanced_settings.method'
#end if
#if $CNV_reference.advanced_settings.segment_method == "cbs"
#set $segment_method_val = "cbs"
--segment-method '$segment_method_val'
#else
--segment-method '$CNV_reference.advanced_settings.segment_method'
#end if
$CNV_reference.advanced_settings.male_reference
$CNV_reference.advanced_settings.countreads
$CNV_reference.advanced_settings.drop_low_coverage
#if str($CNV_reference.CNV_reference_availabel) == "no":
$CNV_reference.advanced_settings.short_names
#if str($CNV_reference.advanced_settings.target_avg_size)
--target-avg-size $CNV_reference.advanced_settings.target_avg_size
#end if
#if str($CNV_reference.advanced_settings.antitarget_avg_size)
--antitarget-avg-size $CNV_reference.advanced_settings.antitarget_avg_size
#end if
#if str($CNV_reference.advanced_settings.antitarget_min_size)
--antitarget-min-size $CNV_reference.advanced_settings.antitarget_min_size
#end if
$CNV_reference.advanced_settings.cluster
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
CNV_reference|input_sample_file: tumor.bam CNV_reference|normal: normal.bam CNV_reference|targets: capture.bed CNV_reference|reference_source|fasta: genome.fasta CNV_reference|reference_source|ref_selector: history CNV_reference|CNV_reference_availabel: no output_section|scatter: True output_section|diagram: True |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
tumor.bam normal.bam capture.bed genome.fasta value |
| Test-2 |
CNV_reference|input_sample_file: tumor.bam CNV_reference|targets: capture.bed CNV_reference|reference_source|fasta: genome.fasta CNV_reference|reference_source|ref_selector: history CNV_reference|CNV_reference_availabel: no output_section|scatter: True output_section|diagram: True |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
tumor.bam capture.bed genome.fasta value |
| Test-3 |
CNV_reference|input_sample_file: tumor.bam CNV_reference|normal: normal.bam CNV_reference|targets: capture.bed CNV_reference|reference_source|fasta: test_buildid CNV_reference|reference_source|ref_selector: cached CNV_reference|CNV_reference_availabel: no output_section|scatter: True output_section|diagram: True |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
tumor.bam normal.bam capture.bed value |
| Test-4 |
CNV_reference|input_sample_file: tumor.bam CNV_reference|reference: reference.cnn CNV_reference|CNV_reference_availabel: yes output_section|scatter: True output_section|diagram: True |
name: value name: value name: value name: value name: value name: value name: value name: value name: value name: value |
tumor.bam reference.cnn value |