Mercurial > repos > morinlab > vardictjava

annotate vardictjava.xml @ 0:fba18d3160d1 draft default tip

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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:37:45 -0400
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fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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1 <tool id="vardictjava" name="VarDictJava" version="1.4.6">
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2 <description>
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3 calls SNVs and indels for tumour-normal pairs.
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4 </description>
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5
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6 <requirements>
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7 <requirement type="package" version="5.18.1">perl</requirement>
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8 <requirement type="package" version="3.2.1">R</requirement>
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9 <requirement type="package" version="1.4.6">vardictjava</requirement>
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10 <requirement type="set_environment">VARDICTJAVA_ROOT_DIR</requirement>
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11 </requirements>
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12
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13 <command detect_errors="aggressive"><![CDATA[
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14 ## LINK BAM INDEX
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15 ln -s $normal ./normal.bam;
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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16 ln -s $normal.metadata.bam_index ./normal.bam.bai;
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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17 ln -s $tumour tumor.bam;
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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18 ln -s $tumour.metadata.bam_index ./tumor.bam.bai;
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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19
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20 ## INDEX REFERENCE FASTA FILE IF FROM HISTORY
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21 #if $reference_source.reference_source_selector == "history":
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22 ln -s $reference_source.ref_file ref.fa;
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23 samtools faidx ref.fa;
fba18d3160d1 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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24 #else if $reference_source.reference_source_selector == "cached"
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25 ln -s $reference_source.ref_file.fields.path ref.fa;
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26 ln -s ${reference_source.ref_file.fields.path}.fai ref.fa.fai;
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27 #end if
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28
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29 ## BUILD BED FILE FROM CHROMOSOME LIST
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30 #if $interval_file:
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31 grep -w -f $interval_file ref.fa.fai > chromosomes.fa.fai;
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32 #else
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33 ln -s ref.fa.fai chromosomes.fa.fai;
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34 #end if
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35 awk 'BEGIN {FS=OFS="\t"} {print $1, "1", $2}' chromosomes.fa.fai > regions.bed;
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36
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37 ## BUILD VARDICT COMMAND
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38 \$VARDICTJAVA_ROOT_DIR/build/install/VarDict/bin/VarDict
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39 -b "./tumor.bam|./normal.bam"
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40 -G ref.fa
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41 -z
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42 -th \${GALAXY_SLOTS:-1}
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43
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44 ## ADVANCED OPTIONS
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45 -f $advancedsettings.f
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46 -k $advancedsettings.k
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47 -r $advancedsettings.r
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48 -B $advancedsettings.B
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49 -Q $advancedsettings.Q
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50 -q $advancedsettings.q
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51 -m $advancedsettings.m
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52 -T $advancedsettings.T
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53 -X $advancedsettings.X
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54 -P $advancedsettings.P
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55 -o $advancedsettings.o
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56 -O $advancedsettings.O
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57 -V $advancedsettings.V
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58
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59 ## CONSTRUCT VCF TABLE
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60 -c 1 -S 2 -E 3 -g 4
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61
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62 ## REGION SPECIFICATION (ENTIRE CHROMOSOMES)
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63 regions.bed
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64
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65 ## POSTPROCESSING
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66 | \$VARDICTJAVA_ROOT_DIR/VarDict/testsomatic.R
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67 | \$VARDICTJAVA_ROOT_DIR/VarDict/var2vcf_somatic.pl
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68 -f $advancedsettings.f
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69
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70 > $all_variants;
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71
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72 ## Filter for PASS variants
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73 awk 'BEGIN {FS=OFS="\t"} substr(\$0, 1, 1) == "#" {print \$0; next} \$7 == "PASS" {print \$0}' $all_variants > $passed_variants
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74 ]]></command>
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75
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76 <inputs>
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77 <conditional name="reference_source">
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78 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome file">
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79 <option value="cached" selected="True">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 name="ref_file" type="select" label="Reference Genome File">
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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 name="ref_file" format="fasta" type="data" label="Reference Genome File" />
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89 </when>
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90 </conditional>
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91
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92 <param name="normal" type="data" format="bam" label="Normal Alignment File" />
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93 <param name="tumour" type="data" format="bam" label="Tumour Alignment File" />
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94 <param name="interval_file" type="data" format="txt" optional="true" label="Chromosomes" help="Restrict SNV calls to the following list of chromosomes (one per line)" />
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95
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96 <section name="advancedsettings" title="Advanced Settings" expanded="False">
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97 <param name="f" type="float" value="0.01" label="Minimum variant allele fraction" />
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98 <param name="k" type="integer" value="1" label="Set to 0 to disable local realignment" />
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99 <param name="r" type="integer" value="2" label="Minimum number of reads supporting the variant" />
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100 <param name="B" type="integer" value="2" label="Minimum number of reads for determining strand bias" />
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101 <param name="Q" type="integer" value="1" label="Minimum mapping quality for reads to be considered" />
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102 <param name="m" type="integer" value="8" label="Maximum number of mismatches before a read is no longer considered (gaps are not counted as mismatches)" />
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103 <param name="T" type="integer" value="0" label="Maximum number of bases considered from 5' end (default: 0, no trimming)" />
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104 <param name="X" type="integer" value="3" label="Maximum number of extended based after indel to look for mismatches" />
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105 <param name="P" type="integer" value="5" label="Maximum average read position for a variant to be considered." />
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106 <param name="q" type="integer" value="25" label="Minimum phred score for a base to be considered a good call" />
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107 <param name="o" type="float" value="1.5" label="Minimum quality ratio [(good_quality_reads)/(bad_quality_reads+0.5)] (based on definition of a good call; see previous option)" />
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108 <param name="O" type="float" value="0" label="Minimum average mapping quality" />
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109 <param name="V" type="float" value="0.05" label="Maximum allowed variant allele fraction in the normal sample" />
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110 </section>
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111 </inputs>
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112
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113 <outputs>
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114 <data name="all_variants" format="vcf" label="VarDict SNVs and Indels (All)" />
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115 <data name="passed_variants" format="vcf" label="VarDict SNVs and Indels (Passed)" />
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116 </outputs>
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117
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118 <help>
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119 <![CDATA[
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120 https://github.com/AstraZeneca-NGS/VarDictJava
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121 ]]>
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122 </help>
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123
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124 <citations>
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125 <expand macro="morinlab_citation" />
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126 <expand macro="galaxy_citation" />
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127 <expand macro="vardict_citation" />
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128 </citations>
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129 </tool>