Command line builder

Command Line Builder (GitHub) is a tool to build a list of command lines from a list of files. Command Line Builder insert automatically the file names in the command line until all the file names are all used. It is possible to substitute file names with or without their extension.

For example, with a file list :

[file01.ext, .. file10.ext]

and the pattern :

bowtie2 -1 /path/Fex[1] -2 /path/Fex[2] | samtools view -bS - > /path/Fne[1].bam

Command Line Builder produces :

bowtie2 -1 /path/file01.ext -2 /path/file02.ext | samtools view -bS - > /path/file01.bam

bowtie2 -1 /path/file03.ext -2 /path/file04.ext | samtools view -bS - > /path/file03.bam

bowtie2 -1 /path/file05.ext -2 /path/file06.ext | samtools view -bS - > /path/file05.bam

bowtie2 -1 /path/file07.ext -2 /path/file08.ext | samtools view -bS - > /path/file07.bam

bowtie2 -1 /path/file09.ext -2 /path/file10.ext | samtools view -bS - > /path/file09.bam