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27
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1 <tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.0">
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17
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2 <description>Remove duplicate reads at the same position</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <macros>
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6 <import>macs2_macros.xml</import>
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7 </macros>
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8 <command>
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9 macs2 filterdup
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19
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10 -i "${ infile }"
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26
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11 -o temp_outfile
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17
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12
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19
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13 --format '${ infile.extension.upper() }'
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17
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14 @effective_genome_size@
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15 @tag_size@
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19
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16 --pvalue "${ pvalue }"
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17
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17 #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
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19
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18 --keep-dup "${ keep_dup_options.user_keepdup }"
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17
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19 #else
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19
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20 --keep-dup "${ keep_dup_options.keep_dup_options_selector }"
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17
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21 #end if
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26
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22 ;
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23 mv temp_outfile "${ outfile }"
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17
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24 </command>
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25 <expand macro="stdio" />
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26 <inputs>
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27 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
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28 <expand macro="conditional_effective_genome_size" />
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29 <expand macro="tag_size" />
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30 <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="default: 1e-5 (--pvalue)" />
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31
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20
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32 <expand macro="keep_duplicates" />
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33
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17
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34 </inputs>
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35 <outputs>
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36 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="infile" value="ChIP_200K_w_dups.bed" ftype="bed"/>
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41 <param name="pvalue" value="1e-5"/>
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42 <param name="keep_dup_options_selector" value="auto"/>
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27
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43 <param name="effective_genome_size_options_selector" value="user_defined" />
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44 <param name="gsize" value="3300000000" />
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17
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45 <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/>
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46 </test>
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47 </tests>
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48 <help>
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49 **What it does**
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50
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51 Remove duplicate reads at the same position, then convert acceptable format to BED format.
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52 filterdup tool from macs2
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53
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54 @citation@
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55 </help>
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26
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56 <expand macro="citations" />
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17
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57 </tool>
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