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1 <tool id="lumpy" name="LUMPY" version="0.2.9">
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2 <description>
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3 a probabilistic framework for structural variant discovery
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="0.1.19">samtools</requirement>
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7 <requirement type="package" version="0.2.9">lumpy</requirement>
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8 <requirement type="set_environment" version="0.2.9">LUMPY_SCRIPTS</requirement>
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9 <requirement type="package" version="1.9">numpy</requirement>
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10 </requirements>
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11 <command>
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12
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13 <!-- Create Symbolic links to bam and bam indexes -->
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14 ln -s $normal normal.bam;
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15 ln -s $normal.metadata.bam_index normal.bam.bai;
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16 ln -s $tumour tumour.bam;
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17 ln -s $tumour.metadata.bam_index tumour.bam.bai;
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18
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19 <!-- EXTRACT DISCORDANT PAIRED END ALIGNMENTS -->
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20 samtools view -F 1294 -b normal.bam | samtools sort - normal.pe;
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21 samtools view -F 1294 -b tumour.bam | samtools sort - tumour.pe;
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22
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23 <!-- EXTRACT SPLIT-READ ALIGNMENTS -->
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24 samtools view -h normal.bam |
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25 \$LUMPY_SCRIPTS/extractSplitReads_BwaMem -i stdin |
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26 samtools view -Sb - |
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27 samtools sort - normal.sr;
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28 samtools view -h tumour.bam |
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29 \$LUMPY_SCRIPTS/extractSplitReads_BwaMem -i stdin |
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30 samtools view -Sb - |
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31 samtools sort - tumour.sr;
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32
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33 <!-- CREATE HISTO FILE -->
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34 samtools view normal.bam |
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35 tail -n+100000 |
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36 \$LUMPY_SCRIPTS/pairend_distro.py -r 150 -X 4 -N 10000 -o normal.pe.histo > normal.stats;
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37 samtools view tumour.bam |
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38 tail -n+100000 |
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39 \$LUMPY_SCRIPTS/pairend_distro.py -r 150 -X 4 -N 10000 -o tumour.pe.histo > tumour.stats;
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40
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41 <!-- Store MEAN and STD in nice format -->
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42 cat -t normal.stats | sed s/\\^\\I/,/g > normal.stats.txt;
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43 cat -t tumour.stats | sed s/\\^\\I/,/g > tumour.stats.txt;
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44
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45 <!-- RUN LUMPY -->
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46
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47 lumpy
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48 -e
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49 -tt $advancedsettings.tt
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50 -mw $advancedsettings.mw
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51 #if $x
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52 -x $x
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53 #end if
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54
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55 -pe
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56 bam_file:normal.pe.sort.bam,
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57 histo_file:normal.pe.histo,
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58 \$(cat normal.stats.txt),
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59 read_length:$advancedsettings.pe_read_length,
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60 min_non_overlap:$advancedsettings.pe_min_non_overlap,
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61 discordant_z:$advancedsettings.pe_discordant_z,
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62 back_distance:$advancedsettings.pe_back_distance,
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63 min_mapping_threshold:$advancedsettings.pe_min_mapping_threshold,
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64 weight:$advancedsettings.pe_weight,
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65 #if $sampleid_source.manual:
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66 id:PE-$sampleid_source.idn
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67 #else:
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68 id:PE-\$(basename $normal)
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69 #end if
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70
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71 -sr
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72 bam_file:normal.sr.sort.bam,
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73 back_distance:$advancedsettings.sr_back_distance,
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74 min_mapping_threshold:$advancedsettings.sr_min_mapping_threshold,
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75 weight:$advancedsettings.sr_weight,
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76 min_clip:$advancedsettings.sr_min_clip,
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77 #if $sampleid_source.manual:
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78 id:SE-$sampleid_source.idn
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79 #else
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80 id:SE-\$(basename $normal)
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81 #end if
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82
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83 -pe
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84 bam_file:n=tumour.pe.sort.bam,
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85 histo_file:tumour.pe.histo,
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86 \$(cat tumour.stats.txt),
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87 read_length:$advancedsettings.pe_read_length,
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88 min_non_overlap:$advancedsettings.pe_min_non_overlap,
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89 discordant_z:$advancedsettings.pe_discordant_z,
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90 back_distance:$advancedsettings.pe_back_distance,
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91 min_mapping_threshold:$advancedsettings.pe_min_mapping_threshold,
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92 weight:$advancedsettings.pe_weight,
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93 #if $sampleid_source.manual:
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94 id:PE-$sampleid_source.idt
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95 #else:
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96 id:PE-\$(basename $tumour)
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97 #end if
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98
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99 -sr
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100 bam_file:tumour.sr.sort.bam,
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101 back_distance:$advancedsettings.sr_back_distance,
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102 min_mapping_threshold:$advancedsettings.sr_min_mapping_threshold,
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103 weight:$advancedsettings.sr_weight,
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104 min_clip:$advancedsettings.sr_min_clip,
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105 #if $sampleid_source.manual:
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106 id:SE-$sampleid_source.idt
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107 #else
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108 id:SE-\$(basename $tumour)
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109 #end if
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110
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111 > $outfile;
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112
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113 </command>
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114 <inputs>
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115 <conditional name="sampleid_source">
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116 <param label="Choose the source to fetch Sample Identifiers" name="sampleid_selector" type="select">
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117 <option value="bamfile">BAM File Name</option>
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118 <option value="manual">Manual</option>
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119 </param>
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120 <when value="manual">
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121 <param name="idn" type="text" label="Tumour ID (Name)"/>
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122 <param name="idt" type="text" label="Normal ID (Name)"/>
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123 </when>
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124 </conditional>
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125 <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
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126 <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
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127 <param type="data" format="bed" name="x" label="Exluded Regions BED file" optional="true"/>
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128 <section name="advancedsettings" title="Advanced Settings" expanded="false">
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129 <param type="integer" value="5" name="mw" label="Minimum Weight for Call"/>
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130 <param type="integer" value="3" name="tt" label="Trim Threshold"/>
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131 <param type="integer" name="pe_back_distance" value="20" label="Paired End Back Distance" help="Distance into the read to add the breakpoint interval"/>
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132 <param type="integer" name="pe_min_mapping_threshold" value="1" label="Paired End Min Mapping Threshold" help="Minimum mapping quality that a read must have to be considered"/>
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133 <param type="integer" name="pe_weight" value="1" label="Paired End Weight" help="Weight of each piece of evidence from this sample"/>
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134 <param type="integer" name="pe_discordant_z" value="4" label="Paired End Discordant Value" help="Number of standard deviations away from the mean to be considered as a normal library size"/>
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135 <param type="integer" name="pe_read_length" value="150" label="Paired End Read Length" help="Length of sequenced reads"/>
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136 <param type="integer" name="pe_min_non_overlap" value="150" label="Paired End Min Non Overlap" help="Number of base pair positions that must be unique to each end of a read pair"/>
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137 <param type="integer" name="sr_back_distance" value="20" label="Split Read Back Distance" help="Distance into the read to add the breakpoint interval"/>
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138 <param type="integer" name="sr_min_mapping_threshold" value="1" label="Split Read Min Mapping Threshold" help="Minimum mapping quality that a read must have to be considered"/>
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139 <param type="integer" name="sr_weight" value="1" label="Split Read Weight" help="Weight of each piece of evidence from this sample"/>
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140 <param type="integer" name="sr_min_clip" value="1" label="Spliy Read Min Clip" help="Minimum number of clipped bases to consider in a split read"/>
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141 </section>
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142 </inputs>
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143 <outputs>
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144 <data type="vcf" name="outfile"/>
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145 </outputs>
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146 </tool> |
