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1 <tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0">
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2 <description>Predict '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 <requirement type="package" version="4.1.0">gnu_awk</requirement>
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6 </expand>
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7 <expand macro="version_command" />
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8 <macros>
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9 <import>macs2_macros.xml</import>
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10 </macros>
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11 <command>
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12 macs2 predictd
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13 -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
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14 @tag_size@
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15 @effective_genome_size@
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16 --bw "${ band_width }"
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17 --mfold "${ mfoldlo }" "${ mfoldhi }"
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18
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19 ## remove the timepoint and strip the output
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20 2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'
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21
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22 > "${ outfile }"
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23
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24 &&
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25
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26 Rscript predictd
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27 </command>
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28 <expand macro="stdio" />
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29 <inputs>
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30 <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" 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. (-i)" />
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31 <expand macro="conditional_effective_genome_size" />
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32 <expand macro="tag_size" />
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33 <expand macro="band_width" />
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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 ${on_string} - d value" />
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44 <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${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 <test>
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48 <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" />
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49 <param name="effective_genome_size_options_selector" value="user_defined" />
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50 <param name="gsize" value="3300000000" />
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51 <param name="tsize" value="-1.0"/>
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52 <param name="band_width" value="300"/>
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53 <param name="mfoldlo" value="5"/>
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54 <param name="mfoldhi" value="50"/>
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55 <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/>
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56 <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
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57 </test>
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58 </tests>
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59 <help>
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60 **What it does**
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61
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62 predictd from macs2
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63
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64
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65 Note that pair-end data is not supposed to work with this command.
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66
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67
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68 @citation@
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69 </help>
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70 <expand macro="citations" />
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71 </tool>
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