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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:12:29 -0400
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0
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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1 <tool id="csvtk_sample" name="csvtk-sample" version="@VERSION@+@GALAXY_VERSION@">
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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2 <description> random proportion of dataset</description>
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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3 <macros>
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4 <import>macros.xml</import>
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_cmd" />
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 ###################
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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11 ## Start Command ##
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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12 ###################
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13
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14 csvtk sample --num-cpus "\${GALAXY_SLOTS:-1}"
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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15
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16 ## Add additional flags as specified ##
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17 #######################################
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18 $global_param.illegal_rows
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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19 $global_param.empty_rows
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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20 $global_param.header
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21 $global_param.lazy_quotes
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22
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23 ## Set Tabular input/output flag if input is tabular ##
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24 #######################################################
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25 #if $in_1.is_of_type("tabular"):
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26 -t -T
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27 #end if
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28
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29 ## Set Input ##
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30 ###############
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31 '$in_1'
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32
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33 ## other ##
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34 ###########
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35 -p '$proportion'
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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36 -s '$seed'
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37 $line_number
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38
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39 ## To output ##
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40 ###############
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41 &> sampled
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42
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43 ]]></command>
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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44 <inputs>
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45 <expand macro="singular_input" />
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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46 <param name="proportion" type="float" argument="-p" value="0.5"
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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47 min="0"
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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48 max="1"
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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49 label="Proportion of Data to Sample"
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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50 />
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51 <param name="seed" type="integer" argument="-s" value="1900"
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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52 label="Random Seed"
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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53 help="Specify a seed number to sample data with"
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54 />
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55 <param name="line_number" type="boolean" checked="false" argument="-n"
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56 truevalue="-n"
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57 falsevalue=""
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58 label="Create column with original line numbers of sampled data"
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59 />
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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60 <expand macro="global_parameters" />
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61 </inputs>
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62 <outputs>
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63 <data format_source="in_1" name="sampled" from_work_dir="sampled" label="${proportion} of ${in_1.name} sampled" />
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="in_1" value="plot.csv" />
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68 <param name="proportion" value="0.5" />
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69 <param name="seed" value="11" />
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70 <output name="sampled" value="sampled_1.csv" />
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71 </test>
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72 <test>
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73 <param name="in_1" value="plot.csv" />
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74 <param name="proportion" value="0.7" />
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75 <param name="seed" value="11" />
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76 <param name="line_number" value="true" />
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77 <output name="sampled" value="sampled_2.csv" />
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78 </test>
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79 </tests>
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80 <help><![CDATA[
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81
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82 Csvtk - Sample Help
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83 -------------------
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84
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85 Info
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86 ####
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87
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88 Csvtk-sample samples a random (as defined by the seed) proportion of a dataset that can be used further.
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89
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90 .. class:: warningmark
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91
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92 Single quotes are not allowed in text inputs!
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93
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94 @HELP_INPUT_DATA@
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95
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96
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97 Usage
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98 #####
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99
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100 To run csvtk-sample, all you need is a valid (as defined above) CSV or TSV file.
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101
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102 **Example**
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103
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104 Input table:
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105
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
106 +-------+--------+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
107 | Group | Length |
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
108 +=======+========+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
109 | 1 | 1500 |
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
110 +-------+--------+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
111 | 2 | 1000 |
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
112 +-------+--------+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
113 | 1 | 1500 |
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
114 +-------+--------+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
115 | 3 | 2000 |
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
116 +-------+--------+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
117
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
118 To get a 0.5 proportion (50% sample) of the population, our input would be 0.5 for the proportion (-p) and then some random seed.
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
119
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
120 Our output could then look as such:
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
121
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
122 +-------+--------+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
123 | Group | Length |
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
124 +=======+========+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
125 | 1 | 1500 |
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
126 +-------+--------+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
127 | 3 | 2000 |
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
128 +-------+--------+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
129
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
130 If we used the same seed, input, and proportion with the "Create column with original line numbers of sampled data"
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
131 set to yes, we would get the following table:
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
132
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
133 +---+-------+--------+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
134 | n | Group | Length |
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
135 +===+=======+========+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
136 | 1 | 1 | 1500 |
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
137 +---+-------+--------+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
138 | 4 | 3 | 2000 |
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
139 +---+-------+--------+
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
140
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
141 --------
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
142
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
143
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
144 @HELP_COLUMNS@
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
145
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
146
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
147 @HELP_END_STATEMENT@
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
148
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
149
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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150 ]]></help>
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
151 <expand macro="citations" />
447272175720 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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152 </tool>