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1 <tool id="region_motif_compare" name="Region Motif Count Compare">
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2 <description>for comparing the motif counts in different region sets</description>
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3 <requirements>
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4 <requirement type="set_environment">RMOTIF_PATH</requirement>
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5 </requirements>
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6 <command interpreter="Rscript">
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7 region_motif_compare.r --args \$RMOTIF_PATH $pwm_file.fields.path $in_tab_1 $in_tab_2
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8 $out_enriched
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9 $out_depleted
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10 $out_plots
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11 </command>
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12 <inputs>
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13 <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/>
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14 <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/>
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15
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16 <param name="pwm_file" type="select" label="Using motif database PWM file">
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17 <options from_data_table="motif_databases"/>
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18 </param>
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19 </inputs>
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20
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21 <outputs>
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22 <data name="out_enriched" format="tabular" label="Enriched Motifs"/>
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23 <data name="out_depleted" format="tabular" label="Depleted Motifs"/>
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24 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/>
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25 </outputs>
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26
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27 <tests>
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28 <test>
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29 <param name="in_tab_1" value="XXX.tab" />
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30 <param name="in_tab_2" value="XXX.tab" />
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31 <param name="pwm_file" value="XXX.meme.txt" />
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32 <output name="out_enriched" file="XXX.tab" />
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33 <output name="out_depleted" file="XXX.tab" />
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34 <output name="out_plots" file="XXX.png" />
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35 </test>
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36 </tests>
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37
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38 <help>
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39 This tools reads in two counts file and determines enriched and depleted
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40 motifs in two different region sets based on poisson calculation with
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41 gc correction.
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42 </help>
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43
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44 </tool> |
