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7
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1 <tool id="macs2_predict" name="Predict" version="2.0.10.0">
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2 <description>d or fragment size from alignment results</description>
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3 <expand macro="requirements">
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4 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
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5 </expand>
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6 <expand macro="version_command" />
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7 <macros>
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8 <import>macs2_macros.xml</import>
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9 </macros>
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10 <command>
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11 macs2 predict
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12 -i #echo ','.join($infiles)#
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13 --tsize $tsize
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14 @effective_genome_size@
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15 --bw $band_width
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16 --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi
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17 > $outfile;
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18
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19 Rscript predicted_model.R > $outfile_image
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20 </command>
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21 <expand macro="stdio" />
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22 <inputs>
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23 <repeat name="infiles" title="ChIP-seq alignment files" min="1"
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24 help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command.">
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25
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26 <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" />
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27 </repeat>
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28
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29 <expand macro="conditional_effective_genome_size" />
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30 <expand macro="tag_size" />
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31
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32 <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
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33 help="This value is only used while building the shifting model. (--bw)" />
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34
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35 <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
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36 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
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37 <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
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38 help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
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39
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40 </inputs>
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41
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42 <outputs>
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43 <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
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44 <data name="outfile_image" format="png" label="${tool.name} on ${on_string} - X-correlation image" />
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45 </outputs>
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46 <tests>
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47 <!--none yet for macs2-->
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48 </tests>
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49 <help>
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50 **What it does**
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51
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52 bdgdiff from macs2
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53
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54
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55 Note that pair-end data is not supposed to work with this command.
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56
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57
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58 ------
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59
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60 **Citation**
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61
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62 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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63
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64 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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65 </help>
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66 </tool>
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