Mercurial > repos > mvdbeek > concatenate_multiple_datasets

annotate catWrapper.xml @ 1:1bf1794dfcf6 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
author mvdbeek
date Fri, 25 Sep 2015 11:07:07 -0400
parents cf750d0edbd8
children 745090cbbf75
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1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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1 <tool id="cat_multiple" name="Concatenate multiple datasets" version="0.2">
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2 <description>tail-to-head</description>
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1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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3 <command><![CDATA[
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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4 cat
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5 #for $file in $input
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1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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6 "$file"
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7 #end for
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1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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8 > "$out_file1"
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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9 ]]>
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10 </command>
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11 <inputs>
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12 <param name="input" type="data" label="Concatenate Dataset" multiple="True"/>
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13 </inputs>
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14 <outputs>
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15 <data name="out_file1" format_source="input" metadata_source="input"/>
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="input" value="1.bed,2.bed"/>
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20 <output name="out_file1" file="cat_wrapper_out1.bed"/>
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21 </test>
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22 </tests>
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23 <help>
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24
1
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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25 .. class:: warningmark
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26
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1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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27 **WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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28 tool does not check if the datasets being concatenated are in the same format.
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1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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30 -----
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31
1
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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32 **What it does**
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33
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1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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34 Concatenates datasets
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35
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1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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36 -----
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37
1
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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38 **Example**
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39
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1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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40 Concatenating Dataset::
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41
1
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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42 chrX 151087187 151087355 A 0 -
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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43 chrX 151572400 151572481 B 0 +
0
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44
1
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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45 with Dataset1::
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1
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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47 chr1 151242630 151242955 X 0 +
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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48 chr1 151271715 151271999 Y 0 +
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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49 chr1 151278832 151279227 Z 0 -
0
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50
1
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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51 and with Dataset2::
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52
1
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53 chr2 100000030 200000955 P 0 +
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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54 chr2 100000015 200000999 Q 0 +
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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55
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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56 will result in the following::
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57
1
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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58 chrX 151087187 151087355 A 0 -
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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59 chrX 151572400 151572481 B 0 +
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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60 chr1 151242630 151242955 X 0 +
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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61 chr1 151271715 151271999 Y 0 +
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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62 chr1 151278832 151279227 Z 0 -
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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63 chr2 100000030 200000955 P 0 +
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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64 chr2 100000015 200000999 Q 0 +
0
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65
1
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66 -----
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67
1
1bf1794dfcf6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concatenate_multiple_datasets commit 1542edc9d7c2b1e9649c52532a5630e23ac5ceda
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68 Adapted from the concatenate tool that comes with galaxy.
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69 </help>
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70 </tool>