Mercurial > repos > bjoern-gruening > bismark
diff bismark_bowtie2_wrapper.xml @ 4:427fb56f2e41 draft default tip
- new options
- fixes
| author | bjoern-gruening |
|---|---|
| date | Fri, 01 Mar 2013 13:39:22 -0500 |
| parents | 36d124f44c0a |
| children |
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--- a/bismark_bowtie2_wrapper.xml Tue Dec 25 05:54:01 2012 -0500 +++ b/bismark_bowtie2_wrapper.xml Fri Mar 01 13:39:22 2013 -0500 @@ -12,7 +12,7 @@ bismark_wrapper.py ## Change this to accommodate the number of threads you have available. - --num-threads 4 + --num-threads 12 --bismark_path \$SCRIPT_PATH @@ -47,16 +47,23 @@ --fasta #end if #else: - --mate-paired - --mate1 $singlePaired.input_mate1 - --mate2 $singlePaired.input_mate2 + --mate-paired + #set $mate1 = list() + #set $mate2 = list() + #for $mate_pair in $singlePaired.mate_list + $mate1.append( str($mate_pair.input_mate1) ) + $mate2.append( str($mate_pair.input_mate2) ) + #end for - #if $singlePaired.input_mate1.ext == "fastqillumina": + --mate1 #echo ','.join($mate1) + --mate2 #echo ','.join($mate2) + + #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina": --phred64-quals --fastq - #elif $singlePaired.input_mate1.ext == "fastqsanger": + #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger": --fastq - #elif $singlePaired.input_mate1.ext == "fasta": + #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta": --fasta #end if @@ -157,8 +164,10 @@ <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." /> </when> <when value="paired"> - <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." /> - <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." /> + <repeat name="mate_list" title="Paired End Pairs" min="1"> + <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." /> + <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." /> + </repeat> <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" /> <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /> </when> @@ -247,7 +256,7 @@ </when> <when value="paired"> <action type="format"> - <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> + <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> </action> </when> </conditional> @@ -267,7 +276,7 @@ </when> <when value="paired"> <action type="format"> - <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> + <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> </action> </when> </conditional> @@ -291,7 +300,7 @@ </when> <when value="paired"> <action type="format"> - <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> + <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> </action> </when> </conditional> @@ -310,7 +319,7 @@ </when> <when value="paired"> <action type="format"> - <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> + <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> </action> </when> </conditional> @@ -353,6 +362,11 @@ .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ + +.. class:: warningmark + +Make sure all your input reads are in the correct and same format. If thats not the case please adjust/convert the filetype with galaxy's build-in converters. + ------ **Input formats** @@ -415,12 +429,7 @@ **Bismark parameter list** -This is an exhaustive list of Bismark options: - ------- - -**OPTIONS** - +This is an exhaustive list of Bismark options. Input::