Mercurial > repos > eugen > bs_seq_test_1
changeset 6:4d48b068b0b4 draft
Deleted selected files
author | eugen |
---|---|
date | Mon, 13 Aug 2012 08:21:18 -0400 |
parents | a6a7cf30cac7 |
children | 34b9847d154d |
files | bismark.xml |
diffstat | 1 files changed, 0 insertions(+), 181 deletions(-) [+] |
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--- a/bismark.xml Mon Aug 13 08:12:54 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,181 +0,0 @@ -<tool id="bismark" name="Bismark Mapper" version="0.7.3"> - <command interpreter="bash"> - bismark_wrapper.sh - ##Reference genome - ref="${indices.fields.path}" - ##Output files (SAM output, Bismark summary) - mapped=$mapped - summary=$summary - ##Temp directory - tempdir=$mapped.files_path - #if str($singlePaired.sPaired) == "single": - library=single - mate1=$singlePaired.sInput1 - #if $singlePaired.sParams.sSettingsType == "full": - fullparam=true - qual=$singlePaired.sParams.qual - seedmms=$singlePaired.sParams.seedmms - seedlen=$singlePaired.sParams.seedlen - maqerr=$singlePaired.sParams.maqerr - directional=$singlePaired.sParams.non_directional - header=$singlePaired.sParams.sam_no_hd - #end if - #else: - library=paired - mate1=$singlePaired.pInput1 - mate2=$singlePaired.pInput2 - #if $singlePaired.pParams.pSettingsType == "full": - fullparam="true" - qual=$singlePaired.pParams.qual - seedmms=$singlePaired.pParams.seedmms - seedlen=$singlePaired.pParams.seedlen - maqerr=$singlePaired.pParams.maqerr - directional=$singlePaired.pParams.non_directional - header=$singlePaired.pParams.sam_no_hd - minins=$singlePaired.pParams.minins - maxins=$singlePaired.pParams.maxins - #end if - #end if - - - </command> - <inputs> - <param name="indices" type="select" label="Select a reference genome"> - <options from_data_table="bismark_bs_indeces"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - - <conditional name="singlePaired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="sInput1" type="data" format="fastq" label="FASTQ file" help="Must have ASCII encoded quality scores"/> - <conditional name="sParams"> - <param name="sSettingsType" type="select" label="Bismark settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> - <option value="preSet">Commonly used</option> - <option value="full">Full parameter list</option> - </param> - <when value="preSet" /> - <when value="full"> - <param name="qual" type="select" label="Select the type of FastQ qualities"> - <option value="--phred33-quals">phred33-quals</option> - <option value="--phred64-quals">phred64-quals</option> - <option value="--solexa-quals">solexa-quals</option> - </param> - <param name="seedmms" type="integer" value="2" label="The maximum number of mismatches permitted in the seed" /> - <param name="seedlen" type="integer" value="28" label="The seed length" /> - <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the seed" /> - <param name="non_directional" type="select" label="Is the library a non-directional one?"> - <option value="">No</option> - <option value="--non_directional">Yes</option> - </param> - <param name="sam_no_hd" type="select" label="Should the SAM header lines (starting with @) be supressed?"> - <option value="">No</option> - <option value="--sam-no-hd">Yes</option> - </param> - </when> <!-- full --> - </conditional> <!-- sParams --> - </when> <!-- single --> - - <when value="paired"> - <param name="pInput1" type="data" format="fastq" label="Forward FASTQ file" /> - <param name="pInput2" type="data" format="fastq" label="Reverse FASTQ file" /> - - <conditional name="pParams"> - <param name="pSettingsType" type="select" label="Bismark settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> - <option value="preSet">Commonly used</option> - <option value="full">Full parameter list</option> - </param> - <when value="preSet" /> - <when value="full"> - <param name="minins" type="integer" value="0" label="The minimum insert size for valid paired-end alignments" /> - <param name="maxins" type="integer" value="500" label="The maximum insert size for valid paired-end alignments" /> - <param name="qual" type="select" label="Select the type of FastQ qualities"> - <option value="--phred33-quals">phred33-quals</option> - <option value="--phred64-quals">phred64-quals</option> - <option value="--solexa-quals">solexa-quals</option> - </param> - <param name="seedmms" type="integer" value="2" label="The maximum number of mismatches permitted in the seed" /> - <param name="seedlen" type="integer" value="28" label="The seed length" /> - <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the seed" /> - <param name="non_directional" type="select" label="Is the library a non-directional one?"> - <option value="">No</option> - <option value="--non_directional">Yes</option> - </param> - <param name="sam_no_hd" type="select" label="Should the SAM header lines (starting with @) be supressed?"> - <option value="">No</option> - <option value="--sam-no-hd">Yes</option> - </param> - </when> <!-- full --> - </conditional> <!-- pParams --> - </when> <!-- paired --> - </conditional> <!-- singlePaired --> - - - </inputs> - <outputs> - <data name="mapped" format="sam" label="Bismark Mapped Reads" /> - <data name="summary" format ="txt" label="Bismark Mapping Summary" /> - </outputs> - <help> -**What it does** - -Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. It's main features are: - - - Bisulfite mapping and methylation calling in one single step - - - Supports single-end and paired-end read alignments - - - Supports ungapped and gapped alignments - - - Alignment seed length, number of mismatches etc. are adjustable - - - Output discriminates between cytosine methylation in CpG, CHG and CHH context - -.. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ - -**Input formats** - -Bismark accepts files in Sanger FASTQ format. - -**Outputs** - -The output is in SAM format, and has the following columns:: - - Column Description - -------- -------------------------------------------------------- - 1 QNAME seq-ID - 2 FLAG this flag tries to take the strand a bisulfite read originated from into account (this is different from ordinary DNA alignment flags!) - 3 RNAME chromosome - 4 POS start position - 5 MAPQ always 255 - 6 CIGAR - 7 RNEXT - 8 PNEXT - 9 TLEN - 10 SEQ - 11 QUAL Phred33 scale - 12 NM-tag edit distance to the reference - 13 XX-tag base-by-base mismatches to the reference, not including indels - 14 XM-tag methylation call string - 15 XR-tag read conversion state for the alignment - 16 XG-tag genome conversion state for the alignment - - </help> - - <tests> - <test> - <param name="sPaired" value="single" /> - <param name="indices" value="bismark" /> - <param name="sInput1" ftype="fastq" value="bismark_test_single.fastq" /> - <param name="sParams" value="preSet" /> - <output name="mapped" ftype="SAM" file="bismark_result_single_1.SAM" /> - <ouput name="summary" ftype="txt" file="bismark_result_single_2.txt" /> - </test> - </tests> -</tool> -