Mercurial > repos > galaxy-australia > kmc

annotate kmc_tools_simple.xml @ 0:ca2743037241 draft default tip

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
author galaxy-australia
date Tue, 27 Sep 2022 05:20:06 +0000
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ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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1 <tool id="kmc_simple" name="KMC simple" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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2 <description>simple operations for two input kmer sets</description>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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3 <xrefs>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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4 <xref type='bio.tools'>kmc</xref>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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5 </xrefs>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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6 <macros>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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7 <import>macros.xml</import>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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8 </macros>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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9 <expand macro="requirements" />
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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10 <expand macro="stdio" />
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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11 <expand macro="version_command" />
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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12 <command><![CDATA[
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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13 mkdir outdir &&
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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14 #for $f in $input_collection_one:
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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15 #if '.kmc_suf' in str($f.element_identifier)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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16 ln -s '${f}' kmers_db_one.kmc_suf &&
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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17 #else
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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18 ln -s '${f}' kmers_db_one.kmc_pre &&
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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19 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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20 #end for
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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21 #for $f in $input_collection_two:
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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22 #if '.kmc_suf' in str($f.element_identifier)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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23 ln -s '${f}' kmers_db_two.kmc_suf &&
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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24 #else
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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25 ln -s '${f}' kmers_db_two.kmc_pre &&
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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26 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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27 #end for
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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28 kmc_tools
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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29 -t\${GALAXY_SLOTS:-4}
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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30 simple
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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31 #if $input_options_cond.input_param == "None":
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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32 kmers_db_one
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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33 kmers_db_two
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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34 #elif $input_options_cond.input_param == "kmc_one_params":
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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35 kmers_db_one
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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36 -ci'$input_options_cond.kmc_db_one_param.min_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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37 -cx'$input_options_cond.kmc_db_one_param.max_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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38 kmers_db_two
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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39 #elif $input_options_cond.input_param == "kmc_two_params":
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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40 kmers_db_one
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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41 kmers_db_two
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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42 -ci'$input_options_cond.kmc_db_two_param.min_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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43 -cx'$input_options_cond.kmc_db_two_param.max_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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44 #elif $input_options_cond.input_param == "both_kmc_params":
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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45 kmers_db_one
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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46 -ci'$input_options_cond.both_db_one_param.min_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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47 -cx'$input_options_cond.both_db_one_param.max_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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48 kmers_db_two
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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49 -ci'$input_options_cond.both_db_two_param.min_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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50 -cx'$input_options_cond.both_db_two_param.max_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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51 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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52 #set $operation_arr=[]
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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53 #for $i,$opt in enumerate($operations)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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54 #silent $operation_arr.append(str($opt.ops.select_operation))
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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55 #if str($opt.ops.select_operation) == "intersect":
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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56 $opt.ops.select_operation
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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57 #if str($opt.ops.add_output_params.oc) != 'None':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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58 '${opt.ops.select_operation}_${opt.ops.add_output_params.oc}_db'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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59 -oc'$opt.ops.add_output_params.oc'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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60 #else
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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61 '${opt.ops.select_operation}_min_db'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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62 -oc'min'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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63 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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64 #if str($opt.ops.add_output_params.min_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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65 -ci'$opt.ops.add_output_params.min_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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66 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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67 #if str($opt.ops.add_output_params.max_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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68 -cx'$opt.ops.add_output_params.max_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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69 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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70 #elif str($opt.ops.select_operation) == "union":
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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71 $opt.ops.select_operation
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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72 #if str($opt.ops.add_output_params.oc) != 'None':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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73 '${opt.ops.select_operation}_${opt.ops.add_output_params.oc}_db'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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74 -oc'$opt.ops.add_output_params.oc'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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75 #else
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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76 '${opt.ops.select_operation}_sum_db'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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77 -oc'sum'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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78 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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79 #if str($opt.ops.add_output_params.min_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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80 -ci'$opt.ops.add_output_params.min_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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81 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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82 #if str($opt.ops.add_output_params.max_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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diff changeset
83 -cx'$opt.ops.add_output_params.max_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
84 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
85 #elif str($opt.ops.select_operation) == "kmers_subtract":
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
86 $opt.ops.select_operation
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
87 ${opt.ops.select_operation}_db
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
88 #if str($opt.ops.add_output_params.min_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
89 -ci'$opt.ops.add_output_params.min_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
90 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
91 #if str($opt.ops.add_output_params.max_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
92 -cx'$opt.ops.add_output_params.max_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
93 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
94 #elif str($opt.ops.select_operation) == "reverse_kmers_subtract":
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
95 $opt.ops.select_operation
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
96 ${opt.ops.select_operation}_db
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
97 #if str($opt.ops.add_output_params.min_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
98 -ci'$opt.ops.add_output_params.min_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
99 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
100 #if str($opt.ops.add_output_params.max_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
101 -cx'$opt.ops.add_output_params.max_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
102 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
103 #elif str($opt.ops.select_operation) == "counters_subtract":
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
104 $opt.ops.select_operation
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
105 #if str($opt.ops.add_output_params.oc) != 'None':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
106 '${opt.ops.select_operation}_${opt.ops.add_output_params.oc}_db'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
107 -oc'$opt.ops.add_output_params.oc'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
108 #else
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
109 '${opt.ops.select_operation}_min_db'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
110 -oc'diff'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
111 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
112 #if str($opt.ops.add_output_params.min_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
113 -ci'$opt.ops.add_output_params.min_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
114 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
115 #if str($opt.ops.add_output_params.max_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
116 -cx'$opt.ops.add_output_params.max_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
117 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
118 #elif str($opt.ops.select_operation) == "reverse_counters_subtract":
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
119 $opt.ops.select_operation
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
120 #if str($opt.ops.add_output_params.oc) != 'None':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
121 '${opt.ops.select_operation}_${opt.ops.add_output_params.oc}_db'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
122 -oc'$opt.ops.add_output_params.oc'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
123 #else
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
124 '${opt.ops.select_operation}_min_db'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
125 -oc'diff'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
126 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
127 #if str($opt.ops.add_output_params.min_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
128 -ci'$opt.ops.add_output_params.min_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
129 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
130 #if str($opt.ops.add_output_params.max_kmer_occurrence) != '':
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
131 -cx'$opt.ops.add_output_params.max_kmer_occurrence'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
132 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
133 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
134 #end for
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
135
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
136 #for $i,$op in enumerate($operation_arr):
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
137 #if str($op) == "kmers_subtract" or str($op) == "reverse_kmers_subtract":
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
138 && cp '${op}'_db.kmc_suf outdir/
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
139 && cp '${op}'_db.kmc_pre outdir/
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
140 2>&1 | tee -a '$out_log'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
141 #else
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
142 && cp '${op}'_*_db.kmc_suf outdir/
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
143 && cp '${op}'_*_db.kmc_pre outdir/
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
144 2>&1 | tee -a '$out_log'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
145 #end if
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
146 #end for
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
147 ]]></command>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
148 <inputs>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
149 <param name="input_collection_one" type="data_collection" collection_type="list" label="KMC db one"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
150 <param name="input_collection_two" type="data_collection" collection_type="list" label="KMC db two"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
151 <conditional name="input_options_cond">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
152 <param name="input_param" type="select" label="Input parameters">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
153 <option value="None" selected="true">Both KMC DB with default parameters</option>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
154 <option value="kmc_one_params">KMC db one only</option>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
155 <option value="kmc_two_params">KMC db two only</option>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
156 <option value="both_kmc_params">Both KMC DB with user parameters</option>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
157 </param>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
158 <when value="None"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
159 <when value="kmc_one_params">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
160 <section name="kmc_db_one_param" title="KMC DB one parameters">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
161 <expand macro="input_option"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
162 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
163 </when>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
164 <when value="kmc_two_params">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
165 <section name="kmc_db_two_param" title="KMC DB two parameters">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
166 <expand macro="input_option"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
167 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
168 </when>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
169 <when value="both_kmc_params">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
170 <section name="both_db_one_param" title="KMC DB one parameters">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
171 <expand macro="input_option"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
172 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
173 <section name="both_db_two_param" title="KMC DB two parameters">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
174 <expand macro="input_option"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
175 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
176 </when>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
177 </conditional>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
178 <repeat name="operations" title="Operations" min="1" max="3">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
179 <conditional name="ops">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
180 <expand macro="simple_operation"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
181 <when value="intersect">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
182 <section name="add_output_params" expanded="false" title="Additional output parameters">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
183 <expand macro="counter_calculation_option"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
184 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
185 </when>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
186 <when value="union">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
187 <section name="add_output_params" expanded="false" title="Additional output parameters">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
188 <expand macro="counter_calculation_option"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
189 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
190 </when>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
191 <when value="kmers_subtract">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
192 <section name="add_output_params" expanded="false" title="Additional output parameters">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
193 <expand macro="none_counter_calculation_option"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
194 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
195 </when>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
196 <when value="reverse_kmers_subtract">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
197 <section name="add_output_params" expanded="false" title="Additional output parameters">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
198 <expand macro="none_counter_calculation_option"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
199 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
200 </when>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
201 <when value="counters_subtract">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
202 <section name="add_output_params" expanded="false" title="Additional output parameters">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
203 <expand macro="counter_calculation_option"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
204 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
205 </when>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
206 <when value="reverse_counters_subtract">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
207 <section name="add_output_params" expanded="false" title="Additional output parameters">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
208 <expand macro="counter_calculation_option"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
209 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
210 </when>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
211 </conditional>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
212 </repeat>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
213 </inputs>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
214 <outputs>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
215 <collection name="kmc_db" type="list" label="${tool.name} on ${on_string}: kmc db">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
216 <discover_datasets pattern="(?P&lt;designation&gt;.+)" format="binary" directory="outdir/" />
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
217 </collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
218 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
219 </outputs>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
220 <tests>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
221 <test>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
222 <!-- #1 test with default parameters -->
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
223 <param name="input_collection_one">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
224 <collection type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
225 <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
226 <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
227 </collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
228 </param>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
229 <param name="input_collection_two">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
230 <collection type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
231 <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
232 <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
233 </collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
234 </param>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
235 <conditional name="input_options_cond">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
236 <param name="input_param" value="None"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
237 </conditional>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
238 <param name="select_operation" value="intersect" />
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
239 <section name="add_output_params">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
240 <param name="oc" value="max"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
241 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
242 <output_collection name="kmc_db" type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
243 <element name="intersect_max_db.kmc_suf" file="intersect_max_db.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
244 <element name="intersect_max_db.kmc_pre" file="intersect_max_db.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
245 </output_collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
246 </test>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
247 <test>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
248 <!-- #2 test with input parameters for KMC DB one only -->
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
249 <param name="input_collection_one">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
250 <collection type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
251 <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
252 <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
253 </collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
254 </param>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
255 <param name="input_collection_two">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
256 <collection type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
257 <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
258 <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
259 </collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
260 </param>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
261 <conditional name="input_options_cond">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
262 <param name="input_param" value="kmc_one_params"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
263 </conditional>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
264 <param name="select_operation" value="intersect" />
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
265 <section name="kmc_db_one_param">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
266 <param name="min_kmer_occurrence" value="3"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
267 <param name="max_kmer_occurrence" value="30"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
268 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
269 <section name="add_output_params">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
270 <param name="oc" value="min"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
271 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
272 <output_collection name="kmc_db" type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
273 <element name="intersect_min_db.kmc_suf" file="intersect_min_db.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
274 <element name="intersect_min_db.kmc_pre" file="intersect_min_db.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
275 </output_collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
276 </test>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
277 <test>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
278 <!-- #3 test with input parameters for KMC DB two only -->
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
279 <param name="input_collection_one">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
280 <collection type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
281 <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
282 <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
283 </collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
284 </param>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
285 <param name="input_collection_two">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
286 <collection type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
287 <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
288 <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
289 </collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
290 </param>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
291 <conditional name="input_options_cond">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
292 <param name="input_param" value="kmc_two_params"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
293 </conditional>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
294 <param name="select_operation" value="union" />
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
295 <section name="kmc_db_two_param">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
296 <param name="min_kmer_occurrence" value="3"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
297 <param name="max_kmer_occurrence" value="30"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
298 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
299 <output_collection name="kmc_db" type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
300 <element name="union_db.kmc_suf" file="union_db.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
301 <element name="union_db.kmc_pre" file="union_db.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
302 </output_collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
303 </test>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
304 <test>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
305 <!-- #4 test with input parameters for both KMC DB -->
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
306 <param name="input_collection_one">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
307 <collection type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
308 <element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
309 <element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
310 </collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
311 </param>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
312 <param name="input_collection_two">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
313 <collection type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
314 <element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
315 <element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
316 </collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
317 </param>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
318 <conditional name="input_options_cond">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
319 <param name="input_param" value="both_kmc_params"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
320 </conditional>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
321 <param name="select_operation" value="counters_subtract" />
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
322 <section name="both_db_one_param">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
323 <param name="min_kmer_occurrence" value="2"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
324 <param name="max_kmer_occurrence" value="20"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
325 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
326 <section name="both_db_two_param">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
327 <param name="min_kmer_occurrence" value="3"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
328 <param name="max_kmer_occurrence" value="30"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
329 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
330 <section name="add_output_params">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
331 <param name="oc" value="sum"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
332 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
333 <output_collection name="kmc_db" type="list">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
334 <element name="counters_subtract_sum_db.kmc_suf" file="counters_subtract_sum_db.kmc_suf"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
335 <element name="counters_subtract_sum_db.kmc_pre" file="counters_subtract_sum_db.kmc_pre"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
336 </output_collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
337 </test>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
338 </tests>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
339 <help><![CDATA[
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
340
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
341 .. class:: infomark
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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diff changeset
342
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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diff changeset
343
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
344 **What it does**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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diff changeset
345
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
346 *KMC simple operation performs set operation on two input KMC's databases*
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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diff changeset
347
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
348 **General Syntax**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
349
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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diff changeset
350 kmc_tools simple <input1 [input1_params]> <input2 [input2_params]> <oper1 output1 [output_params1]> [<oper2 output2 [output_params2]> ...]
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
351
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
352 **Input:**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
353
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
354 - input file - input1 and input2 are the databases generated by KMC ( kmc file suffix - kmc_pre and kmc_suf )
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
355
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
356 **Available Operations:**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
357
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
358 - intersect - output database will contains only k-mers that are present in both input sets
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
359 - union - output database will contains each k-mer present in any of input sets
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
360 - kmers_subtract - difference of input sets based on k-mers. Output database will contains only k-mers that are present in first input set but absent in the second one
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
361 - counters_subtract - difference of input sets based on k-mers and their counters (weaker version of kmers_subtract). Output database will contains all k-mers that are present in first input, beyond those for which counter operation will lead to remove (i.e. counter equal to 0 or negative number)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
362 - reverse_kmers_subtract - same as kmers_subtract but treat input2 as first and input1 as second
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
363 - reverse_counters_subtract - same as counters_subtract but treat input2 as first and input1 as second
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
364
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
365 **Additional Parameters for inputs:**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
366
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
367 - ci<value> - exclude k-mers occurring less than <value> times
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
368 - cx<value> - exclude k-mers occurring more of than <value> times
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
369
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
370 **Additional Parameters for outputs:**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
371
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
372 - ci<value> - exclude k-mers occurring less than <value> times
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
373 - cx<value> - exclude k-mers occurring more of than <value> times
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
374 - cs<value> - maximal value of a counter
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
375 - o<kmc|kff> - output in KMC or KFF format (default: kmc)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
376 - oc<value> - redefine counter calculation mode for equal k-mers
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
377
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
378 **Available oc<value>**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
379
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
380 - min - get lower value of a k-mer counter (default value for intersect operation)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
381 - max - get upper value of a k-mer counter
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
382 - sum - get sum of counters from both databases
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
383 - diff - get difference between counters (default for counters_subtract operation)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
384 - left - get counter from first database (input1)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
385 - right - get counter from second database (input2)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
386
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
387
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
388 **Example(1):**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
389
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
390 - kmc -k27 file1.fastq kmers1 kmc_tmp_dir
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
391 - kmc -k27 file2.fastq kmers2 kmc_tmp_dir
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
392 - kmc_tools simple kmers1 -ci10 -cx200 kmers2 -ci4 -cx100 intersect kmers1_kmers2_intersect -ci20 -cx150
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
393
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
394 **Output(1)**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
395
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
396 - kmers1_kmers2_intersect.kmc_suf (i.e intersect_kmc_suf in galaxy)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
397 - kmers1_kmers2_intersect.kmc_pre (i.e intersect_kmc_pre in galaxy)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
398
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
399 **Example(2):**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
400
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
401 - kmc -k27 file1.fastq kmers1 kmc_tmp_dir
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
402 - kmc -k27 file2.fastq kmers2 kmc_tmp_dir
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
403 - kmc_tools simple kmers1 kmers2 intersect inter_k1_k2_max -ocmax intersect inter_k1_k2_min union union_k1_k2 -ci10
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
404
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
405 **Output(2)**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
406
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
407 - inter_k1_k2_max.kmc_suf (i.e intersect.kmc_suf in galaxy)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
408 - inter_k1_k2_max.kmc_pre (i.e intersect.kmc_pre in galaxy)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
409 - inter_k1_k2_min.kmc_suf (i.e intersect.kmc_suf in galaxy)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
410 - inter_k1_k2_min.kmc_pre (i.e intersect.kmc_pre in galaxy)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
411 - union_k1_k2.kmc_suf (i.e union.kmc_suf in galaxy)
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
412 - union_k1_k2.kmc_pre (i.e union.kmc_pre in galaxy
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
413
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
414 .. class:: infomark
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
415
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
416 **References**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
417
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
418 More information are available on `website <https://github.com/refresh-bio/KMC/blob/master/kmc_tools.pdf>`_.
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
419 ]]></help>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
420 <citations>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
421 <citation type="doi">DOI: 10.1093/bioinformatics/btx304</citation>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
422 <citation type="doi">DOI: 10.1093/bioinformatics/btv022</citation>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
423 <citation type="doi">DOI: 10.1186/1471-2105-14-160</citation>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
424 </citations>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
425 </tool>