Mercurial > repos > joachim-jacob > qualimap_suite
annotate bamqc.xml @ 4:3d690162d629 draft
Added more details for the required dependencies.
| author | Joachim Jacob <joachim.jacob@gmail.com> |
|---|---|
| date | Wed, 20 Mar 2013 09:35:07 +0100 |
| parents | 9537dd9dd18b |
| children |
| rev | line source |
|---|---|
| 2 | 1 |
|
4
3d690162d629
Added more details for the required dependencies.
Joachim Jacob <joachim.jacob@gmail.com>
parents:
3
diff
changeset
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2 <tool id="qualimap_bamqc" name="Analyse SAM/BAM with bamqc" version="1.0.1"> |
| 2 | 3 <!-- Additional info: wrapper compatible with versions ..... --> |
| 4 <description> | |
| 5 to asses mapping quality metrics. | |
| 6 </description> | |
| 7 | |
| 8 <version_command> | |
| 9 qualimap --version | |
| 10 </version_command> | |
| 11 | |
| 12 <requirements> | |
| 13 <requirement type="package">qualimap</requirement> | |
| 14 </requirements> | |
| 15 | |
| 16 <command interpreter="perl"> | |
| 17 ## it is recommended that you write a wrapper for your tool | |
| 18 ## and pass all parameters to that tool, which parses them. | |
| 19 bamqc_wrapper.pl $configfile | |
| 20 </command> | |
| 21 | |
| 22 <inputs> | |
| 23 <param format="sam,bam" name="bam" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." /> | |
| 24 <param type="boolean" name="c" checked="TRUE" truevalue="-c" falsevalue="" label="paint chromosome limits inside charts" /> | |
| 25 <conditional name="customgtf"> | |
| 26 <param name="upload" type="select" label="BETA! Analyze the alignment data for the regions of interest you provide"> | |
| 27 <option value="yes">Yes</option> | |
| 28 <option value="no" selected="true">No</option> | |
| 29 </param> | |
| 30 <when value="yes"> | |
| 31 <param name="gff" type="data" format="bed,gtf,gff3" label="Choose your feature annotation file" help="Provide your BED, GTF or GFF file"/> | |
| 32 <param name="os" type="boolean" checked="FALSE" truevalue="-os" falsevalue="" label="compute also regions outside stats" help="If checked, the information about the reads that are mapped outside of the regions of interest will be also computed and shown in a separate section" /> | |
| 33 <param type="select" name="p" label="The sequencing protocol strand specificity" help="Can be non-strand-specific, forward-stranded orreverse-stranded. This information is required to calculate the number of correct strand reads."> | |
| 34 <option value="NON-STRAND-SPECIFIC">Non-strand-specific</option> | |
| 35 <option value="STRAND-SPECIFIC-FORWARD">Strand-specific forward</option> | |
| 36 <option value="STRAND-SPECIFIC-REVERSE">Strand-specific reverse</option> | |
| 37 </param> | |
| 38 </when> | |
| 39 <when value="no"/> | |
| 40 </conditional> | |
| 41 <param name="hm" type="text" size="3" value="3" label="minimum size for a homopolymer to be considered in indel analysis" help="Only homopolymers of this size or larger will be considered when estimating homopolymer indels count"/> | |
| 42 <param name="nr" type="text" size="6" value="1000" label="number of reads in the chunk" help="In order to reduce the load of I/O, reads are analyzed in chunks. Each chunk contains the selected number of reads which will be loaded into memory and analyzed by a single thread. Smaller numbers may result in lower performance, but also the memory consumption will be reduced. The default value is 1000 reads"/> | |
| 43 </inputs> | |
| 44 | |
| 45 <outputs> | |
| 46 <data format="html" name="bamqc_result" label="${tool.name} on ${on_string}"> | |
| 47 <!-- <data format="html" name="bamqc_result" label="${tool.name} on ${on_string}" from_work_dir="bamqc_output/qualimapReport.html"> --> | |
| 48 </data> | |
| 49 </outputs> | |
| 50 | |
| 51 <configfiles> | |
| 52 <!-- this config file collects all parameter settings --> | |
| 53 <configfile name="configfile"> | |
| 54 ## first we pass some galaxy environment variables | |
| 55 galtemp==${__new_file_path__} | |
| 56 | |
| 57 bamqc_result==$bamqc_result | |
| 58 outputdir==$bamqc_result.files_path | |
| 59 bam==$bam | |
| 60 c==$c | |
| 61 hm==$hm | |
| 62 nr==$nr | |
| 63 #if $customgtf.upload=="yes" | |
| 64 gff==$customgtf.gff | |
| 65 os==$customgtf.os | |
| 66 p==$customgtf.p | |
| 67 #end if | |
| 68 </configfile> | |
| 69 </configfiles> | |
| 70 | |
| 71 <tests> | |
| 72 </tests> | |
| 73 | |
| 74 <help> | |
| 75 **Tool Overview** | |
| 76 | |
| 3 | 77 Bamqc_ allows for simply but throroughly checking of the quality of mapping. |
| 2 | 78 |
| 3 | 79 .. _Bamqc: http://qualimap.bioinfo.cipf.es// |
| 2 | 80 |
| 81 ------ | |
| 82 | |
| 83 </help> | |
| 84 </tool> | |
| 85 |