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1 <tool id="macs2_randsamoke" name="Randomly sample number or percentage" version="2.0.10.0">
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2 <description>of total reads</description>
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3 <requirements>
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4 <requirement type="python-module">macs2</requirement>
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5 <requirement type="python-module">numpy</requirement>
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6 <requirement type="package" version="2.0.10.2">macs2</requirement>
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7 <requirement type="package" version="1.7.1">numpy</requirement>
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8 </requirements>
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9 <command>
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10 macs2 randsample
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11 -t $infile
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12 -o $outfile
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13
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14 --format '$ifile.extension.upper()'
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15
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16 --tsize $tsize
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17 #if str($method_options.method_options_selector ) == 'percentage':
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18 $method_options.percentage
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19 #else:
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20 $method_options.number
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21 #end if
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22
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23 </command>
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24 <inputs>
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25
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26 <!--may need to add a few more formats at later time-->
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27 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
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28 <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will overide the auto detected tag size. DEFAULT: Not set (-1.0) (--tsize)" />
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29
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30 <conditional name="method_options">
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31 <param name="method_options_selector" type="select" label="Select action to be performed">
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32 <option value="percentage">Percentage</option>
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33 <option value="number">Number</option>
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34 </param>
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35 <when value="percentage">
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36 <param name="percentage" type="float" value="80.0" label="Pvalue cutoff for binomial distribution test" help="(--percentage)" />
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37 </when>
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38 <when value="number">
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39 <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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40 </when>
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41 </conditional>
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42
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43 </inputs>
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44 <outputs>
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45 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
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46 </outputs>
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47 <tests>
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48 <!--none yet for macs2-->
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49 </tests>
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50 <help>
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51 **What it does**
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52
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53 randsample tool from macs2
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54 ------
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55
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56 **Citation**
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57
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58 For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
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59
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60 Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
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61 </help>
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62 </tool>
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