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1 <tool id="somatic_sniper" name="SomaticSniper" version="1.0">
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2 <description>identify single nucleotide positions that are different between tumor and normal</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.5.0">somatic-sniper</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7
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8 ## SYMLINK BAM FILES ALONGSIDE INDEX FILES
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9 ln -s $normal normal.bam;
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10 ln -s $normal.metadata.bam_index normal.bam.bai;
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11 ln -s $tumor tumor.bam;
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12 ln -s $tumor.metadata.bam_index tumor.bam.bai;
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13
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14 #if $interval:
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15
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16 for i in \$(cut -f1 $interval); do
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17
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18 #end if
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19
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20
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21 ## BUILD SOMATICSNIPER COMMAND LINE
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2
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22 bam-somaticsniper
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23 -F vcf
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24 -q $advancedsettings.q
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25 -Q $advancedsettings.Q
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26 -T $advancedsettings.T
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27 -N $advancedsettings.N
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28 -r $advancedsettings.r
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29 -n $advancedsettings.n
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30 -t $advancedsettings.t
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31 $advancedsettings.L
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32 $advancedsettings.G
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33 $advancedsettings.p
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34
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35 #if $ref.ref_options == "cached"
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36 -f ${ref.index.fields.path}
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37 #else
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38 -f ${ref.ownFile}
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39 #end if
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40
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41 #if $interval:
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42
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43 <(samtools view -b tumor.bam \$i)
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44 <(samtools view -b normal.bam \$i)
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45
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46 #else:
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47 tumor.bam
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48 normal.bam
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49
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50 #end if
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51
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52 #if $interval:
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53 tmp_\$i.txt
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54 #else:
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55 $variants
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56 #end if
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57 ;
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58
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59 #if $interval:
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60
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61 done;
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62
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63 for i in \$(cut -f1 $interval); do
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64
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65 if [ \$i == \$(cut -f1 $interval | head -n1) ] ; then
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66 cat tmp_\$i.txt > $variants;
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67 else
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68 grep -v ^#.* tmp_\$i.txt >> $variants;
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69 fi ;
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70
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71 done;
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72
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73 #end if
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74
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75
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76
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77 ]]></command>
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78 <inputs>
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79 <conditional name="ref">
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80 <param name="ref_options" type="select" label="Choose the source for the reference genome">
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81 <option value="cached" selected="True">Use a built-in genome</option>
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82 <option value="history">Use a genome from the history</option>
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83 </param>
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84 <when value="cached">
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85 <param name="index" type="select" label="Reference Genome File" >
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2
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86 <options from_data_table="sniper_index" />
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0
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87 </param>
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88 </when>
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89 <when value="history">
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90 <param format="fasta" name="ownFile" type="data" metadata_name="dbkey" label="Reference Genome File" />
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91 </when>
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92 </conditional>
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93 <param format="bam" name="normal" type="data" label="Normal Alignment File" />
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94 <param format="bam" name="tumor" type="data" label="Tumour Alignment File" />
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95 <param type="data" format="txt" optional="true" name="interval" label="Specify Inteval"/>
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96 <section name="advancedsettings" title="Advanced Settings" expanded="False" >
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97 <param name="q" type="integer" value="0" label="Minimum read mapping quality"/>
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98 <param name="Q" type="integer" value="15" label="Minimum somatic variant quality score"/>
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99 <param name="T" type="float" value="0.850000" label="theta in maq consensus calling model (for -c/-g) [0.850000]"/>
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100 <param name="N" type="integer" value="2" label="Ploidy (number of haplotypes)"/>
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101 <param name="r" type="float" value="0.001000" label="Prior probability for differences between haplotypes"/>
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102 <param name="n" type="text" value="NORMAL" label="Normal sample ID"/>
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103 <param name="t" type="text" value="TUMOR" label="Tumour sample ID"/>
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104 <param name="L" type="boolean" truevalue="-L" falsevalue="" checked="true" label="Exclude LOH variants from output" />
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105 <param name="G" type="boolean" truevalue="-G" falsevalue="" checked="true" label="Exclude gain of reference variants from output" />
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106 <param name="p" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Disable priors in somatic calculation (improved sensitivity for solid tumours)" />
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107 </section>
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108 </inputs>
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109 <outputs>
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110 <data name="variants" format="vcf" label="SomaticSniper SNVs" />
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111 </outputs>
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112 <tests>
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113 <test>
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114 <param name="normal" file="sniper_test_normal.bam" />
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115 <param name="tumor" file="sniper_test_tumoral.bam" />
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116 <output name="variants" file="sniper_results.vcf" />
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117 </test>
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118 </tests>
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119 <help>
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120 http://gmt.genome.wustl.edu/packages/somatic-sniper/
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2
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121
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122 this wrapper was developed from https://github.com/morinlab/tools-morinlab/tree/master/tools/somatic_sniper only the requirement and part of the command line have been changed in order to make it suitable for CONDA
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123
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124 </help>
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125 </tool>
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