<commit_before><tool id="fastx_trimmer" name="FastX Trimmer" version="1.0.0">
  <description>to fixed length</description>
 <requirements>
  <requirement type="package" version="0.0.13.2">fastx_trimmer</requirement>
 </requirements>
	<command> 
		fastx_trimmer
	<!--	#if $input.ext == "fastqsanger":
			 -Q 33
		#elif $input.ext == "fastq":
		 	-Q 33
		#elif $input.ext == "fq":
		 	-Q 33
		#end if
		-v -f $first -l $last -->
		#if $Qselect :
			-Q $quality
		#end if
		-f $first
		
		#if $lastSelect :
		
			-l $lastB.last

		#end if
		
		-i $input -o '$output'
		
        </command>
	<inputs>

		<param name="Qselect" type="boolean" label="Use a minimum base score ?" />
		<param name="quality" type="integer" value="33" label="Minimum quality"/>

				
		<param format="fasta,fastq,fastqsanger" name="input" type="data" label="Library to clip" />

		<param name="first" size="4" type="integer" value="1">
			<label>First base to keep</label>
		</param>


		<param name="lastSelect" type="boolean" label="Enter a last base to keep? (By default it will keep the rest of the sequence)" >

		<param name="last" size="4" type="integer" value="21">
			<label>Last base to keep</label>
		</param>



		
		
	</inputs>

	<outputs>
		<data format="input" name="output" metadata_source="input"/>
	</outputs>


	<help>
		**What it does**

This tool trims (cut nucleotides from) sequences in a FASTA/Q file.
  
--------

**Example**<commit_msg>fixed typo<commit_after><tool id="fastx_trimmer" name="FastX Trimmer" version="1.0.0">
  <description>to fixed length</description>
 <requirements>
  <requirement type="package" version="0.0.13.2">fastx_trimmer</requirement>
 </requirements>
	<command> 
		fastx_trimmer
	<!--	#if $input.ext == "fastqsanger":
			 -Q 33
		#elif $input.ext == "fastq":
		 	-Q 33
		#elif $input.ext == "fq":
		 	-Q 33
		#end if
		-v -f $first -l $last -->
		#if $Qselect :
			-Q $quality
		#end if
		-f $first
		
		#if $lastSelect :
		
			-l $last

		#end if
		
		-i $input -o '$output'
		
        </command>
	<inputs>

		<param name="Qselect" type="boolean" label="Use a minimum base score ?" />
		<param name="quality" type="integer" value="33" label="Minimum quality"/>

				
		<param format="fasta,fastq,fastqsanger" name="input" type="data" label="Library to clip" />

		<param name="first" size="4" type="integer" value="1">
			<label>First base to keep</label>
		</param>


		<param name="lastSelect" type="boolean" label="Enter a last base to keep? (By default it will keep the rest of the sequence)" />

		<param name="last" size="4" type="integer" value="21">
			<label>Last base to keep</label>
		</param>



		
		
	</inputs>

	<outputs>
		<data format="input" name="output" metadata_source="input"/>
	</outputs>


	<help>
		**What it does**

This tool trims (cut nucleotides from) sequences in a FASTA/Q file.
  
--------

**Example**
{'fraction_non_alphanumeric': 0.17692307692307693, 'fraction_numerical': 0.014685314685314685, 'mean_word_length': 3.3480243161094223, 'pattern_counts': {'":': 6, '<': 59, '<?xml version=': 0, '>': 59, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 2, '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': '7039929', 'n_tokens_mistral': 1162, 'n_tokens_neox': 997, 'n_words': 280}