annotate groupbyBed.xml @ 11:7308cc546a36 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:35 -0400
parents 607c0576c6ab
children 95a3b2c25bd1
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1 <tool id="bedtools_groupbybed" name="GroupByBed" version="@WRAPPER_VERSION@.0">
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2 <description>group by common cols and summarize other cols</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 bedtools groupby
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11 -i "${inputA}"
7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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12 -g '$group'
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13 -c "${cols}"
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14 -o $operation
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15 > "${output}"
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param format="bed" name="inputA" type="data" label="BED file"/>
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20 <expand macro="choose_columns" />
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21 <param name="group" type="text" value="1,2,3"
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22 label="Specifies which column(s) (1-based) should be used to group the input"
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23 help="Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed. (-g)">
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24 <sanitizer invalid_char="">
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25 <valid initial="string.digits"><add value=","/><add value="-"/></valid>
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26 </sanitizer>
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27 </param>
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28 <param name="operation" type="select" label="Specify the operation" help="(-o)">
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29 <option value="sum" selected="True">Sum - numeric only</option>
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30 <option value="stdev">Stdev - numeric only</option>
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31 <option value="sstdev">Sstdev - numeric only</option>
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32 <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option>
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33 <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option>
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34 <option value="first">First - numeric or text</option>
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35 <option value="last">Last - numeric or text</option>
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36 <expand macro="math_options" />
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37 <expand macro="additional_math_options" />
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data format_source="inputA" name="output" metadata_source="inputA"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
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46 <param name="cols" value="9" />
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47 <param name="group" value="1,2,3" />
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48 <param name="operation" value="sum" />
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49 <output name="output" file="groupbyBed_result1.bed" ftype="bed" />
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50 </test>
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51 <test>
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52 <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
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53 <param name="cols" value="9" />
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54 <param name="group" value="1,2,3" />
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55 <param name="operation" value="min" />
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56 <output name="output" file="groupbyBed_result2.bed" ftype="bed" />
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57 </test>
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58 <test>
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59 <param name="inputA" value="groupbyBed1.bed" ftype="bed" />
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60 <param name="cols" value="9" />
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61 <param name="group" value="1-4" />
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62 <param name="operation" value="median" />
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63 <output name="output" file="groupbyBed_result3.bed" ftype="bed" />
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64 </test>
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65 </tests>
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66 <help>
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67 <![CDATA[
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68 **What it does**
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69
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70 Replicate lines in a file based on columns of comma-separated values.
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71
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72 @REFERENCES@
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73 ]]>
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74 </help>
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75 <expand macro="citations" />
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76 </tool>