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1 <tool id="bwameth" name="bwameth" version="0.20">
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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="0.4.6">toolshed</requirement>
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5 <requirement type="package" version="1.2">samtools</requirement>
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6 <requirement type="package" version="0.7.12">bwa</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
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10 <exit_code range=":-1" />
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11 <regex match="Error:" />
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12 <regex match="Exception:" />
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13 <regex match="Exception :" />
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14 </stdio>
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15 <command interpreter="python">
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16 <![CDATA[
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17 bwameth_wrapper.py
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18 -p "\${GALAXY_SLOTS:-4}"
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19
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20 #if $referenceSource.source != "indexed":
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21 --makeIndex $referenceSource.reference
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22 #else
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23 --premadeIndex $referenceSource.index.fields.path
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24 #end if
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25
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26 #if str($readGroup).strip() != "":
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27 --readGroup "${readGroup}"
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28 #end if
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29
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30 #if $single_or_paired.single_or_paired_opts == 'single':
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31 $single_or_paired.input_singles
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32 #else:
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33 $single_or_paired.input_mate1 $single_or_paired.input_mate2
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34 #end if
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35 ]]>
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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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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 </param>
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61 <when value="single">
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62 <param name="input_singles" type="data" format="fastq" label="FASTQ" help="FASTQ file." />
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63 </when>
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64 <when value="paired">
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65 <param name="input_mate1" type="data" format="fastq" label="First read in pair" help="FASTQ file." />
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66 <param name="input_mate2" type="data" format="fastq" label="Second read in pair" help="FASTQ file." />
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67 </when>
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68 </conditional>
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69 <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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70 </inputs>
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71 <outputs>
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72 <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" />
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="referenceSource" value="history" />
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77 <param name="reference" value="ref.fa" />
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78 <param name="single_or_paired_opts" value="paired" />
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79 <param name="input_mate1" value="t_R1.fastq.gz" />
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80 <param name="input_mate2" value="t_R2.fastq.gz" />
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81 <output file="output.bam" ftype="bam" name="output" compare="sim_size" delta="10000"/>
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82 </test>
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83 </tests>
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84 <help>
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85 <![CDATA[
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86
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87 **What it does**
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88
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89 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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90 ]]>
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91 </help>
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92 </tool>
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