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annotate delly.xml @ 0:e3b753e2ee24 draft default tip

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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:20:05 -0400
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e3b753e2ee24 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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1 <tool id="delly" name="DELLY" version="0.6.1">
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2
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3 <description>structural variant discovery by integrated paired-end and split-read analysis</description>
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4
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5 <macros>
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6 <import>citations.xml</import>
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7 </macros>
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8
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9 <requirements>
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10 <requirement type="package" version="1.55.0">boost</requirement>
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11 <requirement type="package" version="0.6.1">delly</requirement>
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12 <requirement type="set_environment">DELLY_DIR</requirement>
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13 <requirement type="set_environment">BOOST_ROOT_DIR"</requirement>
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14 <requirement type="set_environment">LD_LIBRARY_PATH"</requirement>
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15 <requirement type="set_environment">LIBRARY_PATH"</requirement>
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16 <requirement type="set_environment">CPLUS_INCLUDE_PATH"</requirement>
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17 <requirement type="set_environment">C_INCLUDE_PATH"</requirement>
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18 </requirements>
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19
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20 <command detect_errors="aggressive">
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21
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22 <!-- BAM and BAI linking, (1) link BAM to new BAM file & (2) link BAM metadata to new BAI file -->
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23 #for $i, $s in enumerate( $repeatBam )
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24 ln -s $s.sortedBam ./input$(i).bam;
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25 ln -s $s.sortedBam.metadata.bam_index ./input$(i).bam.bai;
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26 #end for
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27
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28 <!-- Sets args to a list of types selected -->
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29 #if not isinstance( $variant_source_selector_param.value, list ):
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30 #set $args = [ $variant_source_selector_param.value ]
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31 #else:
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32 #set $args = $variant_source_selector_param.value
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33 #end if
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34
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35 <!-- Run Delly Jobs for each type selected -->
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36 #for $option in $args
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37 \$DELLY_DIR/src/delly
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38 -t $option
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39 -o ./output.$(option).vcf
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40 -q $advancedsettings.mapQual
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41 -s $advancedsettings.madCutoff
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42
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43 #if $option == "DEL":
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44 -m $advancedsettings.minFlank
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45 #end if
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46
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47 -u $advancedsettings.genoQual
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48
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49 #if $advancedsettings.vcfgeno
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50 -v $advancedsettings.vcfgeno
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51 #end if
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52
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53 #if $reference_source.reference_source_selector_param == "cached":
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54 -g "${reference_source.reference.fields.path}"
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55 #else:
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56 -g $reference_source.reference
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57 #end if
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58
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59 <!-- add each input bam to command -->
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60 #for $i, $s in enumerate( $repeatBam ):
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61 ./input$(i).bam
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62 #end for
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63 ;
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64 #end for
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65
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66 <!-- Combine VCF Files and Sort Lexographically -->
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67 #set $option = $args[0]
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68 grep ^\# output.$(option).vcf > $outfile;
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69 grep ^\# -v output.$(option).vcf > variants.txt;
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70
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71 <!-- If we called more than a single variant type, concatenate all the other types variant output -->
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72 #if isinstance( $variant_source_selector_param.value, list ):
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73 #for $option in $args[1:]
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74 grep ^\# -v output.$(option).vcf >> variants.txt;
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75 #end for
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76 #end if
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77
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78 <!-- Sort all variant output, assuming that it will sort lexographically by chromosome, then position, ID -->
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79 <!-- In future, maybe develop a script to sort by bam header -->
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80 sort -k1,1d -k2,2n -k3,3d variants.txt > sortedVariants.txt;
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81
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82 <!-- Filter Variants that have Passed Quality Checks -->
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83 #if $filterCalls
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84 awk '{if ($7 == "PASS") print $0;}' sortedVariants.txt >> $outfile;
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85 #else
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86 cat sortedVariants.txt >> $outfile;
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87 #end if
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88
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89 </command>
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90
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91 <inputs>
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92
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93 <!-- REFERENCE OPTIONS -->
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94 <conditional name="reference_source">
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95 <param type="select" name="reference_source_selector_param" label="Choose the source for the reference genome">
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96 <option value="cached" selected="True">Use a built-in genome</option>
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97 <option value="history">Use a genome from the history</option>
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98 </param>
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99 <when value="cached">
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100 <param type="select" name="reference" label="Genome">
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101 <options from_data_table="all_fasta"/>
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102 </param>
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103 </when>
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104 <when value="history">
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105 <param type="data" format="fasta" name="reference" label="Genome"/>
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106 </when>
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107 </conditional>
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108
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109 <!-- VARIANT OPTIONS -->
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110 <param type="select" multiple="True" name="variant_source_selector_param" label="Select variants to identify in samples">
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111 <option value="DEL" selected="true">Deletions</option>
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112 <option value="DUP">Duplications</option>
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113 <option value="INV">Inversions</option>
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114 <option value="TRA">Translocations</option>
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115 </param>
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116 <!--
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117 <param name="interval_file" type="data" format="txt" optional="true" label="Interval file" help="Created by make parallel, only use when parallelism is turned on, note interchromosomal and intrachromosomal events have different interval files"/>
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118 -->
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119 <repeat name="repeatBam" title="Bam Alignment" min="1" default="1" >
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120 <param format="bam" name="sortedBam" type="data" label="File" />
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121 </repeat>
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122 <!-- <param name="excludeFile" type="data" format="bed" optional="true" label="Chromosomes to Exclude"/> -->
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123 <param name="filterCalls" type="boolean" value="false" label="Filter Poor Variant Calls"/>
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124
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125 <section name="advancedsettings" title="Advanced Settings" expanded="false">
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126 <!-- Paired End Options -->
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127 <param name="mapQual" type="integer" value="0" min="0" max="255" label="PE - Minimum Mapping Quality" />
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128 <param name="madCutoff" type="integer" value="9" min="0" max="255" label="PE - Insert Size Cutoff" />
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129
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130 <!-- SR Options -->
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131 <param name="minFlank" type="integer" value="13" label="SR - Minimum Flanking Sequence" />
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132
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133 <!-- Genotyping Options -->
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134 <param format="vcf" name="vcfgeno" type="data" optional="true" label="GT - Input VCF" />
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135 <param name="genoQual" type="integer" value="20" min="0" max="255" label="GT - Minimum Mapping Quality" />
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136 </section>
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137 </inputs>
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138
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139 <outputs>
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140 <data format="vcf" name="outfile" />
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141 </outputs>
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142
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143 <citations>
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144 <expand macro="morinlab_citation"/>
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145 <expand macro="galaxy_citation"/>
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146 <expand macro="delly_citation"/>
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147 </citations>
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148
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149 </tool>