Mercurial > repos > jeremyjliu > region_motif_enrichment

annotate upload/region_motif_compare.xml @ 16:9a84f76db861 draft

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Fixed RMOTIF_PATH env variable for toolshed deployment
author jeremyjliu
date Wed, 12 Nov 2014 15:19:37 -0500
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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 $db_type $in_tab_1 $in_tab_2 $out_enriched $out_depleted $out_plots
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8 </command>
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9 <inputs>
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10 <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/>
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11 <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/>
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12 <param name="db_type" type="select" label="Select Motif Database" >
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13 <option value="t">Test Pouya Subset (hg19)</option>
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14 <option value="p">Pouya Encode Motifs (hg19)</option>
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15 <option value="j">Jaspar and Jolma Motifs (hg19)</option>
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16 <option value="m">Mouse Motifs (mm9)</option>
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17 <option value="c">Pouya, Jaspar, and Jolma Combined (hg19)</option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data name="out_enriched" format="tabular" label="Enriched Motifs"/>
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22 <data name="out_depleted" format="tabular" label="Depleted Motifs"/>
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23 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/>
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24 </outputs>
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25
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26 <help>
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27 This tools reads in two counts file and determines enriched and depleted
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28 motifs in two different region sets based on poisson calculation with
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29 gc correction.
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30 </help>
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31
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32 </tool>