Mercurial > repos > nml > csvtk_concat

annotate concat.xml @ 0:cd31fe25d6ac draft default tip

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:11:07 -0400
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0
cd31fe25d6ac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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1 <tool id="csvtk_concat" name="csvtk-concatenate" version="@VERSION@+@GALAXY_VERSION@">
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2 <description> concatenate CSV/TSV files by rows</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 ###################
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11 ## Start Command ##
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12 ###################
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13
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14 csvtk concat --num-cpus "\${GALAXY_SLOTS:-1}"
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15
cd31fe25d6ac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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16 ## Add additional flags as specified ##
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17 #######################################
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18 $ignore_case
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19 $global_param.illegal_rows
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20 $global_param.empty_rows
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21 $global_param.header
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22 $global_param.lazy_quotes
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23
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24 ## Set Tabular input/output flag if first input is tabular ##
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25 #############################################################
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26 #if $in_1[0].is_of_type("tabular"):
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27 -t -T
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28 #end if
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29
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30 ## Set input files ##
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31 #####################
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32 #for $file in $in_1:
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33 '$file'
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34 #end for
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35
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36 ## Fill unmatched ##
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37 ####################
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38 #if $fill.select == 'yes'
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39 -u '$fill.fill_value'
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40 #end if
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41
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42 ## To output ##
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43 ###############
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44 > concat
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45
cd31fe25d6ac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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46 ]]></command>
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47 <inputs>
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48 <expand macro="multi_input" />
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49 <conditional name="fill">
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50 <param name="select" type="select" label="Fill unmatched columns?">
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51 <option value="yes">Yes</option>
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52 <option value="no">No</option>
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53 </param>
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54 <when value="yes">
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55 <param name="fill_value" type="text" value="-" argument="-u"
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56 optional="false"
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57 label="Fill string"
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58 help="Input character string that will fill unmatched columns. The ' character is not allowed">
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59 <expand macro="text_sanitizer" />
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60 </param>
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61 </when>
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62 <when value="no" />
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63 </conditional>
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64 <expand macro="ignore_case" />
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65 <expand macro="global_parameters" />
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66 </inputs>
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67 <outputs>
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68 <data format_source="in_1" name="concat" from_work_dir="concat" label="${in_1[0].name} concatenated" />
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="in_1" value="test.csv,other.csv,another.csv" />
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73 <conditional name="fill">
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74 <param name="select" value="no" />
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75 </conditional>
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76 <output name="concat" file="concat_2.csv" />
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77 </test>
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78 <test>
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79 <param name="in_1" value="test.csv,other.csv,another.csv" />
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80 <output name="concat" file="concat_1.csv" />
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81 </test>
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82 </tests>
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83 <help><![CDATA[
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84
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85 Csvtk - Collapse Help
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86 ---------------------
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87
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88 Info
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89 ####
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90
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91 Csvtk concatenate CSV/TSV files by rows
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92
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93 **Order is important to input and the first file input will determine the header names!**
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94
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95 .. class:: warningmark
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96
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97 Single quotes are not allowed in text inputs!
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98
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99 @HELP_INPUT_DATA@
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100
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101
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102 Usage
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103 #####
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104
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105 To run csvtk-concatenate, all you need is one or more valid (as defined above) CSV or TSV files (of the same type) to concatenate together.
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106
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107 **Example Concatenate**
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108
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109 ::
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110
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111 If you have the following two files:
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112
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113 +-------+--------+ +-------+------+
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114 | Name | Colour | | Name | Food |
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115 +=======+========+ + +=======+======+
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116 | Steve | Blue | | Fred | Eggs |
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117 +-------+--------+ +-------+------+
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118 | Steve | Ham |
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119 +-------+------+
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120
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121 -----------------------------------------------
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122
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123 They would concatenate to:
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124
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125 +-------+--------+
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126 | Name | Colour |
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127 +=======+========+
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128 | Steve | Blue |
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129 +-------+--------+
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130 | Steve | |
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131 +-------+--------+
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132
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133 If you want, you can fill the empty cell with any set of characters so long as it doesn't contain an apostraphe (')
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134
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135 ----
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136
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137 @HELP_COLUMNS@
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138
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139
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140 @HELP_END_STATEMENT@
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141
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142
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143 ]]></help>
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144 <expand macro="citations" />
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145 </tool>