Mercurial > repos > bgruening > column_arrange_by_header

annotate columnArrange.xml @ 0:f18f67056946 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit 088e73e958b55dc765778641b8a84080cc289f85-dirty
author bgruening
date Fri, 16 Oct 2015 14:31:13 -0400
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f18f67056946 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit 088e73e958b55dc765778641b8a84080cc289f85-dirty
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1 <tool id="bg_column_arrange_by_header" name="Column arrange" version="0.1">
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2 <description>by header name</description>
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3 <requirements>
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4 <requirement type="package" version="0.14.1">pandas</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 <![CDATA[
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8 column_arrange.py
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9 --columns
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10 #for token in $rep_param_columns:
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11 "$token.param_column"
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12 #end for
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13 --in $param_input
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14 --out $output
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param format="tabular" name="param_input" type="data" label="file to rearrange" />
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19 <repeat name ="rep_param_columns" min="1" title="Specify the first few columns by name">
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20 <param name="param_column" type="text" value="" label="column">
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21 <sanitizer>
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22 <valid initial="string.printable">
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23 <remove value="&apos;"/>
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24 </valid>
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25 </sanitizer>
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26 </param>
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27 </repeat>
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28 </inputs>
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29 <outputs>
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30 <data format="tabular" name="output" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="param_input" value="columnarrange_input1.tab"/>
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35 <repeat name="rep_param_columns">
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36 <param name="param_column" value="fname"/>
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37 </repeat>
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38 <repeat name="rep_param_columns">
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39 <param name="param_column" value="age"/>
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40 </repeat>
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41 <output name="out" file="columnarrange_result1.tab"/>
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42 </test>
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43 <test>
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44 <param name="param_input" value="columnarrange_input2.tab"/>
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45 <repeat name="rep_param_columns">
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46 <param name="param_column" value="first name"/>
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47 </repeat>
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48 <repeat name="rep_param_columns">
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49 <param name="param_column" value="nationality"/>
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50 </repeat>
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51 <output name="out" file="columnarrange_result2.tab"/>
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52 </test>
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53 </tests>
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54 <help>
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55 **What it does**
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56
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57 With this tool you can specify (by naming the header) which columns need to be leftmost.
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58 The columns which are not specified will be ordered as before, right of the columns which were specified.
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59
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60 Input file::
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61
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62 AHeader BHeader CHeader DHeader
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63 a b c d
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64 a b c d
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65
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66 Specifying **CHeader** and **BHeader**, as the columns that should be leftmost, generates::
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67
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68 CHeader BHeader AHeader DHeader
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69 c b a d
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70 c b a d
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71
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72 </help>
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73 <citations>
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74 <citation type="bibtex">
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75 @ARTICLE{bgruening_galaxytools,
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76 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
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77 keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
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78 title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
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79 url = {https://github.com/bgruening/galaxytools}
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80 }
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81 </citation>
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82 </citations>
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83 </tool>