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5
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1 <tool id="bcbio-nextgen" name="BCBio" version="1.0">
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2 <command detect_errors="exit_code"><![CDATA[
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3
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3 PATH="\$BCBIO_DIRECTORY/tool_dir/bin:\$BCBIO_DIRECTORY/anaconda/bin:\$PATH" &&
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4 mkdir $everything_else.files_path &&
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5 cd $everything_else.files_path &&
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6 python $__tool_directory__/script.py --workdir `pwd` --output-dir `pwd`/output --template $main --output-conf `pwd`/config.yaml
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7 #if str( $region_file.has_region_file_select ) == "yes":
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8 --bed ${region_file.bed}
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9 #end if
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10 #for $i, $sample in enumerate( $samples )
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7
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11 #if str( $sample.single_or_paired.single_or_paired_selector ) == "single":
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12 --input $sample.single_or_paired.forward:$sample.phenotype
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13 #else:
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14 --input $sample.single_or_paired.forward:$sample.single_or_paired.reverse:$sample.phenotype
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15 #end if
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16 #end for
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17 && bcbio_nextgen.py \$BCBIO_DIRECTORY/galaxy/bcbio_system.yaml `pwd`/config.yaml -t local -n \$BCBIO_CORES &&
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18 zcat final/*/Batch1-ensemble-annotated.vcf.gz > $output_vcf &&
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19 python $__tool_directory__/make_html.py --input-dir $everything_else.files_path --root-html $everything_else
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20 ]]></command>
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21 <configfiles>
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22 <configfile name='main'>
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23 details:
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24 {% for sample in samples -%}
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25 - algorithm:
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26 aligner: $aligner
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27 mark_duplicates: ${mark_duplicates}
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28 remove_lcr: ${remove_lcr}
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29 variantcaller: [$variantcallers]
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30 {% if bed_file_path -%} variant_regions: {{ bed_file_path }}{% endif %}
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31 ensemble:
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32 numpass: 2
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33 align_split_size: false
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34 analysis: $analysis
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35 lane: {{ loop.index }}
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36 description: {{ sample['description'] }}
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37 {% if 'reverse' in sample %}
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38 files: [{{ sample['forward'] }}, {{ sample['reverse'] }}]
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39 {% else %}
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40 files: [{{ sample['forward'] }}]
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41 {% endif %}
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42 genome_build: $build
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43 metadata:
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44 phenotype: {{ sample['phenotype'] }}
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45 batch: Batch1
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46 upload:
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47 dir: ./final
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48 {% endfor %}
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49 </configfile>
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50 </configfiles>
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51 <inputs>
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52 <param name="build" type="select" label="Genome Build">
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53 <option value="GRCh37">GRCh37</option>
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54 <option value="hg19">hg19</option>
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55 <option value="GRCm38">GRCm38</option>
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56 <option value="mm10">mm10</option>
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57 </param>
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58 <param name="analysis" type="select" label="Analysis">
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59 <option value="variant2">variant2</option>
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60 <option value="RNA-seq">RNA-seq</option>
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61 <option value="smallRNA-seq">smallRNA-seq</option>
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62 </param>
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63 <param name="aligner" type="select" label="Aligner">
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64 <option value="bwa">bwa</option>
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65 <option value="bowtie">bowtie</option>
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66 <option value="bowtie2">bowtie2</option>
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67 <option value="hisat2">hisat2</option>
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68 <option value="minimap2">minimap2</option>
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69 <option value="novoalign">novoalign</option>
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70 <option value="snap">snap</option>
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71 <option value="star">star</option>
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72 <option value="tophat2">tophat2</option>
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73 <option value="false">false</option>
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74 </param>
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75 <param name="variantcallers" type="select" multiple="true" label="Variantcallers">
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76 <option value="false">false</option>
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77 <option value="freebayes">freebayes</option>
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78 <option value="gatk-haplotype">gatk-haplotype</option>
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79 <option value="haplotyper">haplotyper</option>
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80 <option value="platypus">platypus</option>
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81 <!--<option value="mutect">mutect</option>-->
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82 <option value="mutect2">mutect2</option>
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83 <option value="scalpel">scalpel</option>
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84 <option value="tnhaplotyper">tnhaplotyper</option>
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85 <option value="tnscope">tnscope</option>
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86 <option value="vardict">vardict</option>
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87 <option value="varscan">varscan</option>
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88 <option value="samtools">samtools</option>
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89 <option value="gatk">gatk</option>
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90 </param>
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91 <param name="mark_duplicates" type="select">
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92 <option value="true" selected="true">true</option>
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93 <option value="false">false</option>
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94 </param>
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95 <param name="remove_lcr" type="select">
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96 <option value="true" selected="true">true</option>
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97 <option value="false">false</option>
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98 </param>
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99 <repeat name="samples" title="Samples" min="1">
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100 <param name="phenotype" type="select" label="Phenotype">
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101 <option value="normal">Normal</option>
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102 <option value="tumor">Tumor</option>
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103 </param>
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104 <conditional name="single_or_paired">
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105 <param name="single_or_paired_selector" type="select">
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106 <option value="single">Single</option>
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107 <option value="paired" selected="true">Paired-End</option>
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108 </param>
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109 <when value="single">
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110 <param type="data" name="forward" format="fastq,fastq.gz,fastqsanger.gz" />
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111 </when>
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112 <when value="paired">
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113 <param type="data" name="forward" format="fastq,fastq.gz,fastqsanger.gz" />
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114 <param type="data" name="reverse" format="fastq,fastq.gz,fastqsanger.gz" />
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115 </when>
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116 </conditional>
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0
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117 </repeat>
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118 <conditional name="region_file">
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119 <param name="has_region_file_select" type="select" label="Do you have a region file">
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120 <option value="yes">Yes</option>
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121 <option value="no" selected="true">No</option>
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122 </param>
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123 <when value="yes">
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124 <param type="data" name="bed" format="bed" />
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125 </when>
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126 </conditional>
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127 </inputs>
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128 <outputs>
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129 <data name="output_vcf" format="vcf"/>
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130 <data name="everything_else" format="html"/>
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131 </outputs>
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132 <help><![CDATA[
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133 TODO: Fill in help.
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134 ]]></help>
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135 </tool>
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