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1 <tool id="pindel" name="Pindel" version="0.2.5b8">
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2
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3 <description>
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4 a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
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5 </description>
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6
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7 <requirements>
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8 <requirement type="package" version="1.3.2">htslib</requirement>
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9 <requirement type="package" version="0.2.5b8">pindel</requirement>
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10 </requirements>
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11
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12 <command detect_errors="aggressive">
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13
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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 touch pindel.txt;
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20 #if $sampleid_source.sampleid_selector.value == "bamfile":
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21 echo -e \$(pwd)/tumour.bam\\t$normal_insert\\t\$(basename $tumour | rev | cut -c 5- | rev) >> pindel.txt;
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22 echo -e \$(pwd)/normal.bam\\t$tumour_insert\\t\$(basename $normal | rev | cut -c 5- | rev) >> pindel.txt;
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23 #else:
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24 echo -e \$(pwd)/tumour.bam\\t$normal_insert\\t$sampleid_source.idt >> pindel.txt;
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25 echo -e \$(pwd)/normal.bam\\t$tumour_insert\\t$sampleid_source.idn >> pindel.txt;
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26 #end if
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27
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28 mkdir outputs;
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29
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30 #if $reference_source.reference_source_selector.value == "cached":
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31 ln -s ${reference_source.ref_file.fields.path} ref.fa;
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32 #else:
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33 ln -s $reference_source.ref_file ref.fa;
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34 samtools faidx ref.fa;
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35 #end if
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36
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37 pindel
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38 -f ref.fa
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39 -i pindel.txt
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40 -o \$(pwd)/outputs/here
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41 $advancedsettings.R
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42 -x $advancedsettings.x
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43 -e $advancedsettings.e
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44 -E $advancedsettings.E
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45 -u $advancedsettings.u
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46 -n $advancedsettings.n
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47 $advancedsettings.r
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48 $advancedsettings.t
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49 $advancedsettings.l
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50 $advancedsettings.k
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51 $advancedsettings.s
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52 $advancedsettings.S
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53 $advancedsettings.I
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54 #if $advancedsettings.include:
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55 -j $advancedsettings.include
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56 #end if
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57 #if $advancedsettings.exclude:
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58 -J $advancedsettings.exclude
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59 #end if
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60 ;
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61
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62 first="true";
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63 for i in \$( ls \$(pwd)/outputs/here* ); do
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64 pindel2vcf -p \$i -r ref.fa -R CHECK_GALAXY_HISTORY -d CHECK_GALAXY_HISTORY -v tmp.vcf;
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65 if [ \$first -eq "true" ] ; then
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66 cat tmp.vcf >> $output;
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67 first="false";
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68 else
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69 grep -v "^#.*" tmp.vcf >> $output;
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70 fi;
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71 done;
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72
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73 </command>
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74
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75 <inputs>
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76
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77 <conditional name="reference_source">
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78 <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
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79 <option value="cached">Use a built-in genome</option>
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80 <option value="history">Use a genome from the history</option>
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81 </param>
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82 <when value="cached">
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83 <param label="Reference Genome File" name="ref_file" type="select">
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84 <options from_data_table="fasta_indexes"/>
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85 </param>
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86 </when>
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87 <when value="history">
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88 <param label="Reference Genome File" name="ref_file" type="data" format="fasta"/>
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89 </when>
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90 </conditional>
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91
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92 <conditional name="sampleid_source">
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93 <param label="Choose the source to open the Sample Id" name="sampleid_selector" type="select">
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94 <option value="bamfile">BAM File Name</option>
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95 <option value="manual">Manual</option>
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96 </param>
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97 <when value="manual">
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98 <param name="idt" type="text" label="Tumour ID (Name)"/>
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99 <param name="idn" type="text" label="Normal ID (Name)"/>
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100 </when>
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101 </conditional>
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102
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103 <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
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104 <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
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105 <param type="integer" name="tumour_insert" value="250" label="Tumour Insert Size" help="suggest running picards collect insert size metrics"/>
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106 <param type="integer" name="normal_insert" value="250" label="Normal Insert Size" help="suggest running picards collect insert size metrics"/>
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107
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108 <section name="advancedsettings" title="Advanced Settings" expanded="false">
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109 <param type="boolean" name="R" checked="true" truevalue="-R true" falsevalue="-R false" label="Search for Discordant Pairs"/>
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110 <param type="integer" name="x" value="2" min="1" max="9" label="Maximum size of structural variations to be detected" help="size = 128 ^ (val - 1)"/>
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111 <param type="float" name="e" value="0.01" max="1.0" label="Expected faraction of sequencing errors"/>
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112 <param type="float" name="E" value="0.95" max="1.0" label="Sensitivity"/>
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113 <param type="float" name="u" value="0.02" max="1.0" label="Maximum allowed mismatch rate"/>
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114 <param type="integer" name="n" value="2" label="Minimum Edit Distance between reads and reference"/>
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115 <param type="boolean" name="r" checked="true" truevalue="-r true" falsevalue="-r false" label="Report Inversions"/>
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116 <param type="boolean" name="t" checked="true" truevalue="-t true" falsevalue="-t false" label="Report Duplications"/>
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117 <param type="boolean" name="l" checked="false" truevalue="-l true" falsevalue="-l false" label="Report Long Insertions"/>
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118 <param type="boolean" name="k" checked="false" truevalue="-k true" falsevalue="-k false" label="Report Breakpoints"/>
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119 <param type="boolean" name="s" checked="false" truevalue="-s true" falsevalue="-s false" label="Report Close Mapped Reads"/>
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120 <param type="boolean" name="S" checked="false" truevalue="-S true" falsevalue="-S false" label="Report Only Close Mapped Reads"/>
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121 <param type="boolean" name="I" checked="false" truevalue="-I true" falsevalue="-I false" label="Report Interchromosomal Events"/>
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122 <param type="data" format="bed" name="include" label="Include Regions" optional="true"/>
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123 <param type="data" format="bed" name="exclude" label="Exclude Regions" optional="true"/>
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124 </section>
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125
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126 </inputs>
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127
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128 <outputs>
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129 <data format="vcf" name="output" />
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130 </outputs>
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131
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132 </tool>
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