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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit 7684f3ec344aadd7a90332e5598a9756855aa177-dirty
author rnateam
date Fri, 15 Sep 2017 14:49:16 -0400
parents 6d3269dc319e
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6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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1 <tool id="AREsite2_REST" name="Get motifs from AREsite2" version="0.1.2">
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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2 <description>AREsite2 REST Interface</description>
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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3 <requirements>
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a3ce813ed604 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit 7684f3ec344aadd7a90332e5598a9756855aa177-dirty
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4 <requirement type="package" version="3.4">python</requirement>
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6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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5 <requirement type="package" version="2.12.4">requests</requirement>
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6 <requirement type="package" version="1.10.0">six</requirement>
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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7 </requirements>
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8 <command>
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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9 <![CDATA[
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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10 python '$__tool_directory__/aresite2.py'
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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11 -g '$gene'
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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12 -m '$motif'
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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13 -s '$species_selector'
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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14 > '$AREsite2_REST_out'
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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15 ]]>
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16 </command>
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6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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18 <inputs>
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19 <param name="gene" type="text" label="Gene ID to search for" help="Try e.g. cxcl2" />
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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20 <param name="species_selector" type="select" label="Select species">
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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21 <option value="Homo_sapiens" selected="true"></option>
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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22 <option value="Mus_musculus"></option>
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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23 <option value="Danio_rerio"></option>
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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24 <option value="Drosophila_melanogaster"></option>
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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25 <option value="Caenorhabditis_elegans"></option>
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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26 </param>
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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27 <param name="motif" type="text" label="Motif to search for" help="Choose a single motif, e.g. ATTTA" />
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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28 </inputs>
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29
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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30 <outputs>
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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31 <data name="AREsite2_REST_out" label="AREsite2_Rest_${motif}_${gene}_${species_selector}" format="bed" />
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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32 </outputs>
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33
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34 <tests>
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35 <test>
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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36 <param name="species" value="Homo_sapiens" />
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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37 <param name="motif" value="ATTTA" />
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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38 <param name="gene" value="Cxcl2" />
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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39 <output name="outputFile" file="AREsite2_Rest_ATTTA_cxcl2_Homo_sapiens.bed" />
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40 </test>
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41 </tests>
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42
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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43 <help>
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44 <![CDATA[
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45 **What it does**
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46
6d3269dc319e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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47 Retrieve motif information in BED format from AREsite2 using its REST API.
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48
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49 ]]>
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50 </help>
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51 <citations>
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52 <citation type="doi">10.1093/nar/gkv1238</citation>
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53 </citations>
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54 </tool>