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annotate cat.xml @ 18:1e974b82380d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
author bgruening
date Tue, 27 Feb 2018 17:10:53 -0500
parents 7725ab6dab67
children 5fef6d08de83
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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 <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 <version_command>
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8 <![CDATA[
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9 cat --version | head -n 1
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10 ]]>
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11 </version_command>
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12 <command>
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13 <![CDATA[
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14 cat
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15 #echo ' '.join(['"%s"' % $file for $file in $inputs])#
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16 #for $q in $queries:
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17 #echo ' '.join(['"%s"' % $file for $file in $q.inputs2])#
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18 #end for
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19 > $out_file1
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20 ]]></command>
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21 <inputs>
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22 <param name="inputs" multiple="true" type="data" format="txt" label="Datasets to concatenate"/>
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23 <repeat name="queries" title="Dataset">
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24 <param name="inputs2" type="data" format="txt" multiple="True" label="Select" />
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25 </repeat>
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26 </inputs>
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27 <outputs>
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28 <data name="out_file1" format_source="inputs" metadata_source="inputs"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="inputs" value="sort_result1.bed,sort_result2.bed,sort_result3.bed"/>
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33 <output name="out_file1" file="cat_result1.txt"/>
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34 </test>
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35 <test>
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36 <param name="inputs" value="sort_result1.bed,sort_result3.bed"/>
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37 <repeat name="queries">
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38 <param name="inputs2" value="sort_result3.bed,sort_result3.bed"/>
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39 </repeat>
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40 <repeat name="queries">
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41 <param name="inputs2" value="sort_result3.bed"/>
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42 </repeat>
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43 <output name="out_file1" file="cat_result2.txt"/>
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44 </test>
8
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45 </tests>
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46 <help>
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47 <![CDATA[
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48
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49 .. class:: warningmark
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51 **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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53 -----
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55 **What it does**
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57 Concatenates datasets
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59 -----
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61 **Example**
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63 Concatenating Dataset::
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65 chrX 151087187 151087355 A 0 -
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66 chrX 151572400 151572481 B 0 +
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68 with Dataset1::
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70 chr1 151242630 151242955 X 0 +
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71 chr1 151271715 151271999 Y 0 +
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72 chr1 151278832 151279227 Z 0 -
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74 and with Dataset2::
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76 chr2 100000030 200000955 P 0 +
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77 chr2 100000015 200000999 Q 0 +
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79 will result in the following::
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81 chrX 151087187 151087355 A 0 -
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82 chrX 151572400 151572481 B 0 +
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83 chr1 151242630 151242955 X 0 +
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84 chr1 151271715 151271999 Y 0 +
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85 chr1 151278832 151279227 Z 0 -
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86 chr2 100000030 200000955 P 0 +
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87 chr2 100000015 200000999 Q 0 +
13
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88
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89 @REFERENCES@
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90 ]]>
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91 </help>
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92 <expand macro="citations" />
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fa7f88da29d7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
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93 </tool>