| Previous changeset 7:be88d0f3f6f2 (2012-11-29) Next changeset 9:385d004f3cb1 (2012-11-30) |
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Commit message:
Deleted selected files |
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removed:
bsmap.xml |
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| diff -r be88d0f3f6f2 -r 3faf4b952701 bsmap.xml --- a/bsmap.xml Thu Nov 29 10:14:57 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,229 +0,0 @@\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\tref="${reference.fields.path}"\n-\t\t\t##Output files (SAM output, BSMAP summary)\n-\t\t\tmapped=$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- <param name="reference" type="select" label="Select a reference genome">\n-\t \t<options from_data_table="all_fasta">\n-\t\t \t<filter type="sort_by" column="2" />\n-\t \t<validator type="no_options" message="No reference genomes are available" />\n- \t\t</options>\n- </param>\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- <param name="sSettingsType" type="select" label="BSMAP settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">\n- <option value="preSet">Commonly used</option>\n- <option value="full">Full parameter list</option>\n- </param>\n- <when value="preSet" />\n- <when value="full">\n-\t <param name="qual" type="select" label="Select the type of FastQ qualities">\n-\t\t<option value="33">phred33-quals</option>\n-\t\t<option value="64">phred64-quals</option>\n-\t </param>\n-\t <param name="threshold" type="integer" value="0" label="Quality threshold in trimming" help="0-40, default=0 (no trim)" min="0" '..b'ismatches 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 <actions>\n-\t\t<action type="metadata" name="dbkey">\n-\t\t <option type="from_data_table" name="bsmap_fasta" column="1" offset="0">\n-\t\t\t<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>\n-\t\t\t<filter type="param_value" ref="reference" column="0"/>\n-\t\t </option>\n-\t\t</action>\n-\t </actions>\t \n-\t</data>\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' |