annotate macros.xml @ 4:df55927535ed draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e6639e130c5bf50f489dd09e38a1cbc712280fff
author iuc
date Fri, 07 Apr 2023 15:02:25 +0000
parents 7c5da353e460
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8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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1 <macros>
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2 <token name="@TOOL_VERSION@">4.11</token>
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3 <!-- HOMER index version compatible with this version of HOMER
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4 This is the HOMER version that introduced the preparsed structure expected
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5 by the current version. -->
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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6 <token name="@IDX_VERSION@">4.11</token>
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7 <token name="@VERSION_SUFFIX@">3</token>
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8 <token name="@PROFILE@">20.05</token>
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9 <xml name="xrefs">
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10 <xrefs>
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11 <xref type="bio.tools">homer</xref>
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12 </xrefs>
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13 </xml>
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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14 <xml name="requirements">
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15 <requirements>
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16 <requirement type="package" version="@TOOL_VERSION@">homer</requirement>
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17 </requirements>
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18 </xml>
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19 <xml name="choose_center">
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20 <conditional name="choose_center">
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21 <param name="center" type="select" label="Do you want to center your sequence on the peak center?">
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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22 <option value="centered" selected="True">Yes</option>
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23 <option value="manual">No, I want asymetric (raise an error if given was chosen above)</option>
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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24 </param>
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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25 <when value="centered"/>
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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26 <when value="manual">
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27 <param name="sizes" type="integer" value="-100" label="sequence start relative to center"/>
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28 </when>
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29 </conditional>
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30 </xml>
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31 <xml name="mask_size">
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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32 <param argument="-mask" type="boolean" truevalue="True" falsevalue="False" label="mask repeats/lower case sequence"/>
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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33 <conditional name="fixed_size">
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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34 <param name="size_fixed" type="select" label="Do you want a fixed fragment size?">
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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35 <option value="fixed" selected="True">Yes</option>
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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36 <option value="given">No, I want to keep the size of my peaks (-size given)</option>
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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37 </param>
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38 <when value="given"/>
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39 <when value="fixed">
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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40 <param argument="-size" type="integer" min="0" value="200" label="fragment size in bp"/>
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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41 <expand macro="choose_center"/>
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42 </when>
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43 </conditional>
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44 </xml>
3
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45 <xml name="geneid_input">
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46 <param name="organism" type="select" label="What is the organism DB to be used?">
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47 <options from_data_table="homer_promoters">
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48 <filter type="sort_by" column="organism"/>
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49 <validator type="no_options" message="No pre-installed organism DBs are available. Contact your galaxy administrator."/>
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50 </options>
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51 </param>
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52 <param name="target_set" type="data" format="tabular" label="List of gene identifiers for the positive set"/>
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53 </xml>
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54 <xml name="citation">
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55 <citations>
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56 <citation type="doi">10.1016/j.molcel.2010.05.004</citation>
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57 </citations>
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58 </xml>
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59 </macros>