Mercurial > repos > bgruening > bismark

annotate bismark2report_wrapper.xml @ 17:aa9bf0f29a9f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
author bgruening
date Wed, 28 Aug 2019 07:08:45 -0400
parents f211753166bd
children
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1 <tool id="bismark_pretty_report" name="Bismark Pretty Report" version="0.22.1" profile="17.01">
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2 <description>Generates a graphical HTML report page from report outputs of Bismark</description>
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3 <requirements>
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4 <requirement type="package" version="0.22.1">bismark</requirement>
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5 <requirement type="package" version="1.8">samtools</requirement>
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6 <requirement type="package" version="2.3.5">bowtie2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 python '$__tool_directory__/bismark2report_wrapper.py'
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11 --alignment_report '$alignment'
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13 #if $additional_reports['dedup']:
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14 --dedup_report '$additional_reports["dedup"]'
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15 #end if
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16 #if $additional_reports['splitting']:
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17 --splitting_report '$additional_reports["splitting"]'
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18 #end if
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19 #if $additional_reports['mbias']:
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20 --mbias_report '$additional_reports["mbias"]'
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21 #end if
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22 #if $additional_reports['nucleotide']:
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23 --nucleotide_report '$additional_reports["nucleotide"]'
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24 #end if
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26 --output_html_report '$output_html_report'
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28 #if $separate_logfile:
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29 --log_report '$log_report'
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30 #end if
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31 ]]>
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32 </command>
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34 <inputs>
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35 <param name="alignment" type="data" format="txt" label="Submit a Bismark mapping report" optional="False"/>
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36 <section name="additional_reports" title="Additional reports to include in the HTML page (optional)"
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37 expanded="True">
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38 <param name="dedup" type="data" format="txt" label="Submit the corresponding Bismark deduplication report"
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39 optional="True" help="Optional output of the module *Bismark Deduplicate*"/>
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40 <param name="splitting" type="data" format="txt" label="Submit the corresponding Bismark splitting report"
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41 optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/>
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42 <param name="mbias" type="data" format="txt" label="Submit the corresponding Bismark M-bias report"
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43 optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/>
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44 <param name="nucleotide" type="data" format="txt" label="Submit the corresponding Bismark nucleotide report"
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45 optional="True" help="Optional output of the module *Bismark Mapping*"/>
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46 </section>
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47 <param name="separate_logfile" type="boolean" truevalue="true" falsevalue="false" checked="False"
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48 label="Create a separate logfile, otherwise logs are added to the dataset info."/>
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49 </inputs>
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50
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51 <outputs>
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52 <data name="output_html_report" format="html"
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53 label="${tool.name} on ${on_string}: Download pretty html report"/>
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54 <data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)">
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55 <filter>( separate_logfile is True )</filter>
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56 </data>
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57 </outputs>
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58
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59 <tests>
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60 <test>
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61 <param name="alignment" value="mapping_report.txt" ftype="txt"/>
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62 <param name="dedup" value="dedup_report.txt" ftype="txt"/>
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63 <param name="splitting" value="output_splitting_report.txt" ftype="txt"/>
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64 <param name="mbias" value="output_mbias_report.txt" ftype="txt"/>
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65 <output name="output_html_report" file="output_html_report.html" ftype="html" lines_diff="8"/>
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66 </test>
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67 </tests>
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68
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69 <help>
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70 <![CDATA[
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71 **What it does**
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73 | This tool uses a Bismark alignment report to generate a graphical HTML report page.
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74 | Optionally, further reports of the Bismark suite such as deduplication, methylation extractor splitting or M-bias reports can be specified as well.
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75
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76 ]]>
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77 </help>
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78 <citations>
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79 <citation type="doi">10.1093/bioinformatics/btr167</citation>
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80 </citations>
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81 </tool>