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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:23:57 -0400
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ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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1 <tool id="csvtk_summary" name="csvtk-summary" version="@VERSION@+@GALAXY_VERSION@">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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2 <description> statistics of selected fields</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 <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 ## Set Up Input ##
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11 ##################
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12
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13 #set input_list = list()
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14 #for $repeat in $field
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15 #silent $input_list.append(str($repeat.column_text.in_text) + ":" + str($repeat.analysis_type))
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16 #end for
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18 #set input_total = ",".join($input_list)
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20 ###################
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21 ## Start Command ##
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22 ###################
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23
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24 csvtk summary --num-cpus "\${GALAXY_SLOTS:-1}"
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25
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26 ## Add additional flags as specified ##
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27 #######################################
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28 $global_param.illegal_rows
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29 $global_param.empty_rows
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30 $global_param.header
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31 $global_param.lazy_quotes
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32
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33 ## Set Tabular input/output flag if input is tabular ##
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34 #######################################################
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35 #if $in_1.is_of_type("tabular"):
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36 -t -T
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37 #end if
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38
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39 ## Set Input ##
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40 ###############
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41 '$in_1'
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42
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43 ## Specify fields ##
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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44 ####################
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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45 -f '$input_total'
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46
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47 ## other ##
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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48 ###########
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49
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50 #if $group_field.select_group != "none"
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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51 -g '$group_field.in_text'
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52 #end if
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53
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54 -s '$extra.separator'
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55 -S '$extra.rand_int'
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56 -n '$decimal_width'
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57 $ignore_non_digits
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58
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59
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60 ## To output ##
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61 ###############
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62 > summary
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63
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64 ]]></command>
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65 <inputs>
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66 <expand macro="singular_input" />
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67 <repeat name="field" title="Select Column and Operator" min="1">
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68 <expand macro="singular_fields_input" />
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69 <param name="analysis_type" type="select" label="Analysis Type" help="Select analysis type to do on the chosen field">
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70 <option value="collapse">Collapse</option>
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71 <option value="count">Count</option>
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72 <option value="countn">Count of Digits (countn)</option>
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73 <option value="countunique">Count Unique</option>
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74 <option value="first">First Value</option>
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75 <option value="last">Last Value</option>
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76 <option value="max">Maximum</option>
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77 <option value="mean">Mean</option>
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78 <option value="median">Median</option>
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79 <option value="min">Minimum</option>
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80 <option value="prod">Product of the Elements</option>
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81 <option value="q1">q1</option>
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82 <option value="q2">q2</option>
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83 <option value="q3">q3</option>
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84 <option value="rand">Random Value</option>
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85 <option value="entropy">Shannon Entropy</option>
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86 <option value="stdev">Standard Deviation</option>
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87 <option value="sum">Sum</option>
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88 <option value="uniq">Unique</option>
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89 <option value="variance">Variance</option>
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90 </param>
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91 </repeat>
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92 <expand macro="groups_input" />
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93 <param name="decimal_width" type="integer" value="2" argument="-n"
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94 label="Number of Decimals"
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95 help="Limit float to N decimal places"
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96 />
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97 <param name="ignore_non_digits" type="boolean" checked="false" argument="-i"
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98 truevalue="-i"
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99 falsevalue=""
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100 label="Ignore non-digits"
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
101 help="Ignore non-digit values in columns. Ex. NA or N/A"
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
102 />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
103 <section name="extra" title="Specific Optional Analysis Modifiers" expanded="false">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
104 <param name="separator" type="text" value="; " argument="-s"
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
105 label="Collapse Separator String"
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
106 help="Input string of characters that will separate collapsed columns. The ' character is not allowed">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
107 <expand macro="text_sanitizer" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
108 </param>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
109 <param name="rand_int" type="integer" value="11" argument="-S"
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
110 label="Random Value Seed"
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
111 help="specify an integer"
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
112 />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
113 </section>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
114 <expand macro="global_parameters" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
115 </inputs>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
116 <outputs>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
117 <data format_source="in_1" name="summary" from_work_dir="summary" label="${in_1.name} summary of analyses" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
118 </outputs>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
119 <tests>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
120 <test>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
121 <param name="in_1" value="plot.csv" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
122 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
123 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
124 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
125 <param name="in_text" value="2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
126 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
127 <param name="analysis_type" value="collapse" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
128 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
129 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
130 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
131 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
132 <param name="in_text" value="3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
133 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
134 <param name="analysis_type" value="count" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
135 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
136 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
137 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
138 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
139 <param name="in_text" value="2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
140 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
141 <param name="analysis_type" value="countn" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
142 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
143 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
144 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
145 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
146 <param name="in_text" value="3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
147 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
148 <param name="analysis_type" value="countunique" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
149 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
150 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
151 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
152 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
153 <param name="in_text" value="2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
154 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
155 <param name="analysis_type" value="entropy" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
156 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
157 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
158 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
159 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
160 <param name="in_text" value="3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
161 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
162 <param name="analysis_type" value="first" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
163 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
164 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
165 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
166 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
167 <param name="in_text" value="2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
168 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
169 <param name="analysis_type" value="last" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
170 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
171 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
172 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
173 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
174 <param name="in_text" value="3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
175 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
176 <param name="analysis_type" value="max" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
177 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
178 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
179 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
180 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
181 <param name="in_text" value="2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
182 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
183 <param name="analysis_type" value="mean" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
184 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
185 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
186 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
187 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
188 <param name="in_text" value="3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
189 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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parents:
diff changeset
190 <param name="analysis_type" value="median" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
191 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
192 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
193 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
194 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
195 <param name="in_text" value="2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
196 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
197 <param name="analysis_type" value="min" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
198 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
199 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
200 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
201 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
202 <param name="in_text" value="3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
203 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
204 <param name="analysis_type" value="prod" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
205 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
206 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
207 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
208 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
209 <param name="in_text" value="2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
210 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
211 <param name="analysis_type" value="q1" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
212 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
213 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
214 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
215 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
216 <param name="in_text" value="3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
217 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
218 <param name="analysis_type" value="q2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
219 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
220 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
221 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
222 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
223 <param name="in_text" value="2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
224 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
225 <param name="analysis_type" value="q3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
226 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
227 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
228 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
229 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
230 <param name="in_text" value="3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
231 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
232 <param name="analysis_type" value="rand" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
233 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
234 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
235 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
236 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
237 <param name="in_text" value="2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
238 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
239 <param name="analysis_type" value="stdev" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
240 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
241 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
242 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
243 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
244 <param name="in_text" value="3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
245 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
246 <param name="analysis_type" value="sum" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
247 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
248 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
249 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
250 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
251 <param name="in_text" value="2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
252 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
253 <param name="analysis_type" value="uniq" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
254 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
255 <repeat name="field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
256 <conditional name="column_text">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
257 <param name="select" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
258 <param name="in_text" value="3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
259 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
260 <param name="analysis_type" value="variance" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
261 </repeat>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
262 <conditional name="group_field">
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
263 <param name="select_group" value="string" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
264 <param name="in_text" value="1" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
265 </conditional>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
266 <output name="summary" >
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
267 <assert_contents>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
268 <has_text text="collapse" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
269 <has_text text="count" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
270 <has_text text="countn" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
271 <has_text text="countunique" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
272 <has_text text="entropy" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
273 <has_text text="first" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
274 <has_text text="last" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
275 <has_text text="max" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
276 <has_text text="mean" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
277 <has_text text="median" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
278 <has_text text="min" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
279 <has_text text="prod" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
280 <has_text text="q1" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
281 <has_text text="q2" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
282 <has_text text="q3" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
283 <has_text text="rand" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
284 <has_text text="stdev" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
285 <has_text text="sum" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
286 <has_text text="uniq" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
287 <has_text text="variance" />
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
288 </assert_contents>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
289 </output>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
290 </test>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
291 </tests>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
292 <help><![CDATA[
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
293
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
294 Csvtk - Summary Help
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
295 --------------------
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
296
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
297 Info
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
298 ####
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
299
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
300 Csvtk Summary works to allow the use of a variety of analysis tools on the selected columns(s) and display one output at the end
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
301
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
302 .. class:: warningmark
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
nml
parents:
diff changeset
303
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304 Single quotes are not allowed in text inputs!
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305
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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306 @HELP_INPUT_DATA@
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307
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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308
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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309 Usage
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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310 #####
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311
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312 To run csvtk-summary, all you need is a valid (as defined above) CSV or TSV file with any column(s) that you want to
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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313 run one of the analyses on.
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314
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315 Analyses include:
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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316
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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317 - Collapse
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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318
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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319 - Count
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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320
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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321 - Count Numbers (countn)
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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322
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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323 - Count Unique
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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324
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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325 - First Value Selection
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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326
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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327 - Last Value Selection
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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328
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329 - Maximum
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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330
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331 - Mean
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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332
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333 - Median
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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334
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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335 - Minimum
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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336
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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337 - q1
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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338
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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339 - q2
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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340
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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341 - q3
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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342
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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343 - Random Value Selection
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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344
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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345 - Shannon Entropy
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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346
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347 - Sum
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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348
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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349 - Unique Values
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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350
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351 - Variance
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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352
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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353 More information on these can be found on the `csvtk website. <https://bioinf.shenwei.me/csvtk/usage/#summary>`_
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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354
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355 **Example Summary Input**
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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356
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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357 Input table:
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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358
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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359 +-------+--------+
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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360 | Group | Length |
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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361 +=======+========+
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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362 | A | 1500 |
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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363 +-------+--------+
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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364 | B | 1000 |
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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365 +-------+--------+
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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366 | B | 1500 |
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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367 +-------+--------+
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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368 | B | 2000 |
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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369 +-------+--------+
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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370
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371 Suppose you wanted to group the values based on column 1 of the input table and then find out the mean lenght and maximum length for each group.
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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372 You would input this into csvtk-summary by creating 2 input repeats where the first one selects "column 2" and an analysis of "mean" and the
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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373 second one selects "column 2" with an analysis of "maximum".
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374
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375 Running this would generate the following output:
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376
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377 +-------+-------------+------------+
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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378 | Group | Length:mean | Length:max |
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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379 +=======+=============+============+
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380 | A | 1500 | 1500 |
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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381 +-------+-------------+------------+
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382 | B | 1500 | 2000 |
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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383 +-------+-------------+------------+
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384
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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385 --------
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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386
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387
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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388 @HELP_COLUMNS@
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389
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390
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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391 @HELP_END_STATEMENT@
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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392
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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393
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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394 ]]></help>
ceb70f0dd898 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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395 <expand macro="citations" />
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396 </tool>