Mercurial > repos > bgruening > bismark
diff bismark_bowtie_wrapper.xml @ 4:243e8f9fb75b draft
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 09 Feb 2015 18:24:41 -0500 |
| parents | 91f07ff056ca |
| children | b100248c35b8 |
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--- a/bismark_bowtie_wrapper.xml Mon Apr 14 16:43:14 2014 -0400 +++ b/bismark_bowtie_wrapper.xml Mon Feb 09 18:24:41 2015 -0500 @@ -7,11 +7,17 @@ <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="0.12.8">bowtie</requirement> </requirements> - <parallelism method="basic"></parallelism> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> <command interpreter="python"> +<![CDATA[ bismark_wrapper.py - --bismark_path \$SCRIPT_PATH + ##--bismark_path \$SCRIPT_PATH ## ## Bismark Genome Preparation, if desired. @@ -53,14 +59,17 @@ --mate1 #echo ','.join($mate1) --mate2 #echo ','.join($mate2) - #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina": - --phred64-quals - --fastq - #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger": - --fastq - #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta": - --fasta - #end if + #for $mate_pair in $singlePaired.mate_list: + #if $mate_pair.input_mate1.ext == "fastqillumina": + --phred64-quals + --fastq + #elif $mate_pair.input_mate1.ext == "fastqsanger": + --fastq + #elif $mate_pair.input_mate1.ext == "fasta": + --fasta + #end if + #break + #end for -I $singlePaired.minInsert -X $singlePaired.maxInsert @@ -123,6 +132,7 @@ #end if #end if +]]> </command> <inputs> <conditional name="refGenomeSource"> @@ -191,7 +201,7 @@ <!-- output Options --> <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" /> <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" /> - <!--end output options --> + <!--end output options --> </when> <!-- full --> </conditional> <!-- params --> <!-- @@ -251,9 +261,9 @@ </action> </when> <when value="paired"> - <action type="format"> + <!--action type="format"> <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> - </action> + </action--> </when> </conditional> </actions> @@ -271,9 +281,9 @@ </action> </when> <when value="paired"> - <action type="format"> + <!--action type="format"> <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> - </action> + </action--> </when> </conditional> </actions> @@ -295,9 +305,9 @@ </action> </when> <when value="paired"> - <action type="format"> + <!--action type="format"> <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> - </action> + </action--> </when> </conditional> </actions> @@ -314,21 +324,20 @@ </action> </when> <when value="paired"> - <action type="format"> + <!--action type="format"> <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> - </action> + </action--> </when> </conditional> </actions> </data> - - </outputs> <tests> </tests> <help> +<![CDATA[ **What it does** @@ -386,8 +395,8 @@ Column Description -------- -------------------------------------------------------- 1 QNAME seq-ID - 2 FLAG this flag tries to take the strand a bisulfite read - originated from into account + 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 @@ -399,12 +408,12 @@ 10 SEQ query SEQuence on the same strand as the reference 11 QUAL Phred33 scale 12 NM-tag edit distance to the reference) - 13 XX-tag base-by-base mismatches to the reference. + 13 XX-tag base-by-base mismatches to the reference. This does not include 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 - + Each read of paired-end alignments is written out in a separate line in the above format. @@ -461,7 +470,7 @@ --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off. --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled - (which can't). The formula for conversion is: + (which can't). The formula for conversion is: phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This is usually the right option for use with (unconverted) reads emitted by the GA Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off. @@ -473,7 +482,7 @@ Alignment:: -n/--seedmms INT The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs - of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the + of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N). -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to @@ -546,5 +555,9 @@ the specified folder does not exist, Bismark will attempt to create it first. The path to the temporary folder can be either relative or absolute. +]]> </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr167</citation> + </citations> </tool>