Mercurial > repos > iuc > fastk_logex

annotate logex.xml @ 5:999e30b75307 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit c91b1ba99124a481c1f6cb1100abd0629974616b
author iuc
date Fri, 16 May 2025 18:49:08 +0000
parents ee15b385e5d2
children
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999e30b75307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit c91b1ba99124a481c1f6cb1100abd0629974616b
iuc
parents: 4
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1 <tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy5" 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
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3 <macros>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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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
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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
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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
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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
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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_${p+1}.tar -C input_files/ -T - &&
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999e30b75307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit c91b1ba99124a481c1f6cb1100abd0629974616b
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42 for file_name in input_files/.output.ktab.*; do
999e30b75307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit c91b1ba99124a481c1f6cb1100abd0629974616b
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43 if [ -f "\$file_name" ]; then
999e30b75307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit c91b1ba99124a481c1f6cb1100abd0629974616b
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44 new_name=\$(echo "\$file_name" | sed "s/\.output\.ktab\./\.$((p+1))\.ktab\./");
999e30b75307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit c91b1ba99124a481c1f6cb1100abd0629974616b
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45 mv "\$file_name" "\$new_name";
999e30b75307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit c91b1ba99124a481c1f6cb1100abd0629974616b
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46 fi
999e30b75307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit c91b1ba99124a481c1f6cb1100abd0629974616b
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47 done &&
3
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48 rm input_files/input_ktab_${p+1}.tar &&
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49 #end for
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50 COUNT=\$(ls -1 input_files/*.ktab 2>/dev/null | wc -l) &&
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51 if [ "\$COUNT" -ge 2 ]; then
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52 #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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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 == 'and':
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 == 'minus':
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57 EXPRESSION="out=\$(seq -s '-' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
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58 #elif $input_type.operation_sel.operation_selector_collection == 'or':
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59 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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60 #elif $input_type.operation_sel.operation_selector_collection == 'xor':
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61 EXPRESSION="out=\$(seq -s '^' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" &&
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62 #elif $input_type.operation_sel.operation_selector_collection == 'custom':
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63 EXPRESSION="out=$input_type.operation_sel.custom_expression" &&
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64 #end if
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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65 Logex -T\${GALAXY_SLOTS:-8} -h "\$EXPRESSION" input_files/*.ktab;
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66 else
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67 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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68 fi &&
0
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69 #end if
3
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70 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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71 cp .*.ktab* logex_ktabs/ &&
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72 tar -cf logex_ktab.tar input_files/ logex_ktabs/
0
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73 ]]></command>
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74 <inputs>
3
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75 <conditional name="input_type">
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76 <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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77 <option value="single">Single Ktab file</option>
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78 <option value="collection">Ktab files Collection</option>
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79 </param>
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80 <when value="single">
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81 <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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82 <param name="input_ktab1_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
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83 <param name="input_ktab2" type="data" format="fastk_ktab" label="Input FastK ktab file (second)"/>
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84 <param name="input_ktab2_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
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85 <param name="operation_selector" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files.">
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86 <option value="and">AND</option>
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87 <option value="or">OR</option>
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88 <option value="minus">Minus</option>
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89 <option value="unionsum">Unionsum</option>
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90 <option value="xor">XOR</option>
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91 </param>
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92 </when>
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93 <when value="collection">
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94 <param name="input_ktab_collection" type="data_collection" collection_type="list" format="fastk_ktab" label="Input FastK ktab Collection"/>
4
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95 <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
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96 <conditional name="operation_sel">
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97 <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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98 <option value="and">AND</option>
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99 <option value="or">OR</option>
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100 <option value="minus">Minus</option>
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101 <option value="unionsum">Unionsum</option>
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102 <option value="xor">XOR</option>
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103 <option value="custom">Custom Logical Expression</option>
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104 </param>
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105 <when value="and"/>
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106 <when value="or"/>
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107 <when value="minus"/>
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108 <when value="unionsum"/>
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109 <when value="xor"/>
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110 <when value="custom">
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111 <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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112 <sanitizer invalid_char="">
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113 <valid>
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114 <add value="+"/>
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115 <add value="-"/>
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116 <add value="|"/>
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117 <add value="."/>
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118 <add value="^"/>
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119 <add value="="/>
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120 <add value="&amp;"/>
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121 </valid>
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122 </sanitizer>
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123 </param>
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124 </when>
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125 </conditional>
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126 </when>
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127 </conditional>
0
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128 </inputs>
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129 <outputs>
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130 <data name="fastk_hist_out" format="fastk_hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Logex .hist file"/>
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131 <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="out.ktab" label="${tool.name} on ${on_string}: Logex .ktab file"/>
2
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132 <data name="fastk_ktab_files" format="fastk_ktab_tar" from_work_dir="logex_ktab.tar" label="${tool.name} on ${on_string}: FastK Logex ktab files"/>
0
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133 </outputs>
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134 <tests>
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135 <test expect_num_outputs="3">
3
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136 <conditional name="input_type">
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137 <param name="input_type_selector" value="single"/>
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138 <param name="input_ktab1" value="fastq1.ktab"/>
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139 <param name="input_ktab1_tar" value="fastk_in1.tar"/>
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140 <param name="input_ktab2" value="fastq2.ktab"/>
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141 <param name="input_ktab2_tar" value="fastk_in2.tar"/>
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142 <param name="operation_selector" value="and"/>
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143 </conditional>
0
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144 <output name="fastk_hist_out" ftype="fastk_hist">
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145 <assert_contents>
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146 <has_size value="262164"/>
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147 </assert_contents>
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148 </output>
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149 <output name="fastk_ktab_out" ftype="fastk_ktab">
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150 <assert_contents>
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151 <has_size value="2064"/>
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152 </assert_contents>
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153 </output>
2
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154 <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
0
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155 <assert_contents>
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156 <has_archive_member path="logex_ktabs/out.ktab"/>
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157 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
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158 <has_archive_member path="input_files/input1.ktab"/>
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159 <has_archive_member path="input_files/.input1.ktab.1"/>
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160 <has_archive_member path="input_files/input2.ktab"/>
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161 <has_archive_member path="input_files/.input2.ktab.1"/>
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162 </assert_contents>
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163 </output>
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164 </test>
3
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165 <test expect_num_outputs="3">
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166 <conditional name="input_type">
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167 <param name="input_type_selector" value="collection"/>
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168 <param name="input_ktab_collection">
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169 <collection type="list">
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170 <element name="input1" value="fastq1.ktab"/>
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171 <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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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
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174 <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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175 <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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176 <element name="input1" value="fastk_in1.tar"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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177 <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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178 </collection>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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179 </param>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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180 <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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181 <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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182 </conditional>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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183 </conditional>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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184 <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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185 <assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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186 <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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187 </assert_contents>
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188 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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189 <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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190 <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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191 <has_size value="2064"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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192 </assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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193 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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194 <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
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195 <assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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196 <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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197 <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
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198 <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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199 <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
200 <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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201 <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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202 </assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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203 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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204 </test>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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205 <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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206 <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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207 <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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208 <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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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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210 <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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211 <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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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 <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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215 <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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216 <element name="input1" value="fastk_in1.tar"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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217 <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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218 </collection>
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219 </param>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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220 <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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221 <param name="operation_selector_collection" value="unionsum"/>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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222 </conditional>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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223 </conditional>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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224 <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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225 <assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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226 <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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227 </assert_contents>
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228 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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229 <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
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230 <assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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231 <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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232 </assert_contents>
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iuc
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233 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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234 <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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235 <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
236 <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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237 <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
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diff changeset
238 <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
239 <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
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diff changeset
240 <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
241 <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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242 </assert_contents>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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243 </output>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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244 </test>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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245 <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
246 <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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247 <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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248 <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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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="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
251 <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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252 </collection>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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253 </param>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
iuc
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254 <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
255 <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
256 <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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257 <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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258 </collection>
f1f6bc33ad2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
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diff changeset
259 </param>
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 <conditional name="operation_sel">
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261 <param name="operation_selector_collection" value="custom"/>
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262 <param name="custom_expression" value="A&amp;.B"/>
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263 </conditional>
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264 </conditional>
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265 <output name="fastk_hist_out" ftype="fastk_hist">
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266 <assert_contents>
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267 <has_size value="262164"/>
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268 </assert_contents>
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269 </output>
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270 <output name="fastk_ktab_out" ftype="fastk_ktab">
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271 <assert_contents>
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272 <has_size value="2064"/>
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273 </assert_contents>
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274 </output>
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275 <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
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276 <assert_contents>
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277 <has_archive_member path="logex_ktabs/out.ktab"/>
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278 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
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279 <has_archive_member path="input_files/1.ktab"/>
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280 <has_archive_member path="input_files/.1.ktab.1"/>
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281 <has_archive_member path="input_files/2.ktab"/>
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282 <has_archive_member path="input_files/.2.ktab.1"/>
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283 </assert_contents>
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284 </output>
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285 </test>
0
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286 </tests>
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287 <help><![CDATA[
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288
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289 Logex tool can perform operations such as AND, OR, XOR, Minus and Unionsum on the input given input Ktab files.
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290
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291 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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292
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293 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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294
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295 ]]></help>
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296 <expand macro="citations"/>
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297 </tool>