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2 <tool id="qualimap_bamqc" name="Analyse SAM/BAM with bamqc" version="0.0.1">
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3 <!-- Additional info: wrapper compatible with versions ..... -->
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4 <description>
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5 to asses mapping quality metrics.
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6 </description>
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7
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8 <version_command>
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9 qualimap --version
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10 </version_command>
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11
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12 <requirements>
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13 <requirement type="package">qualimap</requirement>
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14 </requirements>
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15
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16 <command interpreter="perl">
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17 ## it is recommended that you write a wrapper for your tool
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18 ## and pass all parameters to that tool, which parses them.
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19 bamqc_wrapper.pl $configfile
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20 </command>
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21
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22 <inputs>
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23 <param format="sam,bam" name="bam" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." />
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24 <param type="boolean" name="c" checked="TRUE" truevalue="-c" falsevalue="" label="paint chromosome limits inside charts" />
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25 <conditional name="customgtf">
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26 <param name="upload" type="select" label="BETA! Analyze the alignment data for the regions of interest you provide">
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27 <option value="yes">Yes</option>
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28 <option value="no" selected="true">No</option>
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29 </param>
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30 <when value="yes">
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31 <param name="gff" type="data" format="bed,gtf,gff3" label="Choose your feature annotation file" help="Provide your BED, GTF or GFF file"/>
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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" />
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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.">
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34 <option value="NON-STRAND-SPECIFIC">Non-strand-specific</option>
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35 <option value="STRAND-SPECIFIC-FORWARD">Strand-specific forward</option>
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36 <option value="STRAND-SPECIFIC-REVERSE">Strand-specific reverse</option>
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37 </param>
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38 </when>
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39 <when value="no"/>
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40 </conditional>
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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"/>
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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"/>
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43 </inputs>
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44
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45 <outputs>
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46 <data format="html" name="bamqc_result" label="${tool.name} on ${on_string}">
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47 <!-- <data format="html" name="bamqc_result" label="${tool.name} on ${on_string}" from_work_dir="bamqc_output/qualimapReport.html"> -->
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48 </data>
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49 </outputs>
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50
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51 <configfiles>
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52 <!-- this config file collects all parameter settings -->
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53 <configfile name="configfile">
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54 ## first we pass some galaxy environment variables
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55 galtemp==${__new_file_path__}
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56
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57 bamqc_result==$bamqc_result
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58 outputdir==$bamqc_result.files_path
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59 bam==$bam
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60 c==$c
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61 hm==$hm
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62 nr==$nr
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63 #if $customgtf.upload=="yes"
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64 gff==$customgtf.gff
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65 os==$customgtf.os
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66 p==$customgtf.p
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67 #end if
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68 </configfile>
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69 </configfiles>
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70
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71 <tests>
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72 </tests>
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73
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74 <help>
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75 **Tool Overview**
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76
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77 Bamqc_ allows for simply but throroughly checking of the quality of mapping.
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78
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79 .. _Bamqc: http://qualimap.bioinfo.cipf.es//
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80
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81 ------
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82
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83 </help>
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84 </tool>
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85
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