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1 <tool id="macs2_randsample" name="MACS2 randsample" version="2.0.10.0">
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2 <description>Randomly sample number or percentage of total reads</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 randsample
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19
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10 -t "${ infile }"
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11 -o "${ 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
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15 @tag_size@
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16 #if $method_options.method_options_selector == 'percentage':
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19
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17 --percentage "${ method_options.percentage }"
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17
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18 #else:
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19
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19 --number "${ method_options.number }"
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17
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20 #end if
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21 </command>
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22 <expand macro="stdio" />
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23 <inputs>
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24 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
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25 <expand macro="tag_size" />
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26
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27 <conditional name="method_options">
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28 <param name="method_options_selector" type="select" label="Select action to be performed">
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29 <option value="percentage" selected="true">Percentage</option>
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30 <option value="number">Number</option>
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31 </param>
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32 <when value="percentage">
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33 <param name="percentage" type="float" value="80.0" label="Pvalue cutoff for binomial distribution test" help="(--percentage)" />
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34 </when>
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35 <when value="number">
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36 <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" />
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37 </when>
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38 </conditional>
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39 </inputs>
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40 <outputs>
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41 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
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42 </outputs>
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43 <tests>
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44 <!-- No test, due to the randomness -->
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45 </tests>
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46 <help>
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47 **What it does**
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48
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49 randsample tool from macs2
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50
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51 @citation@
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52 </help>
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53 </tool>
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