Mercurial > repos > iuc > collection_column_join
annotate collection_column_join.xml @ 4:071084070619 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 11d99b82e4e78f3077bc5f6997403b602b8a8423
| author | iuc |
|---|---|
| date | Thu, 28 Feb 2019 05:04:03 -0500 |
| parents | 58228a4d58fe |
| children | 3ddd99c7efee |
| rev | line source |
|---|---|
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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:
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1 <tool id="collection_column_join" name="Column Join" version="0.0.3"> |
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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
parents:
diff
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3 <requirements> |
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dfde09461b1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 52cb707375a11118a7e46612bd5044016abb9903
iuc
parents:
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diff
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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
parents:
diff
changeset
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5 </requirements> |
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2
dfde09461b1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 52cb707375a11118a7e46612bd5044016abb9903
iuc
parents:
1
diff
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6 <command detect_errors="exit_code"><![CDATA[ |
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dfde09461b1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 52cb707375a11118a7e46612bd5044016abb9903
iuc
parents:
1
diff
changeset
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7 #if 'output_shell_script' in str( $include_outputs ).split( "," ): |
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dfde09461b1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 52cb707375a11118a7e46612bd5044016abb9903
iuc
parents:
1
diff
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8 cp '${collection_column_join_script}' '${script_output}' && |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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9 #end if |
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dfde09461b1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 52cb707375a11118a7e46612bd5044016abb9903
iuc
parents:
1
diff
changeset
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10 sh '${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
parents:
diff
changeset
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11 ]]> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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12 </command> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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13 <configfiles> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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14 <configfile name="collection_column_join_script"><![CDATA[ |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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15 #!/bin/sh |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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16 touch header0.tmp && |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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17 touch output0.tmp && |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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18 #set $delimiter = '\t' |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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19 #set $left_identifier_column = $identifier_column |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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20 #set $tail_offset = int( str( $has_header ) ) + 1 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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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
parents:
2
diff
changeset
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22 #if $old_col_in_header: |
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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
diff
changeset
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23 #if $has_header: |
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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
diff
changeset
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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( "${tabular_item.element_identifier}_%s", arr[i] ); ctr++ } }; printf( "\n" ); }' > input_header.tmp && |
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58228a4d58fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents:
2
diff
changeset
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25 tail -n +${tail_offset} "${tabular_item}" | LC_ALL=C sort -t "${delimiter}" -k $identifier_column > input_file.tmp && |
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58228a4d58fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents:
2
diff
changeset
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26 #else: |
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58228a4d58fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents:
2
diff
changeset
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27 awk '{ n = split(\$0,arr,"${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 && |
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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
diff
changeset
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28 LC_ALL=C sort -t "${delimiter}" -k $identifier_column "${tabular_item}" > input_file.tmp && |
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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
diff
changeset
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29 #end if |
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0
2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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30 #else: |
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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
diff
changeset
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31 #if $has_header: |
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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
diff
changeset
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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( "${tabular_item.element_identifier}" ); ctr++ } }; printf( "\n" ); }' > input_header.tmp && |
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58228a4d58fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents:
2
diff
changeset
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33 tail -n +${tail_offset} "${tabular_item}" | LC_ALL=C sort -t "${delimiter}" -k $identifier_column > input_file.tmp && |
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58228a4d58fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents:
2
diff
changeset
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34 #else: |
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58228a4d58fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 9f1c3ab3f41bab8ff962aca1478c75e538e5bf6a
iuc
parents:
2
diff
changeset
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35 awk '{ n = split(\$0,arr,"${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 && |
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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
diff
changeset
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36 LC_ALL=C sort -t "${delimiter}" -k $identifier_column "${tabular_item}" > input_file.tmp && |
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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
diff
changeset
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37 #end if |
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0
2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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38 #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
parents:
diff
changeset
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39 #if $i == 0: |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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40 mv input_file.tmp output${ ( $i + 1 ) % 2 }.tmp && |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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41 #if $has_header: |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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42 awk '{ printf \$${identifier_column}; exit }' "${tabular_item}" > header${ $i % 2 }.tmp && |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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43 #else: |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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44 echo "#KEY" > header${ $i % 2 }.tmp && |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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45 #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
parents:
diff
changeset
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46 #else: |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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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 && |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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48 #set $left_identifier_column = 1 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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49 #end if |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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50 paste -d "${delimiter}" header${ $i % 2 }.tmp input_header.tmp > header${ ( $i + 1 ) % 2 }.tmp && |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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51 #end for |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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52 cat header${ ( $i + 1 ) % 2 }.tmp output${ ( $i + 1 ) % 2 }.tmp > "${tabular_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
parents:
diff
changeset
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53 ]]> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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54 </configfile> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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55 </configfiles> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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56 <inputs> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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57 <param name="input_tabular" type="data" format="tabular" multiple="True" optional="False" label="Tabular files"/> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
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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"/> --> |
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4
071084070619
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 11d99b82e4e78f3077bc5f6997403b602b8a8423
iuc
parents:
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diff
changeset
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59 <param name="identifier_column" type="integer" value="1" min="0" optional="False" label="Identifier column" help="The column that will be used to join the input datasets"/> |
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071084070619
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 11d99b82e4e78f3077bc5f6997403b602b8a8423
iuc
parents:
3
diff
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60 <param name="has_header" type="integer" value="0" min="0" optional="False" label="Number of header lines in each input file" help="If this is set to 0, a header line will be added containing column names as follows: the identifier column will be named #KEY and the other columns are named by the input dataset names/columns. If you have one or more header lines in your input, set this to the number of header lines."/> |
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071084070619
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 11d99b82e4e78f3077bc5f6997403b602b8a8423
iuc
parents:
3
diff
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61 <param name="old_col_in_header" type="boolean" checked="true" label="Add column name to header" help="Disable if you want column headers to only be composed of the input file names, for example, if you want headers like file1 and not file1_column1, see Help section below. Default: Yes"/> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
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62 <param name="fill_char" type="text" value="." optional="False" label="Fill character"/> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
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63 <param name="include_outputs" type="select" multiple="True" label="Additional datasets to create"> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
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64 <option value="output_shell_script" selected="false">Shell script</option> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
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65 </param> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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66 </inputs> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
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67 <outputs> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
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68 <data format="tabular" name="tabular_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
parents:
diff
changeset
|
69 <data format="txt" name="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
parents:
diff
changeset
|
70 <filter>include_outputs and "output_shell_script" in include_outputs</filter> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
|
71 </data> |
|
2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
|
72 </outputs> |
|
2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
|
73 <tests> |
|
2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
|
74 <test> |
|
2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
parents:
diff
changeset
|
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
iuc
parents:
2
diff
changeset
|
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
parents:
diff
changeset
|
79 <param name="fill_char" value="."/> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
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
parents:
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
parents:
diff
changeset
|
82 </test> |
|
2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
|
83 <test> |
|
2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
|
84 <param name="input_tabular" value="in_1_headerless.tabular,in_2_headerless.tabular,in_3_headerless.tabular" ftype="tabular"/> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
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
parents:
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
parents:
diff
changeset
|
88 <param name="fill_char" value="."/> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
diff
changeset
|
89 <param name="include_outputs" /> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
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
parents:
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:
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diff
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92 <test> |
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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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diff
changeset
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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
diff
changeset
|
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:
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diff
changeset
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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:
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diff
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98 <param name="include_outputs" /> |
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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
diff
changeset
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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
parents:
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diff
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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
parents:
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diff
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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"/> |
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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:
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diff
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103 <param name="identifier_column" value="1"/> |
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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
diff
changeset
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104 <param name="has_header" value="0"/> |
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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:
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diff
changeset
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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
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106 <param name="fill_char" value="."/> |
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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
diff
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107 <param name="include_outputs" /> |
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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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108 <output name="tabular_output" file="out_4.tabular" ftype="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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109 </test> |
|
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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110 </tests> |
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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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|
111 <help> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
iuc
parents:
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changeset
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112 <![CDATA[ |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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113 Joins lists of tabular datasets together on a field. |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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114 |
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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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115 ----- |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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116 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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117 **Example** |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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118 |
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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: |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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120 |
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4
071084070619
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 11d99b82e4e78f3077bc5f6997403b602b8a8423
iuc
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121 **First file (in_1)**:: |
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0
2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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122 |
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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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123 #KEY c2 c3 c4 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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124 one 1-1 1-2 1-3 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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125 two 1-4 1-5 1-6 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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126 three 1-7 1-8 1-9 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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127 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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128 |
|
4
071084070619
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 11d99b82e4e78f3077bc5f6997403b602b8a8423
iuc
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129 **Second File (in_2)**:: |
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0
2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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130 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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131 #KEY c2 c3 c4 |
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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 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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133 two 2-4 2-5 2-6 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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134 three 2-7 2-8 2-9 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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135 |
|
4
071084070619
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 11d99b82e4e78f3077bc5f6997403b602b8a8423
iuc
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136 **Third file (in_3)**:: |
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0
2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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137 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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138 #KEY c2 c3 c4 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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139 one 3-3 3-2 3-3 |
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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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140 two 3-4 3-5 3-6 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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141 three 3-7 3-8 3-9 |
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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
iuc
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143 |
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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:: |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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145 |
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4
071084070619
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 11d99b82e4e78f3077bc5f6997403b602b8a8423
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146 #KEY in_1_c2 in_1_c3 in_1_c4 in_2_c2 in_2_c3 in_2_c4 in_3_c2 in_3_c3 in_3_c4 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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147 one 1-1 1-2 1-3 2-1 2-2 2-3 3-3 3-2 3-3 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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148 three 1-7 1-8 1-9 2-7 2-8 2-9 3-7 3-8 3-9 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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149 two 1-4 1-5 1-6 2-4 2-5 2-6 3-4 3-5 3-6 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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150 |
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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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151 |
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071084070619
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 11d99b82e4e78f3077bc5f6997403b602b8a8423
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152 **Joining** the files, using **identifier column of 1** and a **header lines of 1**, but disabling **Add column name to header**, will return:: |
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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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153 |
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071084070619
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 11d99b82e4e78f3077bc5f6997403b602b8a8423
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154 #KEY in_1 in_1 in_1 in_2 in_2 in_2 in_3 in_3 in_3 |
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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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155 one 1-1 1-2 1-3 2-1 2-2 2-3 3-3 3-2 3-3 |
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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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156 three 1-7 1-8 1-9 2-7 2-8 2-9 3-7 3-8 3-9 |
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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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157 two 1-4 1-5 1-6 2-4 2-5 2-6 3-4 3-5 3-6 |
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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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158 |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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159 ]]> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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160 </help> |
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2f120a5c49b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join commit 3b918f5a99ea13ec5acc7cc5fdd310fadb773ac0
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161 <citations> |
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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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1
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> |