Mercurial > repos > iuc > fastk_logex

annotate logex.xml @ 4:ee15b385e5d2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 24dc6373560bd5e409fca84154634f5a528001c3
author iuc
date Wed, 14 May 2025 07:36:23 +0000
parents f1f6bc33ad2e
children 999e30b75307
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4
ee15b385e5d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 24dc6373560bd5e409fca84154634f5a528001c3
iuc
parents: 3
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1 <tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy4" profile="24.2" license="MIT">
0
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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2 <description>Performs binary operations on the generated Ktab files from FASTK suite</description>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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3 <macros>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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4 <import>macros.xml</import>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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5 </macros>
1
a919666df221 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 2df03448c35339ea02f112abb0d0f07b5c41d93e
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6 <expand macro="xrefs"/>
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387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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7 <expand macro="requirements"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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8 <command detect_errors="exit_code"><![CDATA[
3
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9 mkdir -p logex_ktabs &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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10 mkdir -p input_files &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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11 #if $input_type.input_type_selector != 'collection'
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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12 cp '$input_ktab1' input_files/input1.ktab &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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13 ln -s '$input_ktab1_tar' input1.tar &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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14 tar -xf input1.tar &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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15 mv ktabfiles ktabfiles_in1 &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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16 mv "\$(find ktabfiles_in1 -type f -name '*.ktab.1')" "ktabfiles_in1/.input1.ktab.1" &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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17 cp '$input_ktab2' input_files/input2.ktab &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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18 ln -s '$input_ktab2_tar' input2.tar &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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19 tar -xf input2.tar &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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20 mv ktabfiles ktabfiles_in2 &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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21 mv "\$(find ktabfiles_in2 -type f -name '*.ktab.1')" "ktabfiles_in2/.input2.ktab.1" &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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22 mv ktabfiles_in1/.input1.ktab.1 input_files/ &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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23 mv ktabfiles_in2/.input2.ktab.1 input_files/ &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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24 #if $input_type.operation_selector == 'and'
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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25 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&.B' input_files/input1.ktab input_files/input2.ktab &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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26 #elif $input_type.operation_selector == 'or'
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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27 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A|.B' input_files/input1.ktab input_files/input2.ktab &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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28 #elif $input_type.operation_selector == 'minus'
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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29 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A-B' input_files/input1.ktab input_files/input2.ktab &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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30 #elif $input_type.operation_selector == 'xor'
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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31 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A^B' input_files/input1.ktab input_files/input2.ktab &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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32 #elif $input_type.operation_selector == 'unionsum'
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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33 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&+B' input_files/input1.ktab input_files/input2.ktab &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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34 #end if
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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35 #else
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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36 #for $i, $j in enumerate($input_type.input_ktab_collection):
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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37 cp "$j" input_files/${i+1}.ktab &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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38 #end for
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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39 #for $p, $q in enumerate($input_type.input_ktab_collection_tar):
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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40 ln -s "$q" input_files/input_ktab_${p+1}.tar &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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41 tar -tf input_files/input_ktab_${p+1}.tar | grep '/\.[^/]*$' | tar --strip-components=1 -xf input_files/input_ktab_${p+1}.tar -C input_files/ -T - &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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42 rm input_files/input_ktab_${p+1}.tar &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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43 #end for
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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44 COUNT=\$(ls -1 input_files/*.ktab 2>/dev/null | wc -l) &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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45 if [ "\$COUNT" -ge 2 ]; then
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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46 #if $input_type.operation_sel.operation_selector_collection == 'unionsum':
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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47 EXPRESSION="out=\$(seq -s '&+' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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48 #elif $input_type.operation_sel.operation_selector_collection == 'and':
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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49 EXPRESSION="out=\$(seq -s '&.' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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50 #elif $input_type.operation_sel.operation_selector_collection == 'minus':
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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51 EXPRESSION="out=\$(seq -s '-' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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52 #elif $input_type.operation_sel.operation_selector_collection == 'or':
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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53 EXPRESSION="out=\$(seq -s '|.' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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54 #elif $input_type.operation_sel.operation_selector_collection == 'xor':
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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55 EXPRESSION="out=\$(seq -s '^' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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56 #elif $input_type.operation_sel.operation_selector_collection == 'custom':
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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57 EXPRESSION="out=$input_type.operation_sel.custom_expression" &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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58 #end if
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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59 Logex -T\${GALAXY_SLOTS:-8} -h "\$EXPRESSION" input_files/*.ktab;
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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60 else
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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61 echo "ERROR: Logex needs atleast 2 Ktab files" >&2 && exit 1;
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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62 fi &&
0
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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63 #end if
3
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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64 cp *.ktab logex_ktabs/ &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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65 cp .*.ktab* logex_ktabs/ &&
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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66 tar -cf logex_ktab.tar input_files/ logex_ktabs/
0
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67 ]]></command>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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68 <inputs>
3
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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69 <conditional name="input_type">
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70 <param name="input_type_selector" type="select" label="Single Ktab file or Ktab Collection">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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71 <option value="single">Single Ktab file</option>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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72 <option value="collection">Ktab files Collection</option>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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73 </param>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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74 <when value="single">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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75 <param name="input_ktab1" type="data" format="fastk_ktab" label="Input FastK ktab file (first)"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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76 <param name="input_ktab1_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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77 <param name="input_ktab2" type="data" format="fastk_ktab" label="Input FastK ktab file (second)"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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78 <param name="input_ktab2_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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79 <param name="operation_selector" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files.">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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80 <option value="and">AND</option>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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81 <option value="or">OR</option>
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82 <option value="minus">Minus</option>
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83 <option value="unionsum">Unionsum</option>
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84 <option value="xor">XOR</option>
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85 </param>
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86 </when>
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87 <when value="collection">
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88 <param name="input_ktab_collection" type="data_collection" collection_type="list" format="fastk_ktab" label="Input FastK ktab Collection"/>
4
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89 <param name="input_ktab_collection_tar" type="data_collection" collection_type="list" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
3
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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90 <conditional name="operation_sel">
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91 <param name="operation_selector_collection" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files.">
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92 <option value="and">AND</option>
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93 <option value="or">OR</option>
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94 <option value="minus">Minus</option>
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95 <option value="unionsum">Unionsum</option>
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96 <option value="xor">XOR</option>
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97 <option value="custom">Custom Logical Expression</option>
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98 </param>
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99 <when value="and"/>
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100 <when value="or"/>
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101 <when value="minus"/>
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102 <when value="unionsum"/>
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103 <when value="xor"/>
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104 <when value="custom">
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105 <param name="custom_expression" type="text" label="Custom Logical Expression" value="out=" help="Enter a custom logical expression based on number of your input ktab files. For Eg: For 3 Ktab files the expression can be out=(A^B)-C">
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106 <sanitizer invalid_char="">
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107 <valid>
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108 <add value="+"/>
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109 <add value="-"/>
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110 <add value="|"/>
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111 <add value="."/>
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112 <add value="^"/>
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113 <add value="="/>
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114 <add value="&amp;"/>
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115 </valid>
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116 </sanitizer>
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117 </param>
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118 </when>
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119 </conditional>
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120 </when>
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121 </conditional>
0
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122 </inputs>
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123 <outputs>
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124 <data name="fastk_hist_out" format="fastk_hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Logex .hist file"/>
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125 <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="out.ktab" label="${tool.name} on ${on_string}: Logex .ktab file"/>
2
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126 <data name="fastk_ktab_files" format="fastk_ktab_tar" from_work_dir="logex_ktab.tar" label="${tool.name} on ${on_string}: FastK Logex ktab files"/>
0
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127 </outputs>
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128 <tests>
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129 <test expect_num_outputs="3">
3
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130 <conditional name="input_type">
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131 <param name="input_type_selector" value="single"/>
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132 <param name="input_ktab1" value="fastq1.ktab"/>
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133 <param name="input_ktab1_tar" value="fastk_in1.tar"/>
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134 <param name="input_ktab2" value="fastq2.ktab"/>
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135 <param name="input_ktab2_tar" value="fastk_in2.tar"/>
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136 <param name="operation_selector" value="and"/>
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137 </conditional>
0
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138 <output name="fastk_hist_out" ftype="fastk_hist">
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139 <assert_contents>
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140 <has_size value="262164"/>
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141 </assert_contents>
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142 </output>
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143 <output name="fastk_ktab_out" ftype="fastk_ktab">
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144 <assert_contents>
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145 <has_size value="2064"/>
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146 </assert_contents>
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147 </output>
2
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148 <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
0
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149 <assert_contents>
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150 <has_archive_member path="logex_ktabs/out.ktab"/>
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151 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
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152 <has_archive_member path="input_files/input1.ktab"/>
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153 <has_archive_member path="input_files/.input1.ktab.1"/>
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154 <has_archive_member path="input_files/input2.ktab"/>
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155 <has_archive_member path="input_files/.input2.ktab.1"/>
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156 </assert_contents>
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157 </output>
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158 </test>
3
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159 <test expect_num_outputs="3">
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160 <conditional name="input_type">
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161 <param name="input_type_selector" value="collection"/>
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162 <param name="input_ktab_collection">
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163 <collection type="list">
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164 <element name="input1" value="fastq1.ktab"/>
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165 <element name="input2" value="fastq2.ktab"/>
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166 </collection>
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167 </param>
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168 <param name="input_ktab_collection_tar">
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169 <collection type="list">
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170 <element name="input1" value="fastk_in1.tar"/>
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171 <element name="input2" value="fastk_in2.tar"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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172 </collection>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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173 </param>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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174 <conditional name="operation_sel">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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175 <param name="operation_selector_collection" value="and"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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176 </conditional>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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177 </conditional>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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178 <output name="fastk_hist_out" ftype="fastk_hist">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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179 <assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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180 <has_size value="262164"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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181 </assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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182 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
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183 <output name="fastk_ktab_out" ftype="fastk_ktab">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
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184 <assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
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185 <has_size value="2064"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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186 </assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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187 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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188 <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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189 <assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
diff changeset
190 <has_archive_member path="logex_ktabs/out.ktab"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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191 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
diff changeset
192 <has_archive_member path="input_files/1.ktab"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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193 <has_archive_member path="input_files/.1.ktab.1"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
diff changeset
194 <has_archive_member path="input_files/2.ktab"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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195 <has_archive_member path="input_files/.2.ktab.1"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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196 </assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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197 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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198 </test>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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199 <test expect_num_outputs="3">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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200 <conditional name="input_type">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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201 <param name="input_type_selector" value="collection"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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202 <param name="input_ktab_collection">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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203 <collection type="list">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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204 <element name="input1" value="fastq1.ktab"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
205 <element name="input2" value="fastq2.ktab"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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206 </collection>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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207 </param>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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208 <param name="input_ktab_collection_tar">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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209 <collection type="list">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
210 <element name="input1" value="fastk_in1.tar"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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211 <element name="input2" value="fastk_in2.tar"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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212 </collection>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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213 </param>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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214 <conditional name="operation_sel">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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215 <param name="operation_selector_collection" value="unionsum"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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216 </conditional>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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217 </conditional>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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218 <output name="fastk_hist_out" ftype="fastk_hist">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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219 <assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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220 <has_size value="262164"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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221 </assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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222 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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223 <output name="fastk_ktab_out" ftype="fastk_ktab">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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224 <assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
diff changeset
225 <has_size value="2064"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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226 </assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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227 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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228 <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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229 <assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
230 <has_archive_member path="logex_ktabs/out.ktab"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
231 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
diff changeset
232 <has_archive_member path="input_files/1.ktab"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
233 <has_archive_member path="input_files/.1.ktab.1"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
diff changeset
234 <has_archive_member path="input_files/2.ktab"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
235 <has_archive_member path="input_files/.2.ktab.1"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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236 </assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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237 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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238 </test>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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239 <test expect_num_outputs="3">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
240 <conditional name="input_type">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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241 <param name="input_type_selector" value="collection"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
242 <param name="input_ktab_collection">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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243 <collection type="list">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
244 <element name="input1" value="fastq1.ktab"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
245 <element name="input2" value="fastq2.ktab"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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246 </collection>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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247 </param>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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248 <param name="input_ktab_collection_tar">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
249 <collection type="list">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
diff changeset
250 <element name="input1" value="fastk_in1.tar"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
diff changeset
251 <element name="input2" value="fastk_in2.tar"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
252 </collection>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
253 </param>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
parents: 2
diff changeset
254 <conditional name="operation_sel">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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255 <param name="operation_selector_collection" value="custom"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
256 <param name="custom_expression" value="A&amp;.B"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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257 </conditional>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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258 </conditional>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
259 <output name="fastk_hist_out" ftype="fastk_hist">
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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diff changeset
260 <assert_contents>
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iuc
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261 <has_size value="262164"/>
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262 </assert_contents>
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263 </output>
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264 <output name="fastk_ktab_out" ftype="fastk_ktab">
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265 <assert_contents>
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266 <has_size value="2064"/>
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267 </assert_contents>
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268 </output>
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269 <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
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270 <assert_contents>
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271 <has_archive_member path="logex_ktabs/out.ktab"/>
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272 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
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273 <has_archive_member path="input_files/1.ktab"/>
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274 <has_archive_member path="input_files/.1.ktab.1"/>
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275 <has_archive_member path="input_files/2.ktab"/>
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276 <has_archive_member path="input_files/.2.ktab.1"/>
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277 </assert_contents>
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278 </output>
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279 </test>
0
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280 </tests>
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281 <help><![CDATA[
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282
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283 Logex tool can perform operations such as AND, OR, XOR, Minus and Unionsum on the input given input Ktab files.
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284
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285 The tool requires two input Ktab files and their associated files (Generated in the tarball of FASTK tool with .1 extension) as inputs to perform various binary operations.
3
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286
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287 The tool also supports Ktab file collections as input. The user can select the operation to be performed on the input Ktab files.
0
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288
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289 ]]></help>
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290 <expand macro="citations"/>
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291 </tool>