cnvkit_batch: batch.xml annotate

annotate batch.xml @ 4:004311c34527 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 11:53:11 +0000
parents	0d371963d4b9
children

rev	line source
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	1 <tool id="cnvkit_batch" name="CNVkit Batch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	2 <description>Run the CNVkit pipeline on one or more BAM files</description>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	3 <macros>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	4 <import>macros.xml</import>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	5 </macros>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	6 <expand macro="xrefs"/>
1 0c60bd0f4de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22 iuc parents: 0 diff changeset	7 <expand macro="creators"/>
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	8 <expand macro="requirements"/>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	10 ln -s '$CNV_reference.input_sample_file' ./tumor.bam &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	11 ln -s '$CNV_reference.input_sample_file.metadata.bam_index' ./tumor.bam.bai &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	12 #if str($CNV_reference.CNV_reference_availabel) == "yes":
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	13 ln -s '$CNV_reference.reference' ./reference.cnn &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	14 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	15 #if str($CNV_reference.CNV_reference_availabel) == "no":
4 004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	16 #if $CNV_reference.normal
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	17 ln -s '$CNV_reference.normal' ./normal.bam &&
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	18 ln -s '$CNV_reference.normal.metadata.bam_index' ./normal.bam.bai &&
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	19 #end if
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	20 #if $CNV_reference.advanced_settings.antitargets
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	21 ln -s '$CNV_reference.advanced_settings.antitargets' ./antitargets.bed &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	22 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	23 #if $CNV_reference.advanced_settings.annotate
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	24 ln -s '$CNV_reference.advanced_settings.annotate' ./annotate.bed &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	25 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	26 #if $CNV_reference.advanced_settings.access
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	27 ln -s '$CNV_reference.advanced_settings.access' ./access.bed &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	28 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	29 ln -s '$CNV_reference.targets' ./capture.bed &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	30 #if str($CNV_reference.reference_source.ref_selector) == 'history':
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	31 ln -s '$CNV_reference.reference_source.fasta' ./genome.fa &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	32 samtools faidx ./genome.fa 2>&1 \|\| echo 'Error running samtools faidx for indexing fasta reference for CNVkit' >&2 &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	33 #else
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	34 ln -s '$CNV_reference.reference_source.fasta.fields.path' ./genome.fa &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	35 ln -s '${CNV_reference.reference_source.fasta.fields.path}.fai' ./genome.fa.fai &&
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	36 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	37 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	38 #import os
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	39 cnvkit.py batch
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	40 ./tumor.bam
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	41 #if str($CNV_reference.CNV_reference_availabel) == "no":
4 004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	42 #if $CNV_reference.normal
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	43 --normal ./normal.bam
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	44 #else:
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	45 --normal
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	46 #end if
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	47 --targets ./capture.bed
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	48 --fasta ./genome.fa
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	49 #if $CNV_reference.advanced_settings.antitargets
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	50 --antitargets ./antitargets.bed
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	51 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	52 #if $CNV_reference.advanced_settings.annotate
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	53 --annotate ./annotate.bed
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	54 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	55 #if $CNV_reference.advanced_settings.access
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	56 --access ./access.bed
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	57 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	58 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	59 #if str($CNV_reference.CNV_reference_availabel) == "yes":
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	60 --reference ./reference.cnn
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	61 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	62 $output_section.scatter
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	63 $output_section.diagram
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	64 --processes \${GALAXY_SLOTS:-4}
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	65 #if $CNV_reference.advanced_settings.method == "hybrid"
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	66 #set $method_val = "hybrid"
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	67 --method '$method_val'
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	68 #else
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	69 --method '$CNV_reference.advanced_settings.method'
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	70 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	71
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	72 #if $CNV_reference.advanced_settings.segment_method == "cbs"
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	73 #set $segment_method_val = "cbs"
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	74 --segment-method '$segment_method_val'
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	75 #else
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	76 --segment-method '$CNV_reference.advanced_settings.segment_method'
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	77 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	78 $CNV_reference.advanced_settings.male_reference
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	79 $CNV_reference.advanced_settings.countreads
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	80 $CNV_reference.advanced_settings.drop_low_coverage
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	81
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	82 #if str($CNV_reference.CNV_reference_availabel) == "no":
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	83 $CNV_reference.advanced_settings.short_names
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	84 #if str($CNV_reference.advanced_settings.target_avg_size)
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	85 --target-avg-size $CNV_reference.advanced_settings.target_avg_size
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	86 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	87 #if str($CNV_reference.advanced_settings.antitarget_avg_size)
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	88 --antitarget-avg-size $CNV_reference.advanced_settings.antitarget_avg_size
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	89 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	90 #if str($CNV_reference.advanced_settings.antitarget_min_size)
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	91 --antitarget-min-size $CNV_reference.advanced_settings.antitarget_min_size
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	92 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	93 $CNV_reference.advanced_settings.cluster
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	94 #end if
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	95 ]]></command>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	96 <inputs>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	97 <conditional name="CNV_reference">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	98 <param name="CNV_reference_availabel" type="select" label="Build or reuse a copy number reference file (.cnn)?" help="">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	99 <option value="no" selected="True">Build a new copy number reference file</option>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	100 <option value="yes">Reuse a copy number reference file</option>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	101 </param>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	102 <when value="no">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	103 <expand macro="create_CNV_reference_file" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	104 <expand macro="reference_interface" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	105 <section name="advanced_settings" title="Advanced settings" expanded="false">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	106 <expand macro="advanced_no_reference" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	107 <expand macro="shared" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	108 </section>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	109 </when>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	110 <when value="yes">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	111 <expand macro="reuse_an_existing_cnv_reference_file" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	112 <section name="advanced_settings" title="Advanced settings" expanded="false">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	113 <expand macro="shared" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	114 </section>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	115 </when>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	116 </conditional>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	117 <expand macro="output_section" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	118 </inputs>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	119 <outputs>
4 004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	120 <data name="out_sample_bintest" format="cns" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" />
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	121 <data name="out_sample_antitargetcoverage" format="cnn" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" />
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	122 <data name="out_sample_call" format="cns" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	123 <data name="out_sample_targetcoverage_cnn" format="cnn" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" />
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	124 <data name="out_sample_cns" format="cns" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" />
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	125 <data name="out_sample_cnr" format="cnr" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" />
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	126 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture Antitarget" from_work_dir="capture.antitarget.bed">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	127 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	128 </data>
4 004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	129 <data name="out_control_targetcoverage" format="cnn" label="${tool.name} on ${on_string}: Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn">
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	130 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	131 </data>
4 004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	132 <data name="out_control_antitargetcoverage" format="cnn" label="${tool.name} on ${on_string}: Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn">
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	133 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	134 </data>
4 004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	135 <data name="out_reference_cnn" format="cnn" label="${tool.name} on ${on_string}: Copy Number Reference Profile" from_work_dir="reference.cnn">
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	136 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	137 </data>
1 0c60bd0f4de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22 iuc parents: 0 diff changeset	138 <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture Target" from_work_dir="capture.target.bed">
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	139 <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	140 </data>
4 004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	141 <data name="out_reference_target_bed" format="bed" label="${tool.name} on ${on_string}: Reference Target" from_work_dir="reference.target-tmp.bed">
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	142 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	143 </data>
1 0c60bd0f4de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22 iuc parents: 0 diff changeset	144 <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed">
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	145 <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	146 </data>
1 0c60bd0f4de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22 iuc parents: 0 diff changeset	147 <data name="out_sample_diagram_pdf" format="pdf" label="${tool.name} on ${on_string}: Sample Diagram" from_work_dir="tumor-diagram.pdf">
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	148 <filter>output_section['diagram']</filter>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	149 </data>
1 0c60bd0f4de6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22 iuc parents: 0 diff changeset	150 <data name="out_sample_scatter_png" format="png" label="${tool.name} on ${on_string}: Sample Scatter pdf plot " from_work_dir="tumor-scatter.png">
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	151 <filter>output_section['scatter']</filter>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	152 </data>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	153 </outputs>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	154 <tests>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	155 <test expect_num_outputs="13">
2 0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	156 <conditional name="CNV_reference">
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	157 <conditional name="reference_source">
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	158 <param name="ref_selector" value="history"/>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	159 <param name="fasta" ftype="fasta" value="genome.fasta" />
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	160 </conditional>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	161 <param name="CNV_reference_availabel" value="no" />
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	162 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	163 <param name="normal" ftype="bam" value="normal.bam" />
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	164 <param name="targets" ftype="bed" value="capture.bed" />
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	165 </conditional>
2 0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	166 <section name="output_section">
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	167 <param name="scatter" value="1"/>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	168 <param name="diagram" value="1"/>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	169 </section>
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	170 <output name="out_sample_bintest" file="tumor.bintest.cns" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	171 <output name="out_sample_antitargetcoverage">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	172 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	173 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	174 <output name="out_sample_call">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	175 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	176 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	177 <output name="out_sample_cnr">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	178 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	179 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	180 <output name="out_sample_targetcoverage_cnn">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	181 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	182 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	183 <output name="out_sample_cns">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	184 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	185 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	186 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	187 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	188 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
4 004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	189 <output name="out_reference_cnn" file="reference.cnn" ftype="cnn" compare="sim_size">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	190 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	191 </output>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	192 <output name="out_capture_target">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	193 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	194 </output>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	195 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	196 <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	197 </output>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	198 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	199 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	200 </output>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	201 </test>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	202 <test expect_num_outputs="13">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	203 <conditional name="CNV_reference">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	204 <conditional name="reference_source">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	205 <param name="ref_selector" value="history"/>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	206 <param name="fasta" ftype="fasta" value="genome.fasta" />
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	207 </conditional>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	208 <param name="CNV_reference_availabel" value="no" />
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	209 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	210 <param name="method" value="wgs" />
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	211 <param name="targets" ftype="bed" value="capture.bed" />
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	212 </conditional>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	213 <section name="output_section">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	214 <param name="scatter" value="1"/>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	215 <param name="diagram" value="1"/>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	216 </section>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	217 <output name="out_sample_bintest">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	218 <assert_contents><has_text text="chromosome"/></assert_contents>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	219 </output>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	220 <output name="out_sample_antitargetcoverage">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	221 <assert_contents><has_text text="chromosome"/></assert_contents>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	222 </output>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	223 <output name="out_sample_call">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	224 <assert_contents><has_text text="chromosome"/></assert_contents>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	225 </output>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	226 <output name="out_sample_cnr">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	227 <assert_contents><has_text text="chromosome"/></assert_contents>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	228 </output>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	229 <output name="out_sample_targetcoverage_cnn">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	230 <assert_contents><has_text text="chromosome"/></assert_contents>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	231 </output>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	232 <output name="out_sample_cns">
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	233 <assert_contents><has_text text="chromosome"/></assert_contents>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	234 </output>
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	235 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	236
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	237 <output name="out_reference_cnn" file="reference.cnn" ftype="cnn" compare="sim_size">
2 0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	238 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	239 </output>
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	240 <output name="out_capture_target">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	241 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	242 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	243 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	244 <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	245 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	246 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	247 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	248 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	249 </test>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	250 <test expect_num_outputs="13">
2 0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	251 <conditional name="CNV_reference">
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	252 <conditional name="reference_source">
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	253 <param name="ref_selector" value="cached"/>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	254 <param name="fasta" value="test_buildid"/>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	255 </conditional>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	256 <param name="CNV_reference_availabel" value="no" />
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	257 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	258 <param name="normal" ftype="bam" value="normal.bam" />
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	259 <param name="targets" ftype="bed" value="capture.bed" />
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	260 </conditional>
2 0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	261 <section name="output_section">
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	262 <param name="scatter" value="1"/>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	263 <param name="diagram" value="1"/>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	264 </section>
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	265 <output name="out_sample_bintest" file="tumor.bintest.cns" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	266 <output name="out_sample_antitargetcoverage">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	267 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	268 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	269 <output name="out_sample_call">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	270 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	271 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	272 <output name="out_sample_cnr">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	273 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	274 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	275 <output name="out_sample_targetcoverage_cnn">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	276 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	277 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	278 <output name="out_sample_cns">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	279 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	280 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	281 <output name="out_capture_antitarget" file="capture.antitarget.bed" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	282 <output name="out_control_targetcoverage" file="normal.targetcoverage.cnn" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	283 <output name="out_control_antitargetcoverage" file="normal.antitargetcoverage.cnn" />
4 004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	284 <output name="out_reference_cnn" file="reference.cnn" ftype="cnn" compare="sim_size">
2 0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	285 <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	286 </output>
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	287 <output name="out_capture_target">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	288 <assert_contents><has_text_matching expression="chrM"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	289 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	290 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	291 <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	292 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	293 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	294 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	295 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	296 </test>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	297 <test expect_num_outputs="10">
2 0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	298 <conditional name="CNV_reference">
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	299 <param name="CNV_reference_availabel" value="yes" />
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	300 <param name="input_sample_file" ftype="bam" value="tumor.bam" />
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	301 <param name="reference" ftype="tabular" value="reference.cnn" />
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	302 </conditional>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	303 <section name="output_section">
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	304 <param name="scatter" value="1"/>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	305 <param name="diagram" value="1"/>
0d371963d4b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 9d922676808c5f57e9c01b148eec6cc0a63c53e5 iuc parents: 1 diff changeset	306 </section>
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	307 <output name="out_sample_bintest" file="tumor.bintest.cns" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	308 <output name="out_sample_antitargetcoverage">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	309 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	310 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	311 <output name="out_sample_call">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	312 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	313 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	314 <output name="out_sample_cnr">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	315 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	316 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	317 <output name="out_sample_targetcoverage_cnn">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	318 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	319 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	320 <output name="out_sample_cns">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	321 <assert_contents><has_text text="chromosome"/></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	322 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	323 <output name="out_reference_target_bed" file="reference.target-tmp.bed" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	324 <output name="out_reference_antitarget_bed" file="reference.antitarget-tmp.bed" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	325 <output name="out_sample_diagram_pdf" file="tumor-diagram.pdf" ftype="pdf" compare="sim_size">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	326 <assert_contents><has_size value="6000" delta="2000" /></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	327 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	328 <output name="out_sample_scatter_png" file="tumor-scatter.png" ftype="png" compare="sim_size">
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	329 <assert_contents><has_size value="13000" delta="3000" /></assert_contents>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	330 </output>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	331 </test>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	332 </tests>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	333 <help><![CDATA[
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	334 CNVkit pipeline for copy-number changes and allelic imbalances detection
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	335 cnn, cnr and cns are tabuler files extintions:
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	336
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	337 The reference .cnn file has the columns:
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	338 chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	339 of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	340 depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	341
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	342 Target and antitarget bin-level coverages (.cnn)
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	343 chromosome, Start, end, gene, log2 and depth
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	344
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	345 Bin-level log2 ratios (.cnr)
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	346 chromosome, Start, end, gene, log2, depth and proportional weight or reliability (weight)
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	347
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	348 Segmented log2 ratios (.cns)
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	349 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	350
4 004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	351 -----
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	352
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	353 Bin-level log2 ratios (.cnr)
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	354
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	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.
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	356
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	357 .. csv-table::
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	358 :header-rows: 0
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	359
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	360 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	361 "start","Start position of the bin."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	362 "end","End position of the bin."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	363 "gene","Gene name(s) overlapping the bin (if applicable)."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	364 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	365 "depth","Average read depth in the bin."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	366 "weight","Reliability weight of the bin (higher = more reliable)."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	367
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	368 -----
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	369
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	370 Segmented log2 ratios (.cns)
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	371
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	372 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	373
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	374 .. csv-table::
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	375 :header-rows: 0
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	376
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	377 "chromosome","start, end: Genomic coordinates of the segment"
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	378 "gene","Gene(s) overlapping the segment."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	379 "log2","Mean log2 ratio of the segment."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	380 "probes","Mean log2 ratio of the segment."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	381 "depth","Average read depth."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	382 "weight","Reliability weight."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	383 "p_value","Statistical confidence (lower = more significant)."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	384
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	385 -----
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	386
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	387 Copy Number Reference Profile (.cnn)
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	388
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	389 Tabular file defining the reference baseline built from control samples (e.g., normal samples). Used to normalize test samples.
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	390
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	391 .. csv-table::
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	392 :header-rows: 0
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	393
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	394 "chromosome","Genomic chromosome (e.g., chr1, chrX)."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	395 "start","Start position of the bin."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	396 "end","End position of the bin."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	397 "gene","Gene name(s) (if applicable)."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	398 "log2","Reference log2 ratio (typically 0 for diploid regions)."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	399 "depth","Average read depth across control samples."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	400 "spread","Variability (standard deviation) of coverage in controls."
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	401
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	402 -----
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	403
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	404
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	405 Target and Antitarget Bin-level Coverages (.cnn)
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	406
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	407 Two intermediate tabular files containing raw coverage counts for target regions (captured regions) and antitarget regions (background).
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	408
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	409 Target Coverage File (e.g., sample.targetcoverage.cnn):
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	410
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	411 - Columns: chromosome, start, end, gene, reads (raw read count), depth (reads normalized by bin size).
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	412
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	413 - Purpose: Captures on-target sequencing depth.
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	414
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	415 -----
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	416
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	417 Antitarget Coverage File (e.g., sample.antitargetcoverage.cnn):
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	418
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	419 - Columns: Same as target coverage.
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	420
004311c34527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb iuc parents: 2 diff changeset	421 - Purpose: Estimates off-target background noise (corrects for whole-genome effects like tumor ploidy).
0 840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	422 ]]></help>
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	423 <expand macro="citations" />
840fea8d07a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984 iuc parents: diff changeset	424 </tool>

Mercurial > repos > iuc > cnvkit_batch

annotate batch.xml @ 4:004311c34527 draft default tip