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comparison trimmomatic.xml @ 5:f80107cdc406 draft

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Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
author pjbriggs
date Fri, 16 Dec 2016 11:31:55 -0500
parents 14d05f2d511d
children 141bba0e9a77
comparison
equal deleted inserted replaced
4:14d05f2d511d 5:f80107cdc406
1 <tool id="trimmomatic" name="Trimmomatic" version="0.36.0"> 1 <tool id="trimmomatic" name="Trimmomatic" version="0.36.1">
2 <description>flexible read trimming tool for Illumina NGS data</description> 2 <description>flexible read trimming tool for Illumina NGS data</description>
3 <macros>
4 <import>trimmomatic_macros.xml</import>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="0.36">trimmomatic</requirement> 7 <requirement type="package" version="0.36">trimmomatic</requirement>
5 </requirements> 8 </requirements>
6 <stdio> 9 <stdio>
7 <exit_code range="1:" /> 10 <exit_code range="1:" />
8 </stdio> 11 </stdio>
9 <command interpreter="bash"><![CDATA[ 12 <command><![CDATA[
10 trimmomatic.sh 13 @CONDA_TRIMMOMATIC_JAR_PATH@ &&
11 -mx8G 14 @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ &&
12 -jar \$TRIMMOMATIC_DIR/trimmomatic-0.36.jar 15 java -mx8G -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar
13 #if $paired_end.is_paired_end 16 #if $paired_end.is_paired_end
14 PE -threads \${GALAXY_SLOTS:-6} -phred33 17 PE -threads \${GALAXY_SLOTS:-6} -phred33
15 #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type 18 #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type
16 #if $paired_input_type == "pair_of_files" 19 #if $paired_input_type == "pair_of_files"
17 "${paired_end.paired_input_type_conditional.fastq_r1_in}" 20 "${paired_end.paired_input_type_conditional.fastq_r1_in}"
27 #else 30 #else
28 SE -threads \${GALAXY_SLOTS:-6} -phred33 "$fastq_in" "$fastq_out" 31 SE -threads \${GALAXY_SLOTS:-6} -phred33 "$fastq_in" "$fastq_out"
29 #end if 32 #end if
30 ## ILLUMINACLIP option 33 ## ILLUMINACLIP option
31 #if $illuminaclip.do_illuminaclip 34 #if $illuminaclip.do_illuminaclip
32 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_DIR/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold 35 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
33 #end if 36 #end if
34 ## Other operations 37 ## Other operations
35 #for $op in $operations 38 #for $op in $operations
36 ## SLIDINGWINDOW 39 ## SLIDINGWINDOW
37 #if str( $op.operation.name ) == "SLIDINGWINDOW" 40 #if str( $op.operation.name ) == "SLIDINGWINDOW"
58 #end if 61 #end if
59 #if str( $op.operation.name ) == "MAXINFO" 62 #if str( $op.operation.name ) == "MAXINFO"
60 MAXINFO:$op.operation.target_length:$op.operation.strictness 63 MAXINFO:$op.operation.target_length:$op.operation.strictness
61 #end if 64 #end if
62 #end for 65 #end for
66 2>&1 | tee trimmomatic.log &&
67 if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi
63 ]]></command> 68 ]]></command>
64 <inputs> 69 <inputs>
65 <conditional name="paired_end"> 70 <conditional name="paired_end">
66 <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" /> 71 <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" />
67 <when value="no"> 72 <when value="no">