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annotate data_manager/bwameth_index_builder.xml @ 4:a9aa093e2392 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
author iuc
date Tue, 01 Oct 2019 17:53:16 -0400
parents a7fb84abef45
children 5ab25caa7b7d
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a9aa093e2392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
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1 <tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0.1">
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2 <description>builder</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.2.2</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive"><![CDATA[
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10 #if str($sequence_id).strip():
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11 #set $dbkey = $sequence_id
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12 #else:
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13 #set $dbkey = $all_fasta_source.fields.dbkey
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14 #end if
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15
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16 #if str($sequence_name).strip():
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17 #set $name = $sequence_name
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18 #else:
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19 #set $name = $all_fasta_source.fields.name
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20 #end if
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21
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22 python '$__tool_directory__/bwameth_index_builder.py' --output '${out_file}'
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23 --fasta_filename '${all_fasta_source.fields.path}'
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24 --dbkey '${dbkey}'
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25 --name '${name}'
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26 --data_table_name bwameth_indexes
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27 ]]></command>
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28 <inputs>
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29 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
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30 <options from_data_table="all_fasta" />
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31 </param>
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32 <param name="sequence_id" type="text" value="" label="ID for index" help="If not specified, the value from the fasta file is used"/>
a9aa093e2392 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
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33 <param name="sequence_name" type="text" value="" label="Displayed description for sequence" help="If not specified, the value from the fasta file is used"/>
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34 </inputs>
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35 <outputs>
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36 <data name="out_file" format="data_manager_json" />
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37 </outputs>
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38 <help><![CDATA[
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39 .. class:: infomark
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40
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41 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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43 What is BWA-meth?
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44 -----------------
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46 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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47
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48 ]]></help>
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49 <citations>
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50 <citation type="bibtex">@misc{1401.1129,
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51 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
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52 Title = {Fast and accurate alignment of long bisulfite-seq reads},
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53 Year = {2014},
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54 Eprint = {arXiv:1401.1129},
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55 }</citation>
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56 </citations>
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57 </tool>