annotate tools/filters/catWrapper.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="cat1" name="Concatenate datasets">
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2 <description>tail-to-head</description>
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3 <command interpreter="python">
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4 catWrapper.py
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5 $out_file1
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6 $input1
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7 #for $q in $queries
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8 ${q.input2}
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9 #end for
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10 </command>
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11 <inputs>
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12 <param name="input1" type="data" label="Concatenate Dataset"/>
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13 <repeat name="queries" title="Dataset">
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14 <param name="input2" type="data" label="Select" />
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15 </repeat>
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16 </inputs>
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17 <outputs>
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18 <data name="out_file1" format="input" metadata_source="input1"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input1" value="1.bed"/>
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23 <param name="input2" value="2.bed"/>
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24 <output name="out_file1" file="cat_wrapper_out1.bed"/>
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25 </test>
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26 <!--TODO: if possible, enhance the underlying test code to handle this test
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27 the problem is multiple params with the same name "input2"
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28 <test>
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29 <param name="input1" value="1.bed"/>
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30 <param name="input2" value="2.bed"/>
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31 <param name="input2" value="3.bed"/>
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32 <output name="out_file1" file="cat_wrapper_out2.bed"/>
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33 </test>
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34 -->
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35 </tests>
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36 <help>
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37
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38 .. class:: warningmark
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39
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40 **WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format.
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41
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42 -----
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43
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44 **What it does**
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45
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46 Concatenates datasets
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47
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48 -----
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49
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50 **Example**
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51
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52 Concatenating Dataset::
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53
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54 chrX 151087187 151087355 A 0 -
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55 chrX 151572400 151572481 B 0 +
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56
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57 with Dataset1::
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58
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59 chr1 151242630 151242955 X 0 +
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60 chr1 151271715 151271999 Y 0 +
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61 chr1 151278832 151279227 Z 0 -
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62
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63 and with Dataset2::
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64
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65 chr2 100000030 200000955 P 0 +
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66 chr2 100000015 200000999 Q 0 +
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67
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68 will result in the following::
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69
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70 chrX 151087187 151087355 A 0 -
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71 chrX 151572400 151572481 B 0 +
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72 chr1 151242630 151242955 X 0 +
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73 chr1 151271715 151271999 Y 0 +
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74 chr1 151278832 151279227 Z 0 -
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75 chr2 100000030 200000955 P 0 +
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76 chr2 100000015 200000999 Q 0 +
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77
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78 </help>
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79 </tool>