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annotate bismark_deduplicate/bismark_deduplicate_wrapper.xml @ 7:fcadce4d9a06 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
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1 <tool id="bismark_deduplicate" name="Bismark Deduplicate" version="0.16.3">
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2
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3 <description>Deduplicates reads mapped by Bismark</description>
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4 <!--<version_command>bismark version</version_command>-->
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5
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6 <requirements>
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7 <requirement type="package" version="0.1.19">samtools</requirement>
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8 <requirement type="package" version="2.1.0">bowtie2</requirement>
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9 </requirements>
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11 <stdio>
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12 <exit_code range="1:" />
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13 <exit_code range=":-1" />
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14 <regex match="Error:" />
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15 <regex match="Exception:" />
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16 </stdio>
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18 <command interpreter="python">
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19 <![CDATA[
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20 bismark_deduplicate_wrapper.py
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21
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22 --tool_dir "$__tool_directory__"
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23
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24 #if str ( $sPaired ) == "single":
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25 -s
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26 #else
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27 -p
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28 #end if
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29
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30 --input "$mapping_output"
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31
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32 --output_report "$output_report"
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33 --output_bam "$output_bam"
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34
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35 ##--log_report "$log_report"
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36 ]]>
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37 </command>
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38
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39 <inputs>
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40 <param name="sPaired" type="select" label="Is this library mate-paired?" format="bam">
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41 <option value="single">Single-end</option>
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42 <option value="paired">Paired-end</option>
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43 </param>
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44 <param name="mapping_output" type="data" format="bam, sam" label="Submit the resulting bam/sam file from Bismark bisulfite mapper" />
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45 </inputs>
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46
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47 <outputs>
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48 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: deduplicated mapped reads" />
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49 <data name="output_report" format="txt" label="${tool.name} on ${on_string}: deduplication report"/>
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50 <!--<data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)"/>-->
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51 </outputs>
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52
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53 <help>
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54 <![CDATA[
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55 **What it does**
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56
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57 | This tool is supposed to remove alignments to the same position in the genome from the Bismark mapping output (both single and paired-end SAM files), which can arise by e.g. excessive PCR amplification. If sequences align to the same genomic position but on different strands they will be scored individually.
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58 |
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59 | Note that deduplication is not recommended for RRBS-type experiments!
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60 |
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61 | For single-end alignments only use the start-coordinate of a read will be used for deduplication.
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62 | For paired-end alignments the start-coordinate of the first read and the end coordinate of the second read will be used for deduplication.
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63
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64 ]]>
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65 </help>
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66 <citations>
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67 <citation type="doi">10.1093/bioinformatics/btr167</citation>
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68 </citations>
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69 </tool>