Mercurial > repos > nikhil-joshi > sickle
changeset 2:e52679b44700 draft
Uploaded
author | nikhil-joshi |
---|---|
date | Tue, 06 Aug 2013 23:10:54 -0400 |
parents | 7b37c85ba925 |
children | f6ebdaca9925 |
files | sickle/sickle.xml |
diffstat | 1 files changed, 37 insertions(+), 17 deletions(-) [+] |
line wrap: on
line diff
--- a/sickle/sickle.xml Tue Aug 06 23:10:08 2013 -0400 +++ b/sickle/sickle.xml Tue Aug 06 23:10:54 2013 -0400 @@ -5,11 +5,33 @@ sickle $readtype.single_or_paired --quiet #if str($readtype.single_or_paired) == "se": - -f $input_single -t $qual_type -o $output_single + -f $input_single -o $output_single + + #if $input_single.ext == "fastq": + -t sanger + #else if $input_single.ext == "fastqsanger": + -t sanger + #else if $input_single.ext == "fastqillumina": + -t illumina + #else if $input_single.ext == "fastqsolexa": + -t solexa + #end if + #end if #if str($readtype.single_or_paired) == "pe": - -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single -t $qual_type + -f $input_paired1 -r $input_paired2 -o $output_paired1 -p $output_paired2 -s $output_paired_single + + #if $input_paired1.ext == "fastq": + -t sanger + #else if $input_single.ext == "fastqsanger": + -t sanger + #else if $input_single.ext == "fastqillumina": + -t illumina + #else if $input_single.ext == "fastqsolexa": + -t solexa + #end if + #end if #if str($qual_threshold) != "": @@ -31,27 +53,21 @@ <inputs> <conditional name="readtype"> - <param name="single_or_paired" type="select" optional="false" label="Single-End or Paired-End reads?"> + <param name="single_or_paired" type="select" optional="false" label="Single-End or Paired-End reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger."> <option value="se" selected="true">Single-End</option> <option value="pe">Paired-End</option> </param> <when value="se"> - <param format="fastq, fastqsanger" name="input_single" type="data" optional="false" label="Single-End FastQ Reads"/> + <param format="fastq, fastqsanger, fastqillumina, fastqsolexa" name="input_single" type="data" optional="false" label="Single-End FastQ Reads"/> </when> <when value="pe"> - <param format="fastq, fastqsanger" name="input_paired1" type="data" optional="false" label="Paired-End Forward Strand FastQ Reads"/> - <param format="fastq, fastqsanger" name="input_paired2" type="data" optional="false" label="Paired-End Reverse Strand FastQ Reads"/> + <param format="fastq, fastqsanger, fastqillumina, fastqsolexa" name="input_paired1" type="data" optional="false" label="Paired-End Forward Strand FastQ Reads"/> + <param format="fastq, fastqsanger, fastqillumina, fastqsolexa" name="input_paired2" type="data" optional="false" label="Paired-End Reverse Strand FastQ Reads"/> </when> </conditional> - <param name="qual_type" type="select" optional="false" label="Quality type"> - <option value="illumina" selected="true">Illumina</option> - <option value="solexa">Solexa</option> - <option value="sanger">Sanger</option> - </param> - <param name="qual_threshold" value="20" type="integer" optional="true" label="Quality Threshold"> <validator type="in_range" min="0" message="Minimum value is 0"/> </param> @@ -65,19 +81,19 @@ </inputs> <outputs> - <data format="fastq" name="output_single" label="Single-End output of ${tool.name} on ${on_string}"> + <data format_source="input_single" name="output_single" label="Single-End output of ${tool.name} on ${on_string}"> <filter>(readtype['single_or_paired'] == 'se')</filter> </data> - <data format="fastq" name="output_paired1" label="Paired-End forward strand output of ${tool.name} on ${on_string}"> + <data format_source="input_paired1" name="output_paired1" label="Paired-End forward strand output of ${tool.name} on ${on_string}"> <filter>(readtype['single_or_paired'] == 'pe')</filter> </data> - <data format="fastq" name="output_paired2" label="Paired-End reverse strand output of ${tool.name} on ${on_string}"> + <data format_source="input_paired2" name="output_paired2" label="Paired-End reverse strand output of ${tool.name} on ${on_string}"> <filter>(readtype['single_or_paired'] == 'pe')</filter> </data> - <data format="fastq" name="output_paired_single" label="Singletons from Paired-End output of ${tool.name} on ${on_string}"> + <data format_source="input_paired1" name="output_paired_single" label="Singletons from Paired-End output of ${tool.name} on ${on_string}"> <filter>(readtype['single_or_paired'] == 'pe')</filter> </data> </outputs> @@ -89,11 +105,15 @@ Sickle also has an option to discard reads with any Ns in them. -Sickle supports three types of quality values: Illumina, Solexa, and Sanger. Note that the Solexa quality setting is an approximation (the actual conversion is a non-linear transformation). The end approximation is close. Illumina quality refers to qualities encoded with the CASAVA pipeline between versions 1.3 and 1.7. Illumina quality using CASAVA >= 1.8 is Sanger encoded. +Sickle supports three types of quality values: Illumina, Solexa, and Sanger. Note that the Solexa quality setting is an approximation (the actual conversion is a non-linear transformation). The end approximation is close. Illumina quality refers to qualities encoded with the CASAVA pipeline between versions 1.3 and 1.7. Illumina quality using CASAVA >= 1.8 is Sanger encoded. Sickle will get the quality type from the datatype of the file. Note that Sickle will remove the 2nd fastq record header (on the "+" line) and replace it with simply a "+". This is the default format for CASAVA >= 1.8. Sickle also supports gzipped file inputs. + +Copyright: Nikhil Joshi +http://bioinformatics.ucdavis.edu +http://github.com/ucdavis-bioinformatics </help> </tool>