test_description=samtools method rumdup in PE mode
toolshedxml.path=samtools_rmdup.xml
input.input1=input_value
output.output1=output_value
param.bam_paired_end_type.bam_paired_end_type_selector=SE
command.expected=samtools rmdup -s "input_value" "output_value" 2>&1 || echo "Error running samtools rmdup." >&2

test_description=samtools method rumdup in PE mode force SE
toolshedxml.path=samtools_rmdup.xml
input.input1=input_value
output.output1=output_value
param.bam_paired_end_type.bam_paired_end_type_selector=PE
param.bam_paired_end_type.force_se=true
command.expected=samtools rmdup -S "input_value" "output_value" 2>&1 || echo "Error running samtools rmdup." >&2

test_description=samtools method rumdup in PE mode
toolshedxml.path=samtools_rmdup.xml
input.input1=input_value
output.output1=output_value
param.bam_paired_end_type.bam_paired_end_type_selector=PE
command.expected=samtools rmdup "input_value" "output_value" 2>&1 || echo "Error running samtools rmdup." >&2



test_description=grep python script 1
toolshedxml.path=grep.xml
input.input=input_value
param.pattern=[a-z]
param.invert=true
output.out_file1=output_value
command.expected=grep.py -i input_value -o output_value -pattern '[a-z]' -v true


test_description=grep python script 2
toolshedxml.path=grep.xml
input.input=input_value
param.pattern=[a-z]
param.invert=false
output.out_file1=output_value
command.expected=grep.py -i input_value -o output_value -pattern '[a-z]' -v false



test_description=trimmer from fastx 1
toolshedxml.path=fastx_trimmer.xml
input.input=input_value
param.first=2
param.last=12
other.input.ext=
output.output=output_value
command.expected=zcat -f 'input_value' | fastx_trimmer -v -f 2 -l 12 -o output_value

test_description=trimmer from fastx 2
toolshedxml.path=fastx_trimmer.xml
input.input=input_value
output.output=output_value
other.input.ext=
command.expected=zcat -f 'input_value' | fastx_trimmer -v -f 1 -l 21 -o output_value


test_description=sam2bam tool 1
toolshedxml.path=sam_to_bam.xml
input.source.input1=input_value
param.source.index_source=cached
param.source.ref_file=ref_file_value
output.output1=output_value
other.source.index.fields.path=no_authorized
command.expected=sam_to_bam.py --input1=input_value --index=no_authorized --output1=output_value


test_description=sam2bam tool 2
toolshedxml.path=sam_to_bam.xml
input.source.input1=input_value
other.source.index.fields.path=index_fields_value
param.source.index_source=history
input.source.ref_file=ref_file_value
output.output1=output_value
command.expected=sam_to_bam.py --input1=input_value --ref_file=ref_file_value --output1=output_value

test_description=bam2bedgraph tool
toolshedxml.path=bam-to-bedgraph.xml
input.input_bam=input
input.input_bai=index
output.output_bedgraph=output
command.expected=bamCoverage -b input -bai index -o output -of bedgraph

test_description=rmdup
toolshedxml.path=rmdup.xml
input.input=input_value
output.output=output_value
command.expected=picard.jar MarkDuplicates REMOVE_DUPLICATES=true INPUT=input_value OUTPUT=output_value

test_description=trim galore SR
toolshedxml.path=trim_galore.xml
param.is.paired=no
param.quality=30
input.input1=in1.fq
output.output1=out1.fq
command.expected=trim_galore --path_to_cutadapt /tmp/cutadapt-1.8.1/bin/cutadapt --quality 30 -e 0.1 --stringency 1 --length 20 in1.fq ; /RenameOutput.sh in1.fq out1.fq

test_description=trim galore PE
toolshedxml.path=trim_galore.xml
param.is.paired=yes
param.quality=30
input.input1=in1.fq
input.input2=in2.fq
output.output1=out1.fq
output.output2=out2.fq
command.expected=trim_galore --path_to_cutadapt /tmp/cutadapt-1.8.1/bin/cutadapt --quality 30 -e 0.1 --stringency 1 --length 20 --paired in1.fq in2.fq ; /RenameOutput2.sh in1.fq out1.fq ; /RenameOutput3.sh in2.fq out2.fq

test_description=matrix quality filtering
toolshedxml.path=quality-filtering.xml
param.plot.option=yes1
param.detection.threshold=1000
param.expression.option=yes2
param.expression.threshold=2000
param.reads.option=yes3
param.reads.threshold=3000
param.prop.mt=0.11
param.prop.sp=0.22
param.nb.filter=3
input.input1=in1.txt
input.input2=in2.txt
input.input3=in3.txt
output.output1=out1.txt
output.output2=out2.txt
output.output3=out3.txt
command.expected=Rscript scripts/SCQualityChecking.R in1.txt in2.txt in3.txt yes1 1000 2000 yes2 3000 yes3 0.11 0.22 3 out1.txt out2.txt out3.txt


test_description=matrix quality filtering default values
toolshedxml.path=quality-filtering.xml
input.input1=in1.txt
input.input2=in2.txt
input.input3=in3.txt
output.output1=out1.txt
output.output2=out2.txt
output.output3=out3.txt
command.expected=Rscript scripts/SCQualityChecking.R in1.txt in2.txt in3.txt All 10 4000 Endogenous 200000 Endogenous 0.1 0.5 1 out1.txt out2.txt out3.txt

