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20
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1 <tool id="bwameth" name="bwameth" version="0.2.0.2">
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2 <description>Fast and accurate aligner of BS-Seq reads.</description>
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3 <requirements>
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4 <requirement type="package" version="1.2">samtools</requirement>
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5 <requirement type="package" version="0.2.0">bwameth</requirement>
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6 </requirements>
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7 <version_command>bwameth.py --version</version_command>
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8 <command detect_errors="aggressive">
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14
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9 <![CDATA[
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10 #if $referenceSource.source != "indexed":
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17
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11 mkdir index_dir &&
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12 ln -s '$referenceSource.reference' index_dir/genome.fa &&
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13 bwameth.py index index_dir/genome.fa &&
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14 #set index="index_dir/genome.fa"
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14
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15 #else
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17
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16 #set index=$referenceSource.index.fields.path
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14
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17 #end if
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18
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17
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19 bwameth.py
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20 -t "\${GALAXY_SLOTS:-4}"
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20
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21 --reference "${index}"
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17
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22
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14
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23 #if str($readGroup).strip() != "":
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24 --read-group "${readGroup}"
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14
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25 #end if
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26
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27 #if $single_or_paired.single_or_paired_opts == 'single':
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28 $single_or_paired.input_singles
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20
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29 #elif $single_or_paired.single_or_paired_opts == 'paired':
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30 $single_or_paired.input_mate1 $single_or_paired.input_mate2
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20
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31 #else:
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32 $single_or_paired.input_mate1.forward $single_or_paired.input_mate1.reverse
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14
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33 #end if
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20
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34 | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -o output.bam -
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14
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35 ]]>
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20
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36 </command>
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37 <inputs>
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38 <conditional name="referenceSource">
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39 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">
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40 <option value="history" selected="True">Use one from the history</option>
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41 <option value="indexed">Use a built-in index</option>
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42 </param>
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43 <when value="history">
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44 <param name="reference" type="data" format="fasta" metadata_name="dbkey" label="Select a genome" help="in FASTA format" />
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45 </when>
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46 <when value="indexed">
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47 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
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48 <options from_data_table="bwameth_indexes">
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49 <filter type="sort_by" column="2"/>
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50 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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51 </options>
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52 </param>
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53 </when>
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54 </conditional>
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55
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20
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56 <conditional name="single_or_paired">
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57 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
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58 <option value="single">Single-end</option>
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59 <option value="paired">Paired-end</option>
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60 <option value="paired_collection">Paired-end Dataset Collection</option>
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61 </param>
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62 <when value="single">
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63 <param name="input_singles" type="data" format="fastqsanger" label="FASTQ" help="FASTQ file." />
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64 </when>
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65 <when value="paired">
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66 <param name="input_mate1" type="data" format="fastqsanger" label="First read in pair" help="FASTQ file." />
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67 <param name="input_mate2" type="data" format="fastqsanger" label="Second read in pair" help="FASTQ file." />
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68 </when>
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69 <when value="paired_collection">
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70 <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." />
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71 </when>
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72 </conditional>
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73 <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'">
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74 <sanitizer sanitize="False"/>
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75 </param>
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76 </inputs>
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77 <outputs>
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78 <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" />
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79 </outputs>
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80 <tests>
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81 <test>
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82 <param name="referenceSource" value="history" />
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83 <param name="reference" value="ref.fa.gz" />
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84 <param name="single_or_paired_opts" value="paired" />
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85 <param name="input_mate1" value="t_R1.fastq.gz" />
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86 <param name="input_mate2" value="t_R2.fastq.gz" />
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87 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
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88 </test>
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89 <test>
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90 <param name="referenceSource" value="history" />
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91 <param name="reference" value="ref.fa.gz" />
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92 <param name="single_or_paired_opts" value="paired_collection" />
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93 <param name="input_mate1">
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94 <collection type="paired">
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95 <element name="forward" value="t_R1.fastq.gz" />
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96 <element name="reverse" value="t_R2.fastq.gz" />
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97 </collection>
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98 </param>
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99 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
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100 </test>
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101 </tests>
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102 <help>
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103 <![CDATA[
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104
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105 **What it does**
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106
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107 BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool.
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108 ]]>
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20
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109 </help>
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110 <citations>
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111 <citation type="bibtex">@misc{1401.1129,
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112 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
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113 Title = {Fast and accurate alignment of long bisulfite-seq reads},
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114 Year = {2014},
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115 Eprint = {arXiv:1401.1129},
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116 }</citation>
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117 </citations>
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118 </tool>
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