Mercurial > repos > iuc > collection_column_join

annotate collection_column_join.xml @ 3:58228a4d58fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
author iuc
date Fri, 06 Apr 2018 03:44:21 -0400
parents dfde09461b1e
children 071084070619
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58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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1 <tool id="collection_column_join" name="Column Join" version="0.0.3">
2
dfde09461b1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 52cb707375a11118a7e46612bd5044016abb9903
iuc
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2 <description>on Collections</description>
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2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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3 <requirements>
2
dfde09461b1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 52cb707375a11118a7e46612bd5044016abb9903
iuc
parents: 1
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4 <requirement type="package" version="8.25">coreutils</requirement>
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2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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5 </requirements>
2
dfde09461b1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 52cb707375a11118a7e46612bd5044016abb9903
iuc
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6 <command detect_errors="exit_code"><![CDATA[
dfde09461b1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 52cb707375a11118a7e46612bd5044016abb9903
iuc
parents: 1
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7 #if 'output_shell_script' in str( $include_outputs ).split( "," ):
dfde09461b1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 52cb707375a11118a7e46612bd5044016abb9903
iuc
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8 cp '${collection_column_join_script}' '${script_output}' &&
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2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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9 #end if
2
dfde09461b1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 52cb707375a11118a7e46612bd5044016abb9903
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10 sh '${collection_column_join_script}'
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2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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11 ]]>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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12 </command>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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13 <configfiles>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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14 <configfile name="collection_column_join_script"><![CDATA[
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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15 #!/bin/sh
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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16 touch header0.tmp &&
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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17 touch output0.tmp &&
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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18 #set $delimiter = '\t'
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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19 #set $left_identifier_column = $identifier_column
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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20 #set $tail_offset = int( str( $has_header ) ) + 1
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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21 #for $i, $tabular_item in enumerate( $input_tabular ):
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58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
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22 #if $old_col_in_header:
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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23 #if $has_header:
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
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24 head -n ${has_header} "${tabular_item}" | awk '{ n = split(\$0,arr,"${delimiter}"); ctr=1; for(i=1;i<=n;i++){ if( i != $identifier_column ){ if( ctr > 1) {printf("${delimiter}")}; printf( "${tabular_item.element_identifier}_%s", arr[i] ); ctr++ } }; printf( "\n" ); }' > input_header.tmp &&
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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25 tail -n +${tail_offset} "${tabular_item}" | LC_ALL=C sort -t "${delimiter}" -k $identifier_column > input_file.tmp &&
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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26 #else:
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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27 awk '{ n = split(\$0,arr,"${delimiter}"); ctr=1; for(i=1;i<=n;i++){ if( i != $identifier_column ){ if( ctr > 1) {printf("${delimiter}")}; printf( "${tabular_item.element_identifier}_%s", i ); ctr++ } }; exit }' "${tabular_item}" > input_header.tmp &&
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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28 LC_ALL=C sort -t "${delimiter}" -k $identifier_column "${tabular_item}" > input_file.tmp &&
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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29 #end if
0
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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30 #else:
3
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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31 #if $has_header:
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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32 head -n ${has_header} "${tabular_item}" | awk '{ n = split(\$0,arr,"${delimiter}"); ctr=1; for(i=1;i<=n;i++){ if( i != $identifier_column ){ if( ctr > 1) {printf("${delimiter}")}; printf( "${tabular_item.element_identifier}" ); ctr++ } }; printf( "\n" ); }' > input_header.tmp &&
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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33 tail -n +${tail_offset} "${tabular_item}" | LC_ALL=C sort -t "${delimiter}" -k $identifier_column > input_file.tmp &&
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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34 #else:
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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35 awk '{ n = split(\$0,arr,"${delimiter}"); ctr=1; for(i=1;i<=n;i++){ if( i != $identifier_column ){ if( ctr > 1) {printf("${delimiter}")}; printf( "${tabular_item.element_identifier}"); ctr++ } }; exit }' "${tabular_item}" > input_header.tmp &&
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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36 LC_ALL=C sort -t "${delimiter}" -k $identifier_column "${tabular_item}" > input_file.tmp &&
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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37 #end if
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2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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38 #end if
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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39 #if $i == 0:
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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40 mv input_file.tmp output${ ( $i + 1 ) % 2 }.tmp &&
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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41 #if $has_header:
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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42 awk '{ printf \$${identifier_column}; exit }' "${tabular_item}" > header${ $i % 2 }.tmp &&
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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43 #else:
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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44 echo "#KEY" > header${ $i % 2 }.tmp &&
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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45 #end if
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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46 #else:
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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47 LC_ALL=C join -o auto -a 1 -a 2 -1 ${left_identifier_column} -2 ${identifier_column} -t "${delimiter}" -e "${fill_char}" output${ $i % 2 }.tmp input_file.tmp > output${ ( $i + 1 ) % 2 }.tmp &&
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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48 #set $left_identifier_column = 1
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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49 #end if
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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50 paste -d "${delimiter}" header${ $i % 2 }.tmp input_header.tmp > header${ ( $i + 1 ) % 2 }.tmp &&
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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51 #end for
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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52 cat header${ ( $i + 1 ) % 2 }.tmp output${ ( $i + 1 ) % 2 }.tmp > "${tabular_output}"
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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53 ]]>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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54 </configfile>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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55 </configfiles>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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56 <inputs>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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57 <param name="input_tabular" type="data" format="tabular" multiple="True" optional="False" label="Tabular files"/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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58 <!-- <param name="identifier_column" type="data_column" data_ref="input_tabular" value="0" min="0" optional="False" label="Identifier column"/> -->
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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59 <param name="identifier_column" type="integer" value="1" min="0" optional="False" label="Identifier column"/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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60 <param name="has_header" type="integer" value="0" min="0" optional="False" label="Number of Header lines in each item"/>
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58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
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61 <param name="old_col_in_header" type="boolean" checked="true" label="Keep original column header" help="Disable if you want columns headers to be only composed of the input dataset names"/>
0
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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62 <param name="fill_char" type="text" value="." optional="False" label="Fill character"/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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63 <param name="include_outputs" type="select" multiple="True" label="Additional datasets to create">
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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64 <option value="output_shell_script" selected="false">Shell script</option>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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65 </param>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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66 </inputs>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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67 <outputs>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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68 <data format="tabular" name="tabular_output"/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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69 <data format="txt" name="script_output">
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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70 <filter>include_outputs and "output_shell_script" in include_outputs</filter>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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71 </data>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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72 </outputs>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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73 <tests>
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74 <test>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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75 <param name="input_tabular" value="in_1.tabular,in_2.tabular,in_3.tabular" ftype="tabular"/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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76 <param name="identifier_column" value="1"/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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77 <param name="has_header" value="1"/>
3
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
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78 <param name="old_col_in_header" value="true"/>
0
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
79 <param name="fill_char" value="."/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
80 <param name="include_outputs" />
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
81 <output name="tabular_output" file="out_1.tabular" ftype="tabular"/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
82 </test>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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83 <test>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
84 <param name="input_tabular" value="in_1_headerless.tabular,in_2_headerless.tabular,in_3_headerless.tabular" ftype="tabular"/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
85 <param name="identifier_column" value="1"/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
86 <param name="has_header" value="0"/>
3
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
diff changeset
87 <param name="old_col_in_header" value="true"/>
0
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
88 <param name="fill_char" value="."/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
89 <param name="include_outputs" />
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
90 <output name="tabular_output" file="out_2.tabular" ftype="tabular"/>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
91 </test>
3
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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92 <test>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
diff changeset
93 <param name="input_tabular" value="in_1.tabular,in_2.tabular,in_3.tabular" ftype="tabular"/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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94 <param name="identifier_column" value="1"/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
diff changeset
95 <param name="has_header" value="1"/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
diff changeset
96 <param name="old_col_in_header" value="false"/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
diff changeset
97 <param name="fill_char" value="."/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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98 <param name="include_outputs" />
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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99 <output name="tabular_output" file="out_3.tabular" ftype="tabular"/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
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100 </test>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
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101 <test>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
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102 <param name="input_tabular" value="in_1_headerless.tabular,in_2_headerless.tabular,in_3_headerless.tabular" ftype="tabular"/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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103 <param name="identifier_column" value="1"/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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104 <param name="has_header" value="0"/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
diff changeset
105 <param name="old_col_in_header" value="false"/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
diff changeset
106 <param name="fill_char" value="."/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
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107 <param name="include_outputs" />
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
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108 <output name="tabular_output" file="out_4.tabular" ftype="tabular"/>
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
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109 </test>
0
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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110 </tests>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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111 <help>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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112 <![CDATA[
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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113 Joins lists of tabular datasets together on a field.
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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114
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
115 -----
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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116
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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117 **Example**
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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118
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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119 To join three files, with headers, based on the first column:
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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120
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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121 **First file (in_1.tabular)**::
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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122
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
123 #KEY c2 c3 c4
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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124 one 1-1 1-2 1-3
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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diff changeset
125 two 1-4 1-5 1-6
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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126 three 1-7 1-8 1-9
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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127
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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128
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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129 **Second File (in_2.tabular)**::
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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130
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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131 #KEY c2 c3 c4
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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132 one 2-1 2-2 2-3
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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133 two 2-4 2-5 2-6
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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134 three 2-7 2-8 2-9
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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135
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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136 **Third file (in_3.tabular)**::
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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137
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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138 #KEY c2 c3 c4
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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139 one 3-3 3-2 3-3
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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140 two 3-4 3-5 3-6
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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141 three 3-7 3-8 3-9
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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142
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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143
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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144 **Joining** the files, using **identifier column of 1** and a **header lines of 1**, will return::
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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145
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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146 #KEY in_1.tabular_c2 in_1.tabular_c3 in_1.tabular_c4 in_2.tabular_c2 in_2.tabular_c3 in_2.tabular_c4 in_3.tabular_c2 in_3.tabular_c3 in_3.tabular_c4
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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147 one 1-1 1-2 1-3 2-1 2-2 2-3 3-3 3-2 3-3
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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148 three 1-7 1-8 1-9 2-7 2-8 2-9 3-7 3-8 3-9
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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149 two 1-4 1-5 1-6 2-4 2-5 2-6 3-4 3-5 3-6
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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150
3
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
diff changeset
151
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
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152 **Joining** the files, using **identifier column of 1** and a **header lines of 1**, but disabling **Keep original column header**, will return::
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
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diff changeset
153
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
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diff changeset
154 #KEY in_1.tabular in_1.tabular in_1.tabular in_2.tabular in_2.tabular in_2.tabular in_3.tabular in_3.tabular in_3.tabular
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
diff changeset
155 one 1-1 1-2 1-3 2-1 2-2 2-3 3-3 3-2 3-3
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents: 2
diff changeset
156 three 1-7 1-8 1-9 2-7 2-8 2-9 3-7 3-8 3-9
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
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diff changeset
157 two 1-4 1-5 1-6 2-4 2-5 2-6 3-4 3-5 3-6
58228a4d58fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
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158
0
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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159 ]]>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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160 </help>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
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161 <citations>
2f120a5c49b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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162 </citations>
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9c8536c7ed42 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit d46d41c5fec10407bd6b5cb77a11d9b43b82b95e
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163 </tool>