<commit_before><tool id="control_freec" name="control-freec" version="11.6">
    <requirements>
    	<requirement type="package" version="11.6">control-freec</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       freec -conf <config file> -sample <mySample.bam> -control <myControl.bam>
    ]]></command>
    <inputs>
    </inputs>
    <outputs>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool><commit_msg>added configfile and some input parameters<commit_after><tool id="control_freec" name="control-freec" version="11.6">
    <requirements>
    	<requirement type="package" version="11.6">control-freec</requirement>
    </requirements>
    <configfiles>
    	<configfile name="script_file">
			###For more options see: http://boevalab.com/FREEC/tutorial.html#CONFIG ###

			[general]
			chrLenFile = "$chrLenFile"
            window = "${window}"
            ploidy = "${ploidy}"
            outputDir = "${outputDir}"


			#sex=XY
			breakPointType=4
			chrFiles =  /pathToChromosomeFastaFiles/Human/hg19/chromosomes/

			maxThreads=6

			breakPointThreshold=1.2
			noisyData=TRUE
			printNA=FALSE

			readCountThreshold=50

			[sample]
			mateFile = "${input_sample_file}"
			inputFormat = bam
			mateOrientation = 0

			[control]
			mateFile = "${input_control_file}"
			inputFormat = "${input_control_file.format}"
			mateOrientation = 0

			[BAF]
			SNPfile = /bioinfo/users/vboeva/Desktop/annotations/hg19_snp131.SingleDiNucl.1based.txt
			minimalCoveragePerPosition = 5

			[target]
			captureRegions = /EXOME-SEQ/TruSeq_exome_targeted_regions.hg19.bed
    	</configfile>
    </configfiles>
    <command detect_errors="exit_code"><![CDATA[
        freec -conf 
        	$script_file
    ]]></command>
    <inputs>
		<param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample File" help="Sample file in .BAM format."/>
		<param name="input_control_file" type="data" format="bam" multiple="false" label="Control File" help="Control file in .BAM format."/>
    </inputs>
    <outputs>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>
{'fraction_non_alphanumeric': 0.14921946740128558, 'fraction_numerical': 0.014233241505968778, 'mean_word_length': 3.4743326488706368, 'pattern_counts': {'":': 0, '<': 44, '<?xml version=': 0, '>': 44, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4414702', 'n_tokens_mistral': 816, 'n_tokens_neox': 717, 'n_words': 135}