Mercurial > repos > iuc > datamash_ops
annotate datamash-ops.xml @ 3:419027d822d6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
author | iuc |
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date | Sun, 10 Apr 2022 11:41:19 +0000 |
parents | 562f3c677828 |
children | 746e8e4bf929 |
rev | line source |
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3
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
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changeset
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1 <tool id="datamash_ops" name="Datamash" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
0
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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changeset
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2 <description>(operations on tabular data)</description> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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changeset
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3 <macros> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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5 </macros> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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6 <expand macro="requirements" /> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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7 <expand macro="stdio" /> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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8 <command> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
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9 <![CDATA[ |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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10 datamash |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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11 $header_in |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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12 $header_out |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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13 $need_sort |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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14 $print_full_line |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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15 $ignore_case |
3
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
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16 @FIELD_SEPARATOR@ |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
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17 #if str($grouping) != '' |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
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18 --group '$grouping' |
0
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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changeset
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19 #end if |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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20 #for $oper in $operations |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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21 ${oper.op_name} |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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22 ${oper.op_column} |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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23 #end for |
2
562f3c677828
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents:
1
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24 < $in_file > '$out_file' |
0
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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25 ]]> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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26 </command> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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27 <expand macro="inputs_outputs"> |
3
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
changeset
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28 <param argument="--group" name="grouping" type="text" label="Group by fields" help="Group consecutive rows with equal values in the chosen fields. If no columns are specified, each operation is performed in the entire input file. Comma separated list of column indices, e.g. 1,5"> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
changeset
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29 <sanitizer invalid_char=""> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
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changeset
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30 <valid initial="string.digits"> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
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31 <add value="," /> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
changeset
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32 </valid> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
changeset
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33 <mapping initial="none"> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
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changeset
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34 <add source=" " target=""/> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
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changeset
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35 </mapping> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
changeset
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36 </sanitizer> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
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37 <validator message="Invalid value in field. Allowed is a comma separated list of integer values or the empty string" type="regex">(^$)|(^\s*\d+\s*(,\s*\d+\s*)*$)</validator> |
0
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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38 </param> |
3
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
changeset
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39 <param argument="--sort" name="need_sort" type="boolean" truevalue="--sort" falsevalue="" label="Sort input" help="Input file must be sorted by the grouping columns. Enable this option to automatically sort the input."/> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
changeset
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40 <param argument="--header-in" type="boolean" truevalue="--header-in" falsevalue="" label="Input file has a header line" /> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
changeset
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41 <param argument="--header-out" type="boolean" truevalue="--header-out" falsevalue="" label="Print header line" /> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
changeset
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42 <param argument="--full" name="print_full_line" type="boolean" truevalue="--full" falsevalue="" label="Print all fields from input file" /> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
changeset
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43 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" label="Ignore case when grouping" /> |
419027d822d6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
iuc
parents:
2
diff
changeset
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44 <repeat name="operations" default="1" min="1" title="Operation to perform on each group"> |
1
2f3c6f2dcf39
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
parents:
0
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45 <param name="op_name" type="select" label="Type"> |
0
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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changeset
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46 <option value="count">count</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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47 <option value="sum">sum</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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48 <option value="min">minimum</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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49 <option value="max">maximum</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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50 <option value="absmin">Absolute minimum</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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51 <option value="absmax">Absolute maximum</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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52 <option value="mean">Mean</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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53 <option value="pstdev">Population Standard deviantion</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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54 <option value="sstdev">Sample Standard deviantion</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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55 <option value="median">Median</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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56 <option value="q1">1st quartile</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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57 <option value="q3">3rd quartile</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
changeset
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58 <option value="iqr">Inter-quartile range</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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59 <option value="mad">Median Absolute Deviation</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
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60 <option value="pvar">Variance (population)</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
diff
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61 <option value="svar">Variance (sample)</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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62 <option value="sskew">Skewness (sample)</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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63 <option value="pskew">Skewness (population)</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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64 <option value="skurt">Kurtosis (sample)</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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65 <option value="pkurt">Kurtosis (population)</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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66 <option value="jarque">Jarque-Bera Normality test</option> |
2
562f3c677828
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
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67 <option value="dpo">D Agostino-Pearson Omnibus Normality Test</option> |
0
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
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68 <option value="mode">Mode</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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69 <option value="antimode">Anti-Mode</option> |
2
562f3c677828
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents:
1
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70 <option value="rand">One random value from the group</option> |
0
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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71 <option value="unique">Combine all unique values</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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72 <option value="collapse">Combine all values</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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73 <option value="countunique">Count Unique values</option> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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74 </param> |
1
2f3c6f2dcf39
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 5a6df0b54ca66fb588886b4610bbd837cd624fed
iuc
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75 <param name="op_column" data_ref="in_file" label="On column" type="data_column" /> |
0
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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76 </repeat> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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77 </expand> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
iuc
parents:
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78 <tests> |
c4611129661b
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79 <test> |
1
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80 <param name="in_file" value="group_compute_input.txt" ftype="tabular" /> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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81 <param name="grouping" value="2" /> |
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82 <param name="header_in" value="true" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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83 <param name="header_out" value="true" /> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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84 <param name="need_sort" value="true" /> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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85 <param name="print_full_line" value="false" /> |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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86 <param name="ignore_case" value="false" /> |
1
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87 <repeat name="operations"> |
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88 <param name="op_name" value="sum" /> |
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89 <param name="op_column" value="3" /> |
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90 </repeat> |
2
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91 <output file="group_compute_output.txt" name="out_file" ftype="tabular" /> |
0
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92 </test> |
3
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93 <test> |
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94 <param name="in_file" value="group_compute_input.txt" ftype="tsv" /> |
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95 <param name="grouping" value="2" /> |
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96 <param name="header_in" value="true" /> |
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97 <param name="header_out" value="true" /> |
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98 <param name="need_sort" value="true" /> |
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99 <param name="print_full_line" value="false" /> |
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100 <param name="ignore_case" value="false" /> |
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101 <repeat name="operations"> |
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102 <param name="op_name" value="sum" /> |
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103 <param name="op_column" value="3" /> |
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104 </repeat> |
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105 <output file="group_compute_output.txt" name="out_file" ftype="tsv" /> |
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106 </test> |
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107 <test> |
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108 <param name="in_file" value="group_compute_input.csv" ftype="csv" /> |
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109 <param name="grouping" value="2" /> |
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110 <param name="header_in" value="true" /> |
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111 <param name="header_out" value="true" /> |
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112 <param name="need_sort" value="true" /> |
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113 <param name="print_full_line" value="false" /> |
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114 <param name="ignore_case" value="false" /> |
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115 <repeat name="operations"> |
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116 <param name="op_name" value="sum" /> |
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117 <param name="op_column" value="3" /> |
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118 </repeat> |
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119 <output name="out_file" ftype="csv"> |
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120 <assert_contents> |
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121 <has_n_lines n="7"/> |
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122 <has_line line="Arts,1310"/> |
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123 </assert_contents> |
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124 </output> |
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125 </test> |
0
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126 </tests> |
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127 <help> |
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128 <![CDATA[ |
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129 @HELP_HEADER@ |
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130 |
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131 **Syntax** |
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132 |
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133 This tools performs common operations (such as summing, counting, mean, standard-deviation) on input file, based on tabular data. The tool can also optionaly group the input based on a given field. |
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134 |
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135 ----- |
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136 |
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137 **Example 1** |
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138 |
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139 - Find the average score in statistics course of college students, grouped by their college major. The input file has three fields (Name,Major,Score) and a header line:: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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140 |
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141 Name Major Score |
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142 Bryan Arts 68 |
3
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143 Gabriel Health-Medicine 100 |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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144 Isaiah Arts 80 |
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145 Tysza Business 92 |
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146 Zackery Engineering 54 |
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147 ... |
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148 ... |
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149 |
3
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150 - Grouping the input by the second column (*Major*), sorting the input, and performing operations **mean** and **sample standard deviation** on the third column (*Score*), gives:: |
0
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151 |
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152 GroupBy(Major) mean(Score) sstdev(Score) |
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153 Arts 68.9474 10.4215 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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154 Business 87.3636 5.18214 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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155 Engineering 66.5385 19.8814 |
c4611129661b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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156 Health-Medicine 90.6154 9.22441 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
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157 Life-Sciences 55.3333 20.606 |
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158 Social-Sciences 60.2667 17.2273 |
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159 |
3
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160 Note that input needs sorting here, since the column used for grouping (*Major*) is not sorted. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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161 |
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162 This sample file is available at http://www.gnu.org/software/datamash . |
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163 |
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164 **Example 2** |
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165 |
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166 - Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz |
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167 |
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168 - List the number and identifiers of isoforms per gene. The gene identifier is in column 13, the isoform/transcript identifier is in column 2. Grouping by column 13 and performing **count** and **Combine all values** on column 2, gives:: |
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169 |
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170 GroupBy(field-13) count(field-2) collapse(field-2) |
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171 A1BG 1 NM_130786 |
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172 A1BG-AS1 1 NR_015380 |
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173 A1CF 6 NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933 |
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174 A2M 1 NM_000014 |
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175 A2M-AS1 1 NR_026971 |
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176 A2ML1 2 NM_001282424,NM_144670 |
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177 ... |
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178 |
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179 - Count how many transcripts are listed for each chromosome and strand. Chromosome is on column 3, Strand is in column 4. Transcript identifiers are in column 2. Grouping by columns **3,4** and performing operation **count** on column 2, gives:: |
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180 |
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181 GroupBy(field-3) GroupBy(field-4) count(field-2) |
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182 chr1 + 2456 |
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183 chr1 - 2431 |
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184 chr2 + 1599 |
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185 chr2 - 1419 |
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186 chr3 + 1287 |
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187 chr3 - 1249 |
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188 ... |
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189 |
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190 @HELP_FOOTER@ |
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191 ]]> |
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192 </help> |
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193 </tool> |