Mercurial > repos > rnateam > aresite2

annotate aresite2.xml @ 1:ed3a79e21230 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit 4897e30d01fe0ef4742bd58636269fdba5c09603
author rnateam
date Sat, 04 Mar 2017 14:42:30 -0500
parents a203c4ed9166
children bbb027389a54
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a203c4ed9166 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">
a203c4ed9166 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>
a203c4ed9166 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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4 <requirement type="package" version="2.12.4">requests</requirement>
a203c4ed9166 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="1.10.0">six</requirement>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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6 </requirements>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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7 <command>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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8 <![CDATA[
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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9 python '$__tool_directory__/aresite2.py'
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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10 -g '$gene'
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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11 -m '$motif'
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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12 -s '$species_selector'
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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13 > '$AREsite2_REST_out'
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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14 ]]>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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15 </command>
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16
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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17 <inputs>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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18 <param name="gene" type="text" label="Gene ID to search for" help="Try e.g. cxcl2" />
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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19 <param name="species_selector" type="select" label="Select species">
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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20 <option value="Homo_sapiens" selected="true"></option>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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21 <option value="Mus_musculus"></option>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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22 <option value="Danio_rerio"></option>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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23 <option value="Drosophila_melanogaster"></option>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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24 <option value="Caenorhabditis_elegans"></option>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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25 </param>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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26 <param name="motif" type="text" label="Motif to search for" help="Choose a single motif, e.g. ATTTA" />
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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27 </inputs>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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28
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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29 <outputs>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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30 <data name="AREsite2_REST_out" label="AREsite2_Rest_${motif}_${gene}_${species_selector}" format="bed" />
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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31 </outputs>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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32
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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33 <tests>
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34 <test>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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35 <param name="species" value="Homo_sapiens" />
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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36 <param name="motif" value="ATTTA" />
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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37 <param name="gene" value="Cxcl2" />
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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38 <output name="outputFile" file="AREsite2_Rest_ATTTA_cxcl2_Homo_sapiens.bed" />
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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39 </test>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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40 </tests>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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41
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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42 <help>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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43 <![CDATA[
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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44 **What it does**
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45
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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46 Retrieve motif information in BED format from AREsite2 using its REST API.
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47
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48 ]]>
a203c4ed9166 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
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49 </help>
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50 <citations>
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51 <citation type="doi">10.1093/nar/gkv1238</citation>
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52 </citations>
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53 </tool>