Mercurial > repos > sanbi-uwc > trimmomatic
changeset 2:5c5a2a7e9cbb draft
planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 213668d2e5a61c806ad992c201ae6e304c6e0965
| author | sanbi-uwc |
|---|---|
| date | Fri, 20 Jan 2017 13:35:17 -0500 |
| parents | bbe75c52b300 |
| children | f6cb99d6afd3 |
| files | trimmomatic.xml |
| diffstat | 1 files changed, 107 insertions(+), 135 deletions(-) [+] |
line wrap: on
line diff
--- a/trimmomatic.xml Fri Jan 20 08:57:21 2017 -0500 +++ b/trimmomatic.xml Fri Jan 20 13:35:17 2017 -0500 @@ -4,24 +4,21 @@ <requirement type="package" version="0.36">trimmomatic</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ - #if $paired_end.is_paired_end - #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type - #if $paired_input_type == "pair_of_files" - #set r1_ext = $paired_end.paired_input_type_conditional.fastq_r1_in.extension - #set r2_ext = $paired_end.paired_input_type_conditional.fastq_r2_in.extension - ln -s '${paired_end.paired_input_type_conditional.fastq_r1_in}' fastq_r1.'$r1_ext' && - ln -s '${paired_end.paired_input_type_conditional.fastq_r2_in}' fastq_r2.'$r2_ext' && - #else - #set r1_ext = $paired_end.paired_input_type_conditional.fastq_pair.forward.extension - #set r2_ext = $paired_end.paired_input_type_conditional.fastq_pair.reverse.extension - ln -s '${paired_end.paired_input_type_conditional.fastq_pair.forward}' fastq_r1.'$r1_ext' && - ln -s '${paired_end.paired_input_type_conditional.fastq_pair.reverse}' fastq_r2.'$r2_ext' && - #end if + #if $readtype.single_or_paired == "pair_of_files" + #set r1_ext = $readtype.fastq_r1_in.extension + #set r2_ext = $readtype.fastq_r2_in.extension + ln -s '$readtype.fastq_r1_in' fastq_r1.'$r1_ext' && + ln -s '$readtype.fastq_r2_in' fastq_r2.'$r2_ext' && + #elif $readtype.single_or_paired == "collection" + #set r1_ext = $readtype.fastq_pair.forward.extension + #set r2_ext = $readtype.fastq_pair.reverse.extension + ln -s '$readtype.fastq_pair.forward' fastq_r1.'$r1_ext' && + ln -s '$readtype.fastq_pair.reverse' fastq_r2.'$r2_ext' && #else - ln -s '$fastq_in' fastq_in.'$fastq_in.extension' && + ln -s '$fastq_in' fastq_in.'$fastq_in.extension' && #end if bash '${__tool_directory__}/trimmomatic.sh' - #if $paired_end.is_paired_end + #if $readtype.single_or_paired in ["pair_of_files","collection"] PE -threads \${GALAXY_SLOTS:-6} -phred33 fastq_r1.'$r1_ext' fastq_r2.'$r2_ext' fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext' @@ -63,59 +60,50 @@ #end if #end for && - #if $paired_end.is_paired_end - #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type - #if $paired_input_type == "pair_of_files" - mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' && - mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' && - mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' && - mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}' - #else - mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' && - mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' && - mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' && - mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}' - #end if + #if $readtype.single_or_paired == "pair_of_files" + mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' && + mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' && + mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' && + mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}' + #elif $readtype.single_or_paired == "collection" + mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' && + mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' && + mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' && + mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}' #else mv fastq_out.'$fastq_in.extension' '${fastq_out}' #end if ]]></command> <inputs> - <conditional name="paired_end"> - <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="True" /> - <when value="no"> - <param name="fastq_in" type="data" format="fastqsanger|fastqsanger.gz" label="Input FASTQ file" /> - </when> - <when value="yes"> - <conditional name="paired_input_type_conditional"> - <param name="paired_input_type" type="select" label="Input Type"> - <option value="pair_of_files" selected="true">Pair of datasets</option> - <option value="collection">Dataset collection pair</option> + <conditional name="readtype"> + <param name="single_or_paired" type="select" label="Single-end or paired-end reads?"> + <option value="se" selected="true">Single-end</option> + <option value="pair_of_files">Paired-end (two separate input files)</option> + <option value="collection">Paired-end (as collection)</option> </param> - <when value="pair_of_files"> - <param name="fastq_r1_in" type="data" format="fastqsanger|fastqsanger.gz" - label="Input FASTQ file (R1/first of pair)" /> - <param name="fastq_r2_in" type="data" format="fastqsanger|fastqgsanger.gz" - label="Input FASTQ file (R2/second of pair)" /> - </when> + <when value="se"> + <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file" /> + </when> + <when value="pair_of_files"> + <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz" + label="Input FASTQ file (R1/first of pair)" /> + <param name="fastq_r2_in" type="data" format="fastqsanger,fastqgsanger.gz" + label="Input FASTQ file (R2/second of pair)" /> + </when> <when value="collection"> - <param name="fastq_pair" format="fastqsanger|fastqsanger.gz" type="data_collection" - collection_type="paired" - label="Select FASTQ dataset collection with R1/R2 pair" /> + <param name="fastq_pair" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" /> </when> </conditional> - </when> - </conditional> <conditional name="illuminaclip"> <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" /> <when value="yes"> <param name="adapter_fasta" type="select" label="Adapter sequences to use"> - <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option> - <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option> - <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option> - <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option> - <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option> - <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option> + <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option> + <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option> + <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option> + <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option> + <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option> + <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option> </param> <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" /> <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" /> @@ -125,91 +113,77 @@ </conditional> <repeat name="operations" title="Trimmomatic Operation" min="1"> <conditional name="operation"> - <param name="name" type="select" label="Select Trimmomatic operation to perform"> - <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option> - <option value="MINLEN">Drop reads below a specified length (MINLEN)</option> - <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option> - <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option> - <option value="CROP">Cut the read to a specified length (CROP)</option> - <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option> - <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option> - <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option> - </param> - <when value="SLIDINGWINDOW"> - <param name="window_size" type="integer" label="Number of bases to average across" value="4" /> - <param name="required_quality" type="integer" label="Average quality required" value="20" /> - </when> - <when value="MINLEN"> - <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" /> - </when> - <when value="LEADING"> - <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" /> - </when> - <when value="TRAILING"> - <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" /> - </when> - <when value="CROP"> - <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" /> - </when> - <when value="HEADCROP"> - <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" /> - </when> - <when value="AVGQUAL"> - <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" /> - </when> - <when value="MAXINFO"> - <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." /> - <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 (<0.2) favours longer reads, high values (>0.8) favours read correctness." /> - </when> + <param name="name" type="select" label="Select Trimmomatic operation to perform"> + <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option> + <option value="MINLEN">Drop reads below a specified length (MINLEN)</option> + <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option> + <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option> + <option value="CROP">Cut the read to a specified length (CROP)</option> + <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option> + <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option> + <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</option> + </param> + <when value="SLIDINGWINDOW"> + <param name="window_size" type="integer" label="Number of bases to average across" value="4" /> + <param name="required_quality" type="integer" label="Average quality required" value="20" /> + </when> + <when value="MINLEN"> + <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" /> + </when> + <when value="LEADING"> + <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" /> + </when> + <when value="TRAILING"> + <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" /> + </when> + <when value="CROP"> + <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" /> + </when> + <when value="HEADCROP"> + <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" /> + </when> + <when value="AVGQUAL"> + <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" /> + </when> + <when value="MAXINFO"> + <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." /> + <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 (<0.2) favours longer reads, high values (>0.8) favours read correctness." /> + </when> </conditional> </repeat> </inputs> <outputs> - <data name="fastq_out_r1_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 paired)" - format_source="${paired_end.paired_input_type_conditional.fastq_r1_in}"> - <filter>paired_end['is_paired_end']</filter> - <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> + <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in"> + <filter>readtype['single_or_paired'] == "pair_of_files"</filter> </data> - <data name="fastq_out_r2_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 paired)" - format_source="${paired_end.paired_input_type_conditional.fastq_r2_in}"> - <filter>paired_end['is_paired_end']</filter> - <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> + <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in"> + <filter>readtype['single_or_paired'] == "pair_of_files"</filter> </data> - <data name="fastq_out_r1_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 unpaired)" - format_source="${paired_end.paired_input_type_conditional.fastq_r1_in}"> - <filter>paired_end['is_paired_end']</filter> - <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> + <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in"> + <filter>readtype['single_or_paired'] == "pair_of_files"</filter> </data> - <data name="fastq_out_r2_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 unpaired)" - format_source="${paired_end.paired_input_type_conditional.fastq_r1_in}"> - <filter>paired_end['is_paired_end']</filter> - <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter> + <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in"> + <filter>readtype['single_or_paired'] == "pair_of_files"</filter> </data> - <data name="fastq_out" label="${tool.name} on ${paired_end.fastq_in.name}" - format_source="${fastq_in}"> - <filter>not paired_end['is_paired_end']</filter> + <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in"> + <filter>readtype['single_or_paired'] == 'se'</filter> </data> - <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: paired"> - <data name="forward" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 paired)" - format_source="${paired_end.paired_input_type_conditional.fastq_pair.forward}" /> - <data name="reverse" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 paired)" - format_source="${paired_end.paired_input_type_conditional.fastq_pair.reverse}" /> - <filter>paired_end['is_paired_end']</filter> - <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter> + <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: paired"> + <filter>readtype['single_or_paired'] == "collection"</filter> + <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/> + <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/> </collection> - <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: unpaired"> - <data name="forward" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 unpaired)" - format_source="${paired_end.paired_input_type_conditional.fastq_pair.forward}" /> - <data name="reverse" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 unpaired)" - format_source="${paired_end.paired_input_type_conditional.fastq_pair.reverse}" /> - <filter>paired_end['is_paired_end']</filter> - <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter> + <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: unpaired"> + <filter>readtype['single_or_paired'] == "collection"</filter> + <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/> + <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/> </collection> + </outputs> <tests> <test> <!-- Single-end example --> - <param name="is_paired_end" value="no" /> + <param name="single_or_paired" value="se" /> <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> <!-- @@ -221,7 +195,7 @@ </test> <test> <!-- Single-end example - gzipped --> - <param name="is_paired_end" value="no" /> + <param name="single_or_paired" value="se" /> <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" /> <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> <!-- @@ -233,7 +207,7 @@ </test> <test> <!-- Paired-end example - gzipped --> - <param name="is_paired_end" value="yes" /> + <param name="single_or_paired" value="pair_of_files" /> <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" /> <param name="fastq_r2_in" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz" /> <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> @@ -249,7 +223,7 @@ </test> <test> <!-- Paired-end example --> - <param name="is_paired_end" value="yes" /> + <param name="single_or_paired" value="pair_of_files" /> <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> @@ -265,7 +239,7 @@ </test> <test> <!-- Single-end example (cropping) --> - <param name="is_paired_end" value="no" /> + <param name="single_or_paired" value="se" /> <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> <param name="operations_0|operation|name" value="CROP" /> <param name="operations_0|operation|crop" value="10" /> @@ -278,8 +252,7 @@ </test> <test> <!-- Paired-end with dataset collection --> - <param name="is_paired_end" value="yes" /> - <param name="paired_input_type" value="collection" /> + <param name="single_or_paired" value="collection" /> <param name="fastq_pair"> <collection type="paired"> <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> @@ -298,8 +271,7 @@ </test> <test> <!-- Paired-end with dataset collection - gzipped --> - <param name="is_paired_end" value="yes" /> - <param name="paired_input_type" value="collection" /> + <param name="single_or_paired" value="collection" /> <param name="fastq_pair"> <collection type="paired"> <element name="forward" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" /> @@ -318,7 +290,7 @@ </test> <test> <!-- Single-end using AVGQUAL --> - <param name="is_paired_end" value="no" /> + <param name="single_or_paired" value="se" /> <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> <param name="operations_0|operation|name" value="AVGQUAL" /> <param name="operations_0|operation|avgqual" value="30" /> @@ -326,7 +298,7 @@ </test> <test> <!-- Single-end using MAXINFO --> - <param name="is_paired_end" value="no" /> + <param name="single_or_paired" value="se" /> <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> <param name="operations_0|operation|name" value="MAXINFO" /> <param name="operations_0|operation|target_length" value="75" />