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annotate macs2_filterdup.xml @ 53:8f6b37d29df5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
author iuc
date Thu, 25 Jan 2018 02:11:22 -0500
parents 1b3f899ef044
children 644444825ef9
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1 <tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.0">
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2 <description>Remove duplicate reads at the same position</description>
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3 <macros>
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4 <import>macs2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command><![CDATA[
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10 @home_dir@
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11 macs2 filterdup
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12 -i '${ infile }'
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13 -o '${ outfile }'
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14 --format '${ infile.extension.upper() }'
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15 @effective_genome_size@
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16 @tag_size@
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17 --pvalue '${ pvalue }'
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18 #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
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19 --keep-dup '${ keep_dup_options.user_keepdup }'
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20 #else
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21 --keep-dup '${ keep_dup_options.keep_dup_options_selector }'
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22 #end if
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
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27 <expand macro="conditional_effective_genome_size" />
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28 <expand macro="tag_size" />
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29 <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" />
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30 <expand macro="keep_duplicates" />
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32 </inputs>
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33 <outputs>
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34 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="infile" value="ChIP_200K_w_dups.bed" ftype="bed"/>
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39 <param name="pvalue" value="1e-5"/>
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40 <param name="keep_dup_options_selector" value="auto"/>
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41 <param name="effective_genome_size_options_selector" value="user_defined" />
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42 <param name="gsize" value="3300000000" />
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43 <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/>
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44 </test>
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45 </tests>
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46 <help>
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47 <![CDATA[
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48 **What it does**
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49
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50 This is **filterdup** utility from the MACS2_ Package. It removes duplicate reads and converts results to BED format.
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52 .. _MACS2: https://github.com/taoliu/MACS
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54 @citation@
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55 ]]>
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56 </help>
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57 <expand macro="citations" />
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58 </tool>