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1 <tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0">
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2 <description>builder</description>
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3 <requirements>
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1
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4 <requirement type="package" version="0.7.12">bwa</requirement>
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5 <requirement type="package" version="1.2">samtools</requirement>
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6 <requirement type="package" version="0.2.0">bwameth</requirement>
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7 </requirements>
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8 <command detect_errors="aggressive"><![CDATA[
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9 #if str($sequence_id).strip() != "":
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10 #set $dbkey = $sequence_id
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11 #else:
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12 #set $dbkey = $all_fasta_source.fields.dbkey
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13 #end if
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14
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15 #if str($sequence_name).strip() != "":
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16 #set $name = $sequence_name
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17 #else:
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18 #set $name = $all_fasta_source.fields.name
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19 #end if
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20
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21 #if str($sequence_description).strip() != "":
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22 #set $name = $sequence_description
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23 #else:
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24 #set $name = $all_fasta_source.fields.description
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25 #end if
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26
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27 python $__tool_directory__/bwameth_index_builder.py --output "${out_file}"
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28 --fasta_filename "${all_fasta_source.fields.path}"
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29 --dbkey "${dbkey}"
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30 --name "${name}"
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31 --description "${name}"
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32 --data_table_name "bwameth_indexes"
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33 ]]>
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34 </command>
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35 <inputs>
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36 <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
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37 <options from_data_table="all_fasta" />
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38 </param>
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39 <param label="ID for index" name="sequence_id" type="text" value="" help="If not specified, the value from the fasta file is used"/>
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40 <param label="Name for index" name="sequence_name" type="text" value="" help="If not specified, the value from the fasta file is used"/>
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41 <param label="Displayed description for sequence" name="sequence_description" type="text" value="" help="If not specified, the value from the fasta file is used"/>
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42 </inputs>
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43 <outputs>
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44 <data format="data_manager_json" name="out_file" />
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45 </outputs>
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46 <help>
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47 <![CDATA[
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48 .. class:: infomark
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49
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50 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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51
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52 What is BWA-meth?
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53 -----------------
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54
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55 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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56
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57 ]]>
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58 </help>
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59 <citations>
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60 <citation type="bibtex">@misc{1401.1129,
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61 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
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62 Title = {Fast and accurate alignment of long bisulfite-seq reads},
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63 Year = {2014},
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64 Eprint = {arXiv:1401.1129},
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65 }</citation>
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66 </citations>
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67 </tool>
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