Mercurial > repos > sanbi-uwc > trimmomatic

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planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 779c2af9e413bd7098662231d07e6b857161f48d
author sanbi-uwc
date Mon, 23 Jan 2017 07:53:06 -0500
parents 642a39a927c9
children
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4
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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1 <<<<<<< HEAD
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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2 <tool id="trimmomatic" name="Trimmomatic" version="0.36.3">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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3 =======
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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4 <tool id="trimmomatic" name="Trimmomatic" version="0.36.1">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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5 >>>>>>> upstream/master
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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6 <description>flexible read trimming tool for Illumina NGS data</description>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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7 <macros>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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8 <import>trimmomatic_macros.xml</import>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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9 </macros>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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10 <requirements>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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11 <requirement type="package" version="0.36">trimmomatic</requirement>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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12 </requirements>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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13 <<<<<<< HEAD
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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14 <command detect_errors="aggressive"><![CDATA[
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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15 #if $readtype.single_or_paired == "pair_of_files"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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16 #set r1_ext = $readtype.fastq_r1_in.extension
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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17 #set r2_ext = $readtype.fastq_r2_in.extension
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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18 ln -s '$readtype.fastq_r1_in' fastq_r1.'$r1_ext' &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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19 ln -s '$readtype.fastq_r2_in' fastq_r2.'$r2_ext' &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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20 #elif $readtype.single_or_paired == "collection"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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21 #set r1_ext = $readtype.fastq_pair.forward.extension
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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22 #set r2_ext = $readtype.fastq_pair.reverse.extension
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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23 ln -s '$readtype.fastq_pair.forward' fastq_r1.'$r1_ext' &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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24 ln -s '$readtype.fastq_pair.reverse' fastq_r2.'$r2_ext' &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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25 #else
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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26 ln -s '$fastq_in' fastq_in.'$fastq_in.extension' &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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27 #end if
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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28 bash '${__tool_directory__}/trimmomatic.sh'
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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29 #if $readtype.single_or_paired in ["pair_of_files","collection"]
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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30 =======
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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31 <stdio>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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32 <exit_code range="1:" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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33 </stdio>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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34 <command><![CDATA[
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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35 @CONDA_TRIMMOMATIC_JAR_PATH@ &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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36 @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ &&
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37 java -mx8G -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.jar
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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38 #if $paired_end.is_paired_end
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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39 >>>>>>> upstream/master
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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40 PE -threads \${GALAXY_SLOTS:-6} -phred33
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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41 fastq_r1.'$r1_ext' fastq_r2.'$r2_ext'
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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42 fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext'
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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43 fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext'
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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44 #else
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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45 SE -threads \${GALAXY_SLOTS:-6} -phred33 fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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46 #end if
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47 ## ILLUMINACLIP option
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48 #if $illuminaclip.do_illuminaclip
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49 ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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50 #end if
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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51 ## Other operations
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52 #for $op in $operations
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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53 ## SLIDINGWINDOW
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54 #if str( $op.operation.name ) == "SLIDINGWINDOW"
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55 SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality
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56 #end if
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57 ## MINLEN:36
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58 #if str( $op.operation.name ) == "MINLEN"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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59 MINLEN:$op.operation.minlen
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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60 #end if
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61 #if str( $op.operation.name ) == "LEADING"
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62 LEADING:$op.operation.leading
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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63 #end if
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64 #if str( $op.operation.name ) == "TRAILING"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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65 TRAILING:$op.operation.trailing
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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66 #end if
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67 #if str( $op.operation.name ) == "CROP"
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68 CROP:$op.operation.crop
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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69 #end if
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70 #if str( $op.operation.name ) == "HEADCROP"
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71 HEADCROP:$op.operation.headcrop
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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72 #end if
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73 #if str( $op.operation.name ) == "AVGQUAL"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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74 AVGQUAL:$op.operation.avgqual
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75 #end if
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76 #if str( $op.operation.name ) == "MAXINFO"
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77 MAXINFO:$op.operation.target_length:$op.operation.strictness
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78 #end if
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79 #end for
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80 <<<<<<< HEAD
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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81 &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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82 #if $readtype.single_or_paired == "pair_of_files"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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83 mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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84 mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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85 mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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86 mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}'
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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87 #elif $readtype.single_or_paired == "collection"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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88 mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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89 mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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90 mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' &&
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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91 mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}'
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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92 #else
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93 mv fastq_out.'$fastq_in.extension' '${fastq_out}'
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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94 #end if
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95 =======
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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96 2>&1 | tee trimmomatic.log &&
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97 if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi
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98 >>>>>>> upstream/master
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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99 ]]></command>
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100 <inputs>
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101 <conditional name="readtype">
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102 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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103 <option value="se" selected="true">Single-end</option>
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104 <option value="pair_of_files">Paired-end (two separate input files)</option>
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105 <option value="collection">Paired-end (as collection)</option>
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106 </param>
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107 <when value="se">
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108 <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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109 </when>
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110 <when value="pair_of_files">
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111 <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz"
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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112 label="Input FASTQ file (R1/first of pair)" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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113 <param name="fastq_r2_in" type="data" format="fastqsanger,fastqgsanger.gz"
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114 label="Input FASTQ file (R2/second of pair)" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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115 </when>
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116 <when value="collection">
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117 <param name="fastq_pair" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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118 </when>
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119 </conditional>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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120 <conditional name="illuminaclip">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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121 <param name="do_illuminaclip" type="boolean" label="Perform initial ILLUMINACLIP step?" help="Cut adapter and other illumina-specific sequences from the read" truevalue="yes" falsevalue="no" checked="False" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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122 <when value="yes">
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123 <param name="adapter_fasta" type="select" label="Adapter sequences to use">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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124 <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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125 <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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126 <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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127 <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>
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128 <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>
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129 <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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130 </param>
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131 <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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132 <param name="palindrome_clip_threshold" type="integer" label="How accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment" value="30" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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133 <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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134 </when>
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135 <when value="no" /> <!-- empty clause to satisfy planemo lint -->
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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136 </conditional>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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137 <repeat name="operations" title="Trimmomatic Operation" min="1">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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138 <conditional name="operation">
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139 <param name="name" type="select" label="Select Trimmomatic operation to perform">
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140 <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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141 <option value="MINLEN">Drop reads below a specified length (MINLEN)</option>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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142 <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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143 <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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144 <option value="CROP">Cut the read to a specified length (CROP)</option>
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145 <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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146 <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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147 <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option>
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148 </param>
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149 <when value="SLIDINGWINDOW">
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150 <param name="window_size" type="integer" label="Number of bases to average across" value="4" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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151 <param name="required_quality" type="integer" label="Average quality required" value="20" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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152 </when>
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153 <when value="MINLEN">
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154 <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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155 </when>
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156 <when value="LEADING">
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157 <param name="leading" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the start of the read with quality below the threshold will be removed" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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158 </when>
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159 <when value="TRAILING">
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160 <param name="trailing" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the end of the read with quality below the threshold will be removed" />
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161 </when>
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162 <when value="CROP">
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163 <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" />
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164 </when>
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165 <when value="HEADCROP">
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166 <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" />
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167 </when>
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168 <when value="AVGQUAL">
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169 <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" />
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170 </when>
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171 <when value="MAXINFO">
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172 <param name="target_length" type="integer" label="Target read length" value="" help="The read length which is likely to allow the location of the read within the target sequence to be determined." />
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173 <param name="strictness" type="float" label="Strictness" value="" help="Set between zero and one - specifies the balance between preserving read length versus removal of incorrect bases; low values (&lt;0.2) favours longer reads, high values (&gt;0.8) favours read correctness." />
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174 </when>
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175 </conditional>
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176 </repeat>
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177 </inputs>
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178 <outputs>
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179 <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
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180 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
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181 </data>
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182 <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
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183 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
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184 </data>
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185 <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in">
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186 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
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187 </data>
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188 <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in">
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189 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
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190 </data>
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191 <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
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192 <filter>readtype['single_or_paired'] == 'se'</filter>
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193 </data>
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194 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: paired">
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195 <filter>readtype['single_or_paired'] == "collection"</filter>
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196 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
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197 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
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198 </collection>
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199 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: unpaired">
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200 <filter>readtype['single_or_paired'] == "collection"</filter>
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201 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
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202 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
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203 </collection>
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204
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205 </outputs>
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206 <tests>
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207 <test>
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208 <!-- Single-end example -->
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209 <param name="single_or_paired" value="se" />
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210 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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211 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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212 <!--
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213 **NB** outputs have to be specified in order that they appear in the
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214 tool (which is the order they will be written to the history) - the
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215 test framework seems to use the order and ignores the "name" attribute
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216 -->
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217 <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
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218 </test>
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219 <test>
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220 <!-- Single-end example - gzipped -->
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221 <param name="single_or_paired" value="se" />
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222 <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
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223 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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224 <!--
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225 **NB** outputs have to be specified in order that they appear in the
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226 tool (which is the order they will be written to the history) - the
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227 test framework seems to use the order and ignores the "name" attribute
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228 -->
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229 <output name="fastq_out" file="trimmomatic_se_out1.fastq.gz" />
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230 </test>
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231 <test>
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232 <!-- Paired-end example - gzipped -->
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233 <param name="single_or_paired" value="pair_of_files" />
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234 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
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235 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz" />
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236 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
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237 <!--
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238 **NB** outputs have to be specified in order that they appear in the
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239 tool (which is the order they will be written to the history) - the
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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240 test framework seems to use the order and ignores the "name" attribute
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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241 -->
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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diff changeset
242 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq.gz" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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243 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
244 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
245 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
246 </test>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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247 <test>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
248 <!-- Paired-end example -->
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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249 <param name="single_or_paired" value="pair_of_files" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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250 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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251 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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252 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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253 <!--
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
254 **NB** outputs have to be specified in order that they appear in the
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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255 tool (which is the order they will be written to the history) - the
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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256 test framework seems to use the order and ignores the "name" attribute
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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257 -->
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
258 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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259 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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260 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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261 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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262 </test>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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263 <test>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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264 <!-- Single-end example (cropping) -->
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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265 <param name="single_or_paired" value="se" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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266 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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267 <param name="operations_0|operation|name" value="CROP" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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268 <param name="operations_0|operation|crop" value="10" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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269 <!--
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
270 **NB** outputs have to be specified in order that they appear in the
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
271 tool (which is the order they will be written to the history) - the
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
272 test framework seems to use the order and ignores the "name" attribute
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
273 -->
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
274 <output name="fastq_out" file="trimmomatic_se_out2.fastq" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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275 </test>
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sanbi-uwc
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276 <test>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
277 <!-- Paired-end with dataset collection -->
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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278 <param name="single_or_paired" value="collection" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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279 <param name="fastq_pair">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
280 <collection type="paired">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
281 <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
282 <element name="reverse" value="Illumina_SG_R2.fastq" ftype="fastqsanger"/>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
283 </collection>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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284 </param>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
285 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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286 <output_collection name="fastq_out_paired" type="paired">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
287 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
parents:
diff changeset
288 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
289 </output_collection>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
290 <output_collection name="fastq_out_unpaired" type="paired">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
291 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
292 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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293 </output_collection>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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294 </test>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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295 <test>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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296 <!-- Paired-end with dataset collection - gzipped -->
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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297 <param name="single_or_paired" value="collection" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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298 <param name="fastq_pair">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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299 <collection type="paired">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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300 <element name="forward" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
301 <element name="reverse" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz"/>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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302 </collection>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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303 </param>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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304 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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diff changeset
305 <output_collection name="fastq_out_paired" type="paired">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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306 <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq.gz" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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307 <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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308 </output_collection>
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sanbi-uwc
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309 <output_collection name="fastq_out_unpaired" type="paired">
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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310 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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311 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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312 </output_collection>
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sanbi-uwc
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313 </test>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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314 <test>
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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315 <!-- Single-end using AVGQUAL -->
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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316 <param name="single_or_paired" value="se" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
sanbi-uwc
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317 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
642a39a927c9 planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit b30cac62484ba664a19a02a6817752f4f2b140bf
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318 <param name="operations_0|operation|name" value="AVGQUAL" />
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319 <param name="operations_0|operation|avgqual" value="30" />
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320 <output name="fastq_out" file="trimmomatic_avgqual.fastq" />
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321 </test>
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322 <test>
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323 <!-- Single-end using MAXINFO -->
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324 <param name="single_or_paired" value="se" />
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325 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
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326 <param name="operations_0|operation|name" value="MAXINFO" />
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327 <param name="operations_0|operation|target_length" value="75" />
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328 <param name="operations_0|operation|strictness" value="0.8" />
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329 <output name="fastq_out" file="trimmomatic_maxinfo.fastq" />
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330 </test>
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331 </tests>
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332 <help><![CDATA[
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333 .. class:: infomark
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334
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335 **What it does**
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336
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337 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and
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338 single ended data.
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339
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340 This tool allows the following trimming steps to be performed:
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341
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342 * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read
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343 * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average
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344 quality within the window falls below a threshold
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345 * **MINLEN:** Drop the read if it is below a specified length
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346 * **LEADING:** Cut bases off the start of a read, if below a threshold quality
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347 * **TRAILING:** Cut bases off the end of a read, if below a threshold quality
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348 * **CROP:** Cut the read to a specified length
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349 * **HEADCROP:** Cut the specified number of bases from the start of the read
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350 * **AVGQUAL:** Drop the read if the average quality is below a specified value
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351 * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to
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352 maximise the value of each read
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353
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354 If ILLUMINACLIP is requested then it is always performed first; subsequent options
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355 can be mixed and matched and will be performed in the order that they have been
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356 specified.
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357
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358 .. class:: warningmark
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359
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360 Note that trimming operation order is important.
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361
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362 -------------
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363
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364 .. class:: infomark
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365
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366 **Inputs**
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367
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368 For single-end data this Trimmomatic tool accepts a single FASTQ file; for
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369 paired-end data it will accept either two FASTQ files (R1 and R2), or a
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370 dataset collection containing the R1/R2 FASTQ pair.
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371
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372 .. class:: infomark
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373
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374 **Outputs**
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375
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376 For paired-end data a particular strength of Trimmomatic is that it retains the
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377 pairing of reads (from R1 and R2) in the filtered output files:
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378
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379 * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where
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380 both have survived filtering.
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381 * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where
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382 one of the pair failed the filtering steps.
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383
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384 .. class:: warningmark
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385
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386 If the input consists of a dataset collection with the R1/R2 FASTQ pair then
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387 the outputs will also inclue two dataset collections: one for the 'paired'
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388 outputs and one for the 'unpaired' (as described above)
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389
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390 Retaining the same order and number of reads in the filtered output fastq files is
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391 essential for many downstream analysis tools.
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392
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393 For single-end data the output is a single FASTQ file containing just the filtered
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394 reads.
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395
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396 -------------
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397
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398 .. class:: infomark
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399
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400 **Credits**
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401
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402 This Galaxy tool has been developed within the Bioinformatics Core Facility at the
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403 University of Manchester. It runs the Trimmomatic program which has been developed
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404 within Bjorn Usadel's group at RWTH Aachen university.
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405
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406 Trimmomatic website (including documentation):
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407
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408 * http://www.usadellab.org/cms/index.php?page=trimmomatic
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409
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410 The reference for Trimmomatic is:
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411
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412 * Bolger, A.M., Lohse, M., &amp; Usadel, B. (2014). Trimmomatic: A flexible trimmer
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413 for Illumina Sequence Data. Bioinformatics, btu170.
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414
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415 Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you
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416 use it.
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417 ]]></help>
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418 <citations>
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419 <!--
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420 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
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421 Can be either DOI or Bibtex
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422 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
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423 -->
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424 <citation type="doi">10.1093/bioinformatics/btu170</citation>
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425 </citations>
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426 </tool>