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annotate kmc.xml @ 3:87ddc8ca7859 draft default tip

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planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
author galaxy-australia
date Wed, 02 Oct 2024 09:52:40 +0000
parents c97f8a687258
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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1 <tool id="kmc" name="KMC Counter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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2 <description>K-mer counting and filtering of reads</description>
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c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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3 <macros>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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4 <import>macros.xml</import>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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5 </macros>
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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6 <xrefs>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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7 <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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8 </xrefs>
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"
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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[
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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13 mkdir output &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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14 #if $data_type.select == 'individual'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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15 #for $input_file in $data_type.individual_file
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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16 #if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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17 #if $input_file.ext.endswith(".gz")
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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18 #set $ext='.fastq.gz'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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19 #else
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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20 #set $ext='.fastq'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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21 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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22 ln -s '$input_file' 'in$ext' &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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23 #elif $input_file.is_of_type("fasta","fasta.gz"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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24 #if $input_file.ext.endswith(".gz")
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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25 #set $ext='.fasta.gz'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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26 #else
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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27 #set $ext='.fasta'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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28 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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29 ln -s '$input_file' 'in$ext' &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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30 #elif $input_file.is_of_type("bam"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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31 ln -s '$input_file' in.bam &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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32 #elif $input_file.is_of_type("kmc_suf"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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33 #if $input_file.ext.endswith(".kmc_suf")
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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34 #set $suf_ext='.kmc_suf'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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35 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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36 #if $input_file.ext.endswith(".kmc_pre")
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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37 #set $pre_ext='.kmc_pre'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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38 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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39 ln -s '$input_file' 'in$suf_ext' &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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40 ln -s '$input_file' 'in$pre_ext' &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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41 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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42 #end for
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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43 #else
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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44 mkdir input_dir &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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45 #import re
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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46 #for $input_file in $data_type.collection_file
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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47 #if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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48 #if $input_file.ext.endswith(".gz")
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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49 #set $ext='.fastq.gz'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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50 #else
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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51 #set $ext='.fastq'
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52 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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53 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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54 ln -s '$input_file' 'input_dir/${identifier}' &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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55 #elif $input_file.is_of_type("fasta","fasta.gz"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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56 #if $input_file.ext.endswith(".gz")
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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57 #set $ext='.fasta.gz'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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58 #else
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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59 #set $ext='.fasta'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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60 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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61 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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62 ln -s '$input_file' 'input_dir/${identifier}' &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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63 #elif $input_file.is_of_type("bam"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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64 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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65 ln -s '$input_file' 'input_dir/${identifier}' &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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66 #elif $input_file.is_of_type("kmc_suf"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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67 #if $input_file.ext.endswith(".kmc_suf")
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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68 #set $suf_ext='.kmc_suf'
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69 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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70 #if $input_file.ext.endswith(".kmc_pre")
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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71 #set $pre_ext='.kmc_pre'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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72 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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73 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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74 ln -s '$input_file' 'input_dir/${identifier}' &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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75 ln -s '$input_file' 'input_dir/${identifier}' &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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76 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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77 #end for
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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78 ls -ld input_dir/* | awk '{print $9}' >> files.list &&
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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79 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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80
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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81 kmc
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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82 -t\${GALAXY_SLOTS:-4}
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
83 #if $params.k:
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
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84 -k'$params.k'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
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85 #end if
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
86 -m\${GALAXY_MEMORY_GB:-4}
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
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87 #if $params.j:
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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88 -j'$statistic'
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
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89 #end if
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
90 #if $params.p:
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
91 -p'$params.p'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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92 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
93 #if $params.ci:
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
94 -ci'$params.ci'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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95 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
96 #if $params.cs:
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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97 -cs'$params.cs'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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98 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
99 #if $params.cx:
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
100 -cx'$params.cx'
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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101 #end if
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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102 #if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
103 -fq
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
104 #elif $input_file.is_of_type("fasta","fasta.gz"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
105 #if $data_type.select == "individual":
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
106 -fa
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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107 #else
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
108 -fm
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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109 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
110 #elif $input_file.is_of_type("bam"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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111 -fbam
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
112 #elif $input_file.is_of_type("kmc_suf"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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113 -fkmc
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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114 #end if
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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115
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
116 #if $input_file.is_of_type('fastq.gz','fasta.gz','fastqsanger.gz'):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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117 -f
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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118 #end if
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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119
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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120 #if $data_type.select == 'individual'
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
121 #if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
122 #if $input_file.ext.endswith(".gz")
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
123 in.fastq.gz
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
124 #else
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
125 in.fastq
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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126 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
127 #elif $input_file.is_of_type("fasta","fasta.gz"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
128 #if $input_file.ext.endswith(".gz")
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
129 in.fasta.gz
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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130 #else
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
131 in.fasta
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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132 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
133 #elif $input_file.is_of_type("bam"):
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
134 in.bam
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
135 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
136 #else
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
137 @files.list
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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138 #end if
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
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diff changeset
139 output/kmer_"$params.k"
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
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140 .
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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141
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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142 ]]></command>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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143 <inputs>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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144 <expand macro="macro_input" />
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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145 <section name="params" title="parameter" expanded="false">
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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146 <param argument="-k" type="integer" value="25" label="k-mer length (k from 1 to 256; default: 25)" />
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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147 <param argument="-p" type="integer" value="9" label="signature length (5, 6, 7, 8, 9, 10, 11); default: 9"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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148 <param argument="-ci" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
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149 <param argument="-cs" type="integer" value="255" label="maximal value of a counter (default: 255)"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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150 <param argument="-cx" type="integer" value="1000000000" label="xclude k-mers occurring more of than [value] times (default: 1e9)"/>
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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151 <param argument="-j" type="boolean" truevalue="-j" falsevalue="" checked="True" label="file name with execution summary in JSON format"/>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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152 </section>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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153 </inputs>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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154 <outputs>
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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155 <data name="statistic" format="json" label="${tool.name} on ${on_string}">
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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156 <filter>params['j']</filter>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
157 </data>
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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diff changeset
158 <collection name="kmc_db" type="list" label="${tool.name} on ${on_string}: kmc db">
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
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parents: 0
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159 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="output" format="binary" />
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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160 </collection>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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161 </outputs>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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162 <tests>
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
163 <test expect_num_outputs="2">
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
164 <!-- #1 test individual fasta file -->
2
c97f8a687258 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 1
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165 <param name="individual_file" value="test.fasta" ftype="fasta"/>
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
166 <param name="k" value="27" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
167 <param name="ci" value="2" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
168 <param name="cs" value="255" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
169 <output_collection name="kmc_db" type="list">
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
170 <element name="kmer_27.kmc_pre" file="kmer_27.kmc_pre" ftype="binary" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
171 <element name="kmer_27.kmc_suf" file="kmer_27.kmc_suf" ftype="binary" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
172 </output_collection>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
173 <output name="statistic" ftype="json">
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
174 <assert_contents>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
175 <has_text text="1st_stage"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
176 <has_text text="2nd_stage"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
177 <has_text text="Stats"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
178 </assert_contents>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
179 </output>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
180 </test>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
181 <!-- output file is too large for testing; comment out to test on local machine with update_test_data option -->
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
182 <!-- <test expect_num_outputs="2"> -->
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
183 <!-- #2 test individual fastq file -->
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
184 <!-- <param name="individual_file" value="filtered_1.fastq" ftype="fastq"/>
0
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
185 <param name="k" value="25" />
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
186 <param name="p" value="9" />
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
parents:
diff changeset
187 <param name="ci" value="2" />
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
188 <param name="cs" value="255" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
189 <output_collection name="kmc_db" type="list">
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
190 <element name="kmer_25.kmc_pre" file="kmer_25.kmc_pre" ftype="binary" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
191 <element name="kmer_25.kmc_suf" file="kmer_25.kmc_suf" ftype="binary" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
192 </output_collection>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
193 <output name="statistic" ftype="json">
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
194 <assert_contents>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
195 <has_text text="1st_stage"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
196 <has_text text="2nd_stage"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
197 <has_text text="Stats"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
198 </assert_contents>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
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199 </output>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
200 </test> -->
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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201 <!-- output file is too large for testing; comment out to test on local machine -->
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
202 <!-- <test expect_num_outputs="2"> -->
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
203 <!-- #3 test collection fastq with common parameters -->
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
204 <!-- <param name="k" value="29" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
205 <param name="m" value="12" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
206 <param name="p" value="9" />
0
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
207 <param name="ci" value="2" />
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
208 <param name="cs" value="255" />
1
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
209 <conditional name="data_type">
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
210 <param name="select" value="collection"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
211 <param name="collection_file">
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
212 <collection type="list">
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
213 <element name="filtered_1.fastq" value="filtered_1.fastq" ftype="fastq"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
214 <element name="filtered_2.fastq" value="filtered_2.fastq" ftype="fastq"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
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215 </collection>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
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diff changeset
216 </param>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
217 </conditional>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
218 <output_collection name="kmc_db">
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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219 <element name="kmer_29.kmc_suf" file="kmer_29.kmc_suf" ftype="binary" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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220 <element name="kmer_29.kmc_pre" file="kmer_29.kmc_pre" ftype="binary" />
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
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221 </output_collection>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
222 <output name="statistic" ftype="json">
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
223 <assert_contents>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
224 <has_text text="1st_stage"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
225 <has_text text="2nd_stage"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
parents: 0
diff changeset
226 <has_text text="Stats"/>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
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227 </assert_contents>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
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228 </output>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
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229 </test>
c7fda6e88567 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
galaxy-australia
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230 -->
0
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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231 </tests>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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232 <help><![CDATA[
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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233
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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diff changeset
234 .. class:: infomark
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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235
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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236 **What it does**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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237
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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diff changeset
238 *K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.*
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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239
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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240
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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241 **Input**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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242
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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243 - input file - FASTA, FASTQ and BAM. Also, gipped versions of FASTA and FASTQ.
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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244
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
245 **Example:**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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246
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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247 - kmc -k27 -m24 NA19238.fastq NA.res /data/kmc_tmp_dir/
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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248 - kmc -k27 -m24 @files.lst NA.res /data/kmc_tmp_dir/
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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249
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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250 **Output**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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251
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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252 - filename.res.kmc_suf
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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253 - filename.res.kmc_pre
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
galaxy-australia
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254
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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256 .. class:: infomark
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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257
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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258 **References**
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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259
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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260 More information are available on `website <http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about>`_.
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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261 ]]></help>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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262 <citations>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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263 <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"
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264 <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"
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265 <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"
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266 </citations>
ca2743037241 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
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267 </tool>