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bsmap.xml |
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| diff -r 4f9b7eaecbd4 -r 413c742682f7 bsmap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bsmap.xml Fri Nov 30 09:14:33 2012 -0500 |
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| b'@@ -0,0 +1,237 @@\n+<tool id="bsmap" name="BSMAP Mapper">\n+\t<requirements>\n+\t <requirement type=\'package\'>\n+\t\tbsmap\n+\t </requirement>\n+\t</requirements>\n+ <command interpreter="bash">\n+ bsmap_wrapper.sh\n+\t\t\t##Reference genome\n+\t\t\t##ref="${reference.fields.path}"\n+\t\t\t#if $refGenomeSource.genomeSource == "history":\n+\t\t\t\tref="${refGenomeSource.myFile}"\n+\t\t\t#else\n+\t\t\t\tref="${refGenomeSource.builtinFile.fields.path}"\n+\t\t\t#end if\n+\t\t\t##Output files (SAM output, BSMAP summary)\n+\t\t\tmapped=$mapped\n+\t\t\t##Temp directory\n+\t\t\ttempdir=$mapped.files_path\n+\t\t\tsummary=$summary\n+\t\t\t#if str($singlePaired.sPaired) == "single":\n+\t\t\t library="single"\n+\t\t\t mate1=$singlePaired.sInput1\n+\t\t\t #if str($singlePaired.sParams.sSettingsType) == "full":\n+\t\t\t fullparam=true\n+\t\t\t qual=$singlePaired.sParams.qual\n+\t\t\t threshold=$singlePaired.sParams.threshold\n+\t\t\t lowqual=$singlePaired.sParams.lowqual\n+\t\t\t adapter=$singlePaired.sParams.adapter\n+\t\t\t firstn=$singlePaired.sParams.firstn\n+\t\t\t repeat_reads=$singlePaired.sParams.repeat_reads\n+\t\t\t seed_size=$singlePaired.sParams.seed_size\n+\t\t\t mismatch=$singlePaired.sParams.mismatch\n+\t\t\t equal_best=$singlePaired.sParams.equal_best\n+\t\t\t start=$singlePaired.sParams.start\n+\t\t\t end=$singlePaired.sParams.end\n+\t\t\t index_interval=$singlePaired.sParams.index_interval\n+\t\t\t seed_random=$singlePaired.sParams.seed_random\n+\t\t\t rrbs=$singlePaired.sParams.rrbs\n+\t\t\t mode=$singlePaired.sParams.mode\n+\t\t\t align_info=$singlePaired.sParams.align_info \n+\t\t\t #end if\n+\t\t\t#else:\n+\t\t\t library="paired"\n+\t\t\t mate1=$singlePaired.pInput1\n+\t\t\t mate2=$singlePaired.pInput2\n+\t\t\t unpaired=$unpaired\n+\t\t\t #if str($singlePaired.pParams.pSettingsType) == "full": \n+\t\t\t fullparam=true\n+\t\t\t qual=$singlePaired.pParams.qual\n+\t\t\t threshold=$singlePaired.pParams.threshold\n+\t\t\t lowqual=$singlePaired.pParams.lowqual\n+\t\t\t adapter=$singlePaired.pParams.adapter\n+\t\t\t firstn=$singlePaired.pParams.firstn\n+\t\t\t repeat_reads=$singlePaired.pParams.repeat_reads\n+\t\t\t seed_size=$singlePaired.pParams.seed_size\n+\t\t\t mismatch=$singlePaired.pParams.mismatch\n+\t\t\t equal_best=$singlePaired.pParams.equal_best\n+\t\t\t start=$singlePaired.pParams.start\n+\t\t\t end=$singlePaired.pParams.end\n+\t\t\t index_interval=$singlePaired.pParams.index_interval\n+\t\t\t seed_random=$singlePaired.pParams.seed_random\n+\t\t\t rrbs=$singlePaired.pParams.rrbs\n+\t\t\t mode=$singlePaired.pParams.mode\n+\t\t\t align_info=$singlePaired.pParams.align_info \n+\t\t\t maxinsert=$singlePaired.pParams.maxinsert \n+\t\t\t mininsert=$singlePaired.pParams.mininsert \n+\t\t\t #end if\n+\t\t\t#end if\n+ </command>\n+ <inputs>\n+\n+ <conditional name="refGenomeSource">\n+ <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in reference?">\n+ <option value="builtin">Use a built-in reference</option>\n+ <option value="history">Use one from the history</option>\n+ </param>\n+ <when value="builtin">\n+ <param name="builtinFile" type="select" label="Select the reference genome">\n+ <options from_data_table="bsmap_fasta">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No reference genomes are available" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="myFile" type="data" format="fasta" label="Select the reference genome" />\n+ </when> \n+ </conditional>\n+ \n+ <conditional name="singlePaired">\n+ <param name="sPaired" type="select" label="Is this library mate-paired?">\n+ <option value="single">Single-end</option>\n+ <option value="paired">Paired-end</option>\n+ </param>\n+ <when value="single">\n+ <param name="sInput1" type="data" format="fastq,fasta" label="FASTQ file" help="Must have ASCII encoded quality scores"/>\n+ <conditional name="sParams">\n+ '..b'+\t <option value="0">none(unique hit only)</option>\n+\t <option value="1">random one</option>\n+\t </param>\n+\t \n+\t <param name="seed_size" type="integer" value="16" label="Seed size" min="8" max="16" help="default=16(WGBS mode), 12(RRBS mode)" />\n+\t <param name="mismatch" type="integer" value="2" label="Maximum number of mismatches allowed on a read" max="15" />\n+\t <param name="equal_best" type="integer" value="20" label="Maximum number of equal best hits to count" max="1000" />\n+\t <param name="start" type="integer" value="1" label="Start from the Nth read or read pair" />\n+\t <param name="end" type="integer" value="4294967295" label="End at the Nth read or read pair" />\n+\t <param name="index_interval" type="integer" value="4" label="Index interval" />\n+\t <param name="seed_random" type="integer" value="-1" label="Seed for random number generation used in selecting multiple hits" help="other seed values generate pseudo random number based on read index number, to allow reproducible mapping results" />\n+\t <param name="rrbs" type="text" value="none" label="Activating RRBS mapping mode and set restriction enzyme digestion sites" help="digestion position marked by \'-\', example: -D C-CGG for MspI digestion. default: none (whole genome shotgun bisulfite mapping mode)" />\n+\t <param name="mode" type="select" label="Set mapping strand information">\n+\t\t<option value="0">only map to 2 forward strands</option>\n+\t\t<option value="1">map SE or PE reads to all 4 strands</option>\n+\t </param>\n+\t <param name="align_info" type="text" value="none" label="Set alignment information for the additional nucleotide transition" help="is in the form of two different nucleotides N1N2,indicating N1 in the reads could be mapped to N2 in the reference sequences. default: -M TC, corresponds to C=>U(T) transition in bisulfite conversion. example: -M GA could be used to detect A=>I(G) transition in RNA editing." />\n+\n+\t \n+ </when> <!-- full -->\n+ </conditional> <!-- pParams -->\n+ </when> <!-- paired -->\n+ </conditional> <!-- singlePaired -->\n+ \n+ \n+ </inputs>\n+ <outputs>\n+ <data name="mapped" format="sam" label="BSMAP Mapped Reads" />\n+\t<data name="summary" format="txt" label="BSMAP Mapping Summary" />\n+\t<data name="unpaired" format ="sam" label="BSMAP Unpaired Hits">\n+\t <filter>(singlePaired[\'sPaired\'] == \'paired\')</filter>\n+\t</data>\n+\n+ </outputs>\n+ <help>\n+**What it does**\n+\n+BSMAP is a short reads mapping software for bisulfite sequencing reads. It has the following features:\n+\n+ - read length up to 144 nt, allow up to 15 mismatches, gap size up to 3 bp.\n+\n+ - support single end and pair end mapping. support multi-thread mapping.\n+\n+ - support both "Lister protocol" (sequence 2 forward strands only) and "Cokus protocol" (sequence all 4 bisulfite converted strands)\n+\n+ - reads are directly mapped to original reference genome sequence, no need to preprocess the reads and reference genome to convert C to T.\n+\n+ - support both whole genome bisulfite sequencing (WGBS) mode and reduced representation bisulfite sequencing (RRBS) mode, allow changing the digestion site information to support different digestion enzymes for RRBS.\n+\n+ - allow trimming adapter sequences and low quality nucleotides from the 3\'end of reads\n+\n+ - allow trade off between speed/memory usage/mapping sensitivity. For human genome, the RRBS mode uses ~3GB. In WGBS mode, the typical memory usage is ~9GB, but can be as low as 5GB.\n+\n+ - allow alignment for other nucleotide transitions, for example, can be set to detect the A=>I(G) transition in RNA editing.\n+\n+.. _BSMAP: http://code.google.com/p/bsmap/\n+\n+**Input formats**\n+\n+BSMAP accepts files in FASTA/FASTQ format.\n+\n+**Outputs**\n+\n+The output contains the following files:\n+\n+ - mapped reads in SAM format\n+ \n+ - mapping summary\n+ \n+ - unpaired hits (only for paired-end mapping)\n+ \n+ </help>\n+ \n+ <tests>\n+ </tests>\n+</tool>\n+\n' |