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18
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
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6 <requirement type="package" version="4.11.1">meme</requirement>
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7 <requirement type="package" version="0.5">multigps</requirement>
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8 </requirements>
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9 </xml>
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10 <xml name="stdio">
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11 <stdio>
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12 <exit_code range="1:"/>
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13 <exit_code range=":-1"/>
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14 <regex match="Error:"/>
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15 <regex match="Exception:"/>
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16 </stdio>
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17 </xml>
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18 <xml name="rd_cond">
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19 <conditional name="read_distribution_cond">
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20 <param name="read_distribution" type="select" label="Use read distribution file for this replicate?" help="Selecting No uses default distribution.">
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21 <option value="no" selected="True">No</option>
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22 <option value="yes">Yes</option>
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23 </param>
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24 <when value="yes">
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25 <param name="read_distribution_file" type="data" format="tabular" label="Read distribution file" />
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26 </when>
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27 <when value="no" />
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28 </conditional>
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29 </xml>
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30 <xml name="frc_param">
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31 <param name="fixed_read_count" type="select" label="Use fixed per-base read count limit for this replicate?" help="Selecting No uses a global per-base limit that is estimated from a Poisson distribution.">
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32 <option value="no" selected="True">No</option>
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33 <option value="yes">Yes</option>
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34 </param>
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35 </xml>
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36 <xml name="motif_finding_params">
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37 <param name="memenmotifs" type="integer" min="0" value="3" label="Number of motifs MEME should find for each condition" />
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38 <param name="mememinw" type="integer" min="0" value="6" label="Minimum motif width for MEME" />
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39 <param name="mememaxw" type="integer" min="0" value="16" label="Maximum motif width for MEME" />
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40 </xml>
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41 <xml name="citations">
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42 <citations>
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43 <citation type="doi">10.1371/journal.pcbi.1003501</citation>
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44 </citations>
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45 </xml>
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46 </macros>
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