Mercurial > repos > iuc > fastk_logex

annotate logex.xml @ 2:52ae020a27eb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit de98c1736ab624bff379c3e83ccfc19cb2995684
author iuc
date Wed, 19 Feb 2025 11:16:37 +0000
parents a919666df221
children f1f6bc33ad2e
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52ae020a27eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit de98c1736ab624bff379c3e83ccfc19cb2995684
iuc
parents: 1
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1 <tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT">
0
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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2 <description>Performs binary operations on the generated Ktab files from FASTK suite</description>
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iuc
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3 <macros>
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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
iuc
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6 <expand macro="xrefs"/>
0
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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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
iuc
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8 <command detect_errors="exit_code"><![CDATA[
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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9 mkdir -p logex_ktabs
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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10 && mkdir -p input_files
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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11 && cp '$input_ktab1' input_files/input1.ktab
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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12 && ln -s '$input_ktab1_tar' input1.tar
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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13 && tar -xf input1.tar
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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14 && mv ktabfiles ktabfiles_in1
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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15 && mv "\$(find ktabfiles_in1 -type f -name '*.ktab.1')" "ktabfiles_in1/.input1.ktab.1"
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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16 && cp '$input_ktab2' input_files/input2.ktab
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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17 && ln -s '$input_ktab2_tar' input2.tar
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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18 && tar -xf input2.tar
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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19 && mv ktabfiles ktabfiles_in2
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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20 && mv "\$(find ktabfiles_in2 -type f -name '*.ktab.1')" "ktabfiles_in2/.input2.ktab.1"
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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21 && mv ktabfiles_in1/.input1.ktab.1 input_files/
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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22 && mv ktabfiles_in2/.input2.ktab.1 input_files/ &&
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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23 #if $operation_selector == 'and':
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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24 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&.B' input_files/input1.ktab input_files/input2.ktab
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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25 #elif $operation_selector == 'or':
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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26 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A|.B' input_files/input1.ktab input_files/input2.ktab
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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27 #elif $operation_selector == 'minus':
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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28 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A-B' input_files/input1.ktab input_files/input2.ktab
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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29 #elif $operation_selector == 'xor':
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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30 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A^B' input_files/input1.ktab input_files/input2.ktab
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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31 #elif $operation_selector == 'unionsum':
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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32 Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&+B' input_files/input1.ktab input_files/input2.ktab
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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33 #end if
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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34 && cp *.ktab logex_ktabs/
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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35 && cp .*.ktab* logex_ktabs/
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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36 && tar -cf logex_ktab.tar input_files/ logex_ktabs/
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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37 ]]></command>
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iuc
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38 <inputs>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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39 <param name="input_ktab1" type="data" format="fastk_ktab" label="Input FastK ktab file (first)"/>
2
52ae020a27eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit de98c1736ab624bff379c3e83ccfc19cb2995684
iuc
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40 <param name="input_ktab1_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
0
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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41 <param name="input_ktab2" type="data" format="fastk_ktab" label="Input FastK ktab file (second)"/>
2
52ae020a27eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit de98c1736ab624bff379c3e83ccfc19cb2995684
iuc
parents: 1
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42 <param name="input_ktab2_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/>
0
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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43 <param name="operation_selector" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files.">
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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44 <option value="and">AND</option>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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45 <option value="or">OR</option>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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46 <option value="minus">Minus</option>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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47 <option value="unionsum">Unionsum</option>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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48 <option value="xor">XOR</option>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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49 </param>
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50 </inputs>
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51 <outputs>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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52 <data name="fastk_hist_out" format="fastk_hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Logex .hist file"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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53 <data name="fastk_ktab_out" format="fastk_ktab" from_work_dir="out.ktab" label="${tool.name} on ${on_string}: Logex .ktab file"/>
2
52ae020a27eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit de98c1736ab624bff379c3e83ccfc19cb2995684
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54 <data name="fastk_ktab_files" format="fastk_ktab_tar" from_work_dir="logex_ktab.tar" label="${tool.name} on ${on_string}: FastK Logex ktab files"/>
0
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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55 </outputs>
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56 <tests>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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57 <test expect_num_outputs="3">
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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58 <param name="input_ktab1" value="fastq1.ktab"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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59 <param name="input_ktab1_tar" value="fastk_in1.tar"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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60 <param name="input_ktab2" value="fastq2.ktab"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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61 <param name="input_ktab2_tar" value="fastk_in2.tar"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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62 <param name="operation_selector" value="AND"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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63 <output name="fastk_hist_out" ftype="fastk_hist">
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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64 <assert_contents>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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65 <has_size value="262164"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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66 </assert_contents>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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67 </output>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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68 <output name="fastk_ktab_out" ftype="fastk_ktab">
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69 <assert_contents>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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70 <has_size value="2064"/>
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71 </assert_contents>
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72 </output>
2
52ae020a27eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit de98c1736ab624bff379c3e83ccfc19cb2995684
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73 <output name="fastk_ktab_files" ftype="fastk_ktab_tar">
0
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74 <assert_contents>
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75 <has_archive_member path="logex_ktabs/out.ktab"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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76 <has_archive_member path="logex_ktabs/.out.ktab.1"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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77 <has_archive_member path="input_files/input1.ktab"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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78 <has_archive_member path="input_files/.input1.ktab.1"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
iuc
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79 <has_archive_member path="input_files/input2.ktab"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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80 <has_archive_member path="input_files/.input2.ktab.1"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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81 </assert_contents>
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82 </output>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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83 </test>
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84 </tests>
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85 <help><![CDATA[
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86
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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87 Logex tool can perform operations such as AND, OR, XOR, Minus and Unionsum on the input given input Ktab files.
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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88
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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89 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.
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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90
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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91 ]]></help>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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92 <expand macro="citations"/>
387a1695d800 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 56658d5048382715413718dd2d41c9751e886608
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93 </tool>