<commit_before><tool id="expectedkmercoverage" name="ExpKmerCov" version="1.0.0">
	<command interpreter='perl'>
		ExpKmerCov.pl 
		#for $i in $files:

			#if $i.input_file_or_user.selection == "Manual" :
				--read_length $i.input_file_or_user.read_length --num_reads $i.input_file_or_user.num_reads
			#else :
				--read_length `head -n 1 $i.input_file_or_user.length_file` --num_reads `tail -n 1 $i.input_file_or_user.count_file`
			#end if
				
		#end for

		--genome_size $genome_size
		
		#if $range_input.range_select == "Manual" :
		
			--kmer_range $kmer_range_min,$kmer_range_max,$kmer_range_inc 
		
		#else :
			
			--kmer_range `cat $range_file `
			
		#end if
		> $output
	</command> 
	<inputs>
		<repeat name="files" title="Files">
			<conditional name="input_file_or_user" >
				<param name="selection" type="select" label="Input reads length and count manually or from a file?">
					<option value="Manual"> Manual</option>
					<option value="File" > File </option>
				</param>			
				<when value="Manual">	
					<param name="read_length" type="integer" value="0" label="read_length"/>
					<param name="num_reads" type="integer" value="0" label="nums_reads" />
				</when>
					
				<when value="File">
					<param name="length_file" type="data" label= "The reads length file" />
				</when>	
			</conditional>
		</repeat>
		<param name="genome_size" type="integer" value="0" label="Estimate for genome size" />
		<conditional name="range_input">
			<param name="range_select" type="select" label="Select input option for Kmer range"  > 
				<option value="Manual">Manual</option>
				<option value="File">File</option>
			</param>
			
			
			
			<when value="Manual">
				<param name="kmer_range_min" type="integer" value="0" label="The minimum of the kmer range" />
				<param name="kmer_range_max" type="integer" value="0" label="The maximum of the kmer range" />
				<param name="kmer_range_inc" type="integer" value="0" label="The even increment of the kmer range" />
			</when>	
		
			<when value="File">
			
				<param name="range_file" type="data" format="txt" label="The range file"/>
			
			</when>
		</conditional>
		
	</inputs>
	<outputs>
		<data format="txt" name="output"/>
	</outputs>
</tool>
<commit_msg>fixed problems with expected kmer input that came from no longer using the read counts tool and from adding a kmer range file option<commit_after><tool id="expectedkmercoverage" name="ExpKmerCov" version="1.0.0">
	<command interpreter='perl'>
		ExpKmerCov.pl 
		#for $i in $files:

			#if $i.input_file_or_user.selection == "Manual" :
				--read_length $i.input_file_or_user.read_length --num_reads $i.input_file_or_user.num_reads
			#else :
				--read_length `head -n 1 $i.input_file_or_user.length_file` --num_reads `tail -n 1 $i.input_file_or_user.length_file`
			#end if
				
		#end for

		--genome_size $genome_size
		
		#if $range_input.range_select == "Manual" :
		
			--kmer_range $range_input.kmer_range_min,$range_input.kmer_range_max,$range_input.kmer_range_inc 
		
		#else :
			
			--kmer_range `cat $range_file `
			
		#end if
		> $output
	</command> 
	<inputs>
		<repeat name="files" title="Files">
			<conditional name="input_file_or_user" >
				<param name="selection" type="select" label="Input reads length and count manually or from a file?">
					<option value="Manual"> Manual</option>
					<option value="File" > File </option>
				</param>			
				<when value="Manual">	
					<param name="read_length" type="integer" value="0" label="read_length"/>
					<param name="num_reads" type="integer" value="0" label="nums_reads" />
				</when>
					
				<when value="File">
					<param name="length_file" type="data" label= "The reads length file" />
				</when>	
			</conditional>
		</repeat>
		<param name="genome_size" type="integer" value="0" label="Estimate for genome size" />
		<conditional name="range_input">
			<param name="range_select" type="select" label="Select input option for Kmer range"  > 
				<option value="Manual">Manual</option>
				<option value="File">File</option>
			</param>
			
			
			
			<when value="Manual">
				<param name="kmer_range_min" type="integer" value="0" label="The minimum of the kmer range" />
				<param name="kmer_range_max" type="integer" value="0" label="The maximum of the kmer range" />
				<param name="kmer_range_inc" type="integer" value="0" label="The even increment of the kmer range" />
			</when>	
		
			<when value="File">
			
				<param name="range_file" type="data" format="txt" label="The range file"/>
			
			</when>
		</conditional>
		
	</inputs>
	<outputs>
		<data format="txt" name="output"/>
	</outputs>
</tool>

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{'dir': 'git-commits-cleaned', 'id': '5702647', 'n_tokens_mistral': 1916, 'n_tokens_neox': 1579, 'n_words': 377}