Mercurial > repos > jeremyjliu > region_motif_enrichment

annotate region_motif_compare.xml @ 1:1de6f7f3d513 draft

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author jeremyjliu
date Tue, 05 Aug 2014 13:57:32 -0400
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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 <command interpreter="bash">
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4 /usr/bin/R --slave --vanilla -f $GALAXY_ROOT_DIR/tools/my_tools/region_motif_compare.r --args $GALAXY_ROOT_DIR $db_type $in_tab_1 $in_tab_2 $out_enriched $out_depleted $out_plots
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5 </command>
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6 <inputs>
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7 <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/>
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8 <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/>
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9 <param name="db_type" type="select" label="Select Motif Database" >
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10 <option value="t">Test Pouya Subset (hg19)</option>
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11 <option value="p">Pouya Encode Motifs (hg19)</option>
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12 <option value="j">Jaspar and Jolma Motifs (hg19)</option>
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13 <option value="m">Mouse Motifs (mm9)</option>
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14 <option value="c">Pouya, Jaspar, and Jolma Combined (hg19)</option>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data name="out_enriched" format="tabular" label="Enriched Motifs"/>
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19 <data name="out_depleted" format="tabular" label="Depleted Motifs"/>
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20 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/>
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21 </outputs>
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22
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23 <help>
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24 This tools reads in two counts file and determines enriched and depleted
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25 motifs in two different region sets based on poisson calculation with
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26 gc correction.
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27 </help>
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28
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29 </tool>