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annotate cat.xml @ 10:c78b1767db2b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
author bgruening
date Fri, 26 Feb 2016 12:22:54 -0500
parents d9819ccb9ca7
children 3c685c4106b3
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1 <tool id="tp_cat" name="Concatenate datasets" version="0.1.0">
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2 <description>tail-to-head (cat)</description>
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3 <requirements>
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4 <requirement type="package" version="8.22">gnu_coreutils</requirement>
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5 </requirements>
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6 <version_command>
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7 <![CDATA[
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8 cat --version | head -n 1
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9 ]]>
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10 </version_command>
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11 <command>
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12 <![CDATA[
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13 cat
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14 #echo ' '.join(['"%s"' % $file for $file in $inputs])#
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15 #for $q in $queries:
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16 #echo ' '.join(['"%s"' % $file for $file in $q.inputs2])#
8
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17 #end for
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18 > $out_file1
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19 ]]></command>
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20 <inputs>
9
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21 <param name="inputs" multiple="true" type="data" format="txt" label="Datasets to concatenate"/>
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22 <repeat name="queries" title="Dataset">
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23 <param name="inputs2" type="data" format="txt" multiple="True" label="Select" />
9
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24 </repeat>
8
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25 </inputs>
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26 <outputs>
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27 <data name="out_file1" format_source="inputs" metadata_source="inputs"/>
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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="inputs" value="sort_result1.bed,sort_result2.bed,sort_result3.bed"/>
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32 <output name="out_file1" file="cat_result1.txt"/>
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33 </test>
9
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34 <test>
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35 <param name="inputs" value="sort_result1.bed,sort_result3.bed"/>
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36 <repeat name="queries">
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37 <param name="inputs2" value="sort_result3.bed,sort_result3.bed"/>
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38 </repeat>
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39 <repeat name="queries">
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40 <param name="inputs2" value="sort_result3.bed"/>
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41 </repeat>
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42 <output name="out_file1" file="cat_result2.txt"/>
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43 </test>
8
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44 </tests>
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45 <help>
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46 <![CDATA[
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47
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48 .. class:: warningmark
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49
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50 **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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52 -----
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53
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54 **What it does**
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55
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56 Concatenates datasets
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58 -----
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59
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60 **Example**
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62 Concatenating Dataset::
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64 chrX 151087187 151087355 A 0 -
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65 chrX 151572400 151572481 B 0 +
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67 with Dataset1::
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68
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69 chr1 151242630 151242955 X 0 +
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70 chr1 151271715 151271999 Y 0 +
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71 chr1 151278832 151279227 Z 0 -
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73 and with Dataset2::
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75 chr2 100000030 200000955 P 0 +
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76 chr2 100000015 200000999 Q 0 +
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78 will result in the following::
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80 chrX 151087187 151087355 A 0 -
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81 chrX 151572400 151572481 B 0 +
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82 chr1 151242630 151242955 X 0 +
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83 chr1 151271715 151271999 Y 0 +
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84 chr1 151278832 151279227 Z 0 -
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85 chr2 100000030 200000955 P 0 +
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86 chr2 100000015 200000999 Q 0 +
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87 ]]></help>
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88 </tool>