Mercurial > repos > iuc > join_files_by_id

annotate join_files_by_id.xml @ 0:d212d12aee5e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
author iuc
date Wed, 09 Aug 2017 17:44:54 -0400
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d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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1 <tool id="join_files_by_id" name="Join datasets by identifier column" version="1.0">
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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2 <requirements>
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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3 <requirement type="package" version="1.10.4">r-data.table</requirement>
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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4 </requirements>
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iuc
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5 <command detect_errors="exit_code"><![CDATA[
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iuc
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6 Rscript '$__tool_directory__/join_files.R'
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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7 --out='$out_file1'
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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8 --he='$header'
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9 --jc='$field'
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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10 --sep='$delimiter'
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11 --nc='$null_str'
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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12 --in='$input1'
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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13 #for $q in $queries
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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14 --in='${q.input}'
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15 #end for
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16 ]]></command>
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17 <inputs>
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18 <param name="header" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Header" help="If header is true, the column name used for joining need to be the same in all datasets"/>
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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19 <param name="delimiter" type="select" label="Delimited by">
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20 <option value="ta">Tab</option>
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21 <option value="do">Dot</option>
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22 <option value="co">Comma</option>
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23 <option value="un">Underscore</option>
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24 <option value="da">Dash</option>
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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25 <option value="sp">Space</option>
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26 </param>
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27 <param name="null_str" type="select" label="Select mismatch character">
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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28 <option value="0">0</option>
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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29 <option value="-">-</option>
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30 <option value="">"empty"</option>
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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31 <option value="NA">NA</option>
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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32 </param>
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33 <param name="input1" type="data" format="tabular" label="Select table" help="Single dataset selection only to preserve the order"/>
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34 <repeat name="queries" min="1" title="Select table">
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35 <param name="input" type="data" format="tabular" label="Select table" help="Single dataset selection only to preserve the order"/>
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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36 </repeat>
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
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37 <param name="field" type="data_column" data_ref="input1" label="Column used for joining" />
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
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38 </inputs>
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39 <outputs>
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40 <data name="out_file1" format="tabular" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="header" value="1"/>
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45 <param name="null_str" value="0"/>
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46 <param name="delimiter" value="ta"/>
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47 <param name="input1" value="df1.txt"/>
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48 <repeat name="queries">
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49 <param name="input" value="df2.txt"/>
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50 </repeat>
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51 <repeat name="queries">
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52 <param name="input" value="df3.txt"/>
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53 </repeat>
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54 <param name="field" value="1"/>
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55 <output name="out_file1" file="df.txt"/>
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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59 **What it does**
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60
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61 Joins datasets by identifier column
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62
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63 -----
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64
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65 '''Example'''
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66
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67 Dataset 1:
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68
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69 +--------+--------+---------+
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70 | name | counts | percent |
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71 +========+========+=========+
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72 | gene 1 | 10 | 0.3 |
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73 +--------+--------+---------+
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74 | gene 2 | 20 | 0.2 |
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75 +--------+--------+---------+
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76 | gene 3 | 20 | 0.2 |
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77 +--------+--------+---------+
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78
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79
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80 and Dataset 2:
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81
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82 +--------+--------+---------+
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83 | name | counts | percent |
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84 +========+========+=========+
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85 | gene 1 | 13 | 0.5 |
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86 +--------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
87 | gene 4 | 4 | 0.4 |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
88 +--------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
89
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
90
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
91 and Dataset 3:
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
92
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
93 +--------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
94 | name | counts | percent |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
95 +========+========+=========+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
96 | gene 1 | 10 | 0.3 |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
97 +--------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
98 | gene 3 | 12 | 0.2 |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
99 +--------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
100 | gene 4 | 4 | 0.4 |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
101 +--------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
102 | gene 5 | 19 | 0.6 |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
103 +--------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
104
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
105
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
106 will result in the following:
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
107
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
108 +--------+--------+---------+--------+---------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
109 | name | counts | percent | counts | percent | counts | percent |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
110 +========+========+=========+========+=========+========+=========+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
111 | gene 1 | 10 | 0.3 | 13 | 0.5 | 10 | 0.3 |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
112 +--------+--------+---------+--------+---------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
113 | gene 2 | 20 | 0.2 | 0 | 0 | 0 | 0 |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
114 +--------+--------+---------+--------+---------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
115 | gene 3 | 12 | 0.2 | 0 | 0 | 12 | 0.2 |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
116 +--------+--------+---------+--------+---------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
117 | gene 4 | 0 | 0 | 4 | 0.4 | 4 | 0.4 |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
118 +--------+--------+---------+--------+---------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
119 | gene 5 | 0 | 0 | 0 | 0 | 19 | 0.6 |
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
120 +--------+--------+---------+--------+---------+--------+---------+
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
121
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
122 For help contact: jochen.bick@usys.ethz.ch
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
123 ]]></help>
d212d12aee5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id commit a835a0b20127f485a6af4b466bb29d58d63541ea
iuc
parents:
diff changeset
124 </tool>