Mercurial > repos > artbio > concatenate_multiple_datasets

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
author artbio
date Sun, 11 Mar 2018 18:19:40 -0400
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6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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1 <tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="0.3">
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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2 <description>tail-to-head</description>
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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3 <command><![CDATA[
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4 #if $headers == "No":
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5 cat
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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6 #for $file in $input
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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7 "$file"
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8 #end for
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9 > "$out_file1"
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10 #else:
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11 #for $file in $input
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12 printf "# ${file.element_identifier}\n" >> "$out_file1" &&
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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13 cat "$file" >> "$out_file1" &&
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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14 #end for
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15 sleep 1
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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16 #end if
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="headers" type="select" label="include dataset names">
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21 <option value="No" selected="true">No</option>
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22 <option value="Yes">Yes</option>
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23 </param>
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24 <param name="input" type="data" label="Concatenate Dataset" multiple="True"/>
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25 </inputs>
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26 <outputs>
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27 <data name="out_file1" format_source="input" metadata_source="input"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="headers" value="No" />
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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32 <param name="input" value="1.bed,2.bed"/>
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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33 <output name="out_file1" file="cat_wrapper_out1.bed"/>
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34 </test>
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35 <test>
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36 <param name="headers" value="Yes" />
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37 <param name="input" value="1.bed,2.bed"/>
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38 <output name="out_file1" file="cat_wrapper_out2.bed"/>
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39 </test>
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40
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41 </tests>
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42 <help>
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44 .. class:: warningmark
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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46 **WARNING:** This tool does not check if the datasets being concatenated are in the same format.
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47
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48 -----
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50 **What it does**
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51
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52 Concatenates datasets
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54 -----
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56 **Example**
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58 Concatenating Dataset::
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60 chrX 151087187 151087355 A 0 -
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61 chrX 151572400 151572481 B 0 +
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62
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63 with Dataset1::
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64
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65 chr1 151242630 151242955 X 0 +
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66 chr1 151271715 151271999 Y 0 +
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67 chr1 151278832 151279227 Z 0 -
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68
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69 and with Dataset2::
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70
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71 chr2 100000030 200000955 P 0 +
6f54dc6b37da planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 732cefeff9a38b50f23820441422d4df3974b922
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72 chr2 100000015 200000999 Q 0 +
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74 will result in the following::
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75
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76 chrX 151087187 151087355 A 0 -
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77 chrX 151572400 151572481 B 0 +
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78 chr1 151242630 151242955 X 0 +
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79 chr1 151271715 151271999 Y 0 +
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80 chr1 151278832 151279227 Z 0 -
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81 chr2 100000030 200000955 P 0 +
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82 chr2 100000015 200000999 Q 0 +
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84 -----
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86 Adapted from galaxy's catWrapper.xml to allow multiple input files.
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87
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88 </help>
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89 </tool>