Mercurial > repos > iuc > colibread_commet

annotate macros.xml @ 1:dc31aacc886b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
author iuc
date Fri, 24 Nov 2017 12:45:22 -0500
parents 0b9a713ece1d
children a4d4b2564a2a
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0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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1 <macros>
1
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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2 <xml name="discosnp_requirements">
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
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3 <requirements>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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4 <requirement type="package" version="2.3.0">discosnp</requirement>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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5 </requirements>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
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6 </xml>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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8 <token name="@DISCOSNP_VERSION@">2.3.0</token>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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0
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10 <token name="@discosnp_single_reads@"><![CDATA[
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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11 #for $input in $input_type_options.list_reads
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dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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12 #set $filename = os.path.basename(str($input)) + "." + $input.ext
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0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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13 ln -sf '${input}' '${filename}' &&
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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14 echo '${filename}' >> input.lst &&
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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15 #end for
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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16 ]]></token>
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dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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0
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18 <token name="@discosnp_paired_reads@"><![CDATA[
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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19 #for $i, $paired in enumerate( $input_type_options.list_paired_reads )
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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1
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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21 #set $filenameFWD = os.path.basename(str($paired.forward)) + "." + $paired.forward.ext
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0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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22 ln -sf '${paired.forward}' '${filenameFWD}' &&
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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23
1
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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24 #set $filenameREV = os.path.basename(str($paired.reverse)) + "." + $paired.reverse.ext
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0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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25 ln -sf '${paired.reverse}' '${filenameREV}' &&
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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27 echo '${filenameFWD}' > "paired_${i}.lst" &&
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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28 echo '${filenameREV}' >> "paired_${i}.lst" &&
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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29 echo "paired_${i}.lst" >> input.lst &&
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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31 #end for
0b9a713ece1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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32 ]]></token>
1
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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34 <xml name="discosnp_inputs">
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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35 <conditional name="input_type_options">
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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36 <param name="input_type" type="select" label="Input options">
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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37 <option value="single">Single end reads</option>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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38 <option value="paired">Paired end reads</option>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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39 <option value="mix">Both single and paired reads</option>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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40 </param>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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41 <when value="single">
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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42 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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43 </when>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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44 <when value="paired">
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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45 <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" />
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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46 </when>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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47 <when value="mix">
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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48 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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49 <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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50 </when>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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51 </conditional>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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52 </xml>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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53
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54 <xml name="discosnp_options">
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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55 <param argument="-D" type="integer" label="Deletion size" value="0" help="If different of 0, discoSnp will search for deletions of size from 1 to D included"/>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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56 <param argument="-P" type="integer" label="Maximum SNPs per bubble" value="1" help="discoSnp will search up to P SNPs in a unique bubble"/>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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57 <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" />
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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58 <param argument="-k" type="integer" label="Size of kmers" value="31" />
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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59
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60 <conditional name="coverage_options_type" >
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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61 <param name="coverage_options" type="select" label="Coverage option">
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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62 <option value="auto"></option>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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63 <option value="custom"></option>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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64 </param>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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65 <when value="auto" />
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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66 <when value="custom">
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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67 <param argument="-c" type="text" label="Minimal coverage per read set" value="4" help="e.g. 4 / 4,5,17 / 4,auto,auto"/>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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68 </when>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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69 </conditional>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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70
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71 <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" />
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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72 <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" />
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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73
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74 </xml>
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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75
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76 <token name="@discosnp_inputs@"><![CDATA[
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77 -r input.lst
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78 -b ${b}
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79 -D ${D}
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80 -P ${P}
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81 ${low_complexity}
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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82 -k ${k}
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83
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84 #if str($coverage_options_type.coverage_options) == 'auto'
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85 -c auto
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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86 #else
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87 -c '${coverage_options_type.c}'
dc31aacc886b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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88 #end if
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89 -C ${C}
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90 -d ${d}
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91 ]]></token>
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92
0
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93 <token name="@lordec_inputs@"><![CDATA[
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94 -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }"
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95 -i '${program_type_choice.i}'
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96 -k ${program_type_choice.k}
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97 -s ${program_type_choice.s}
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98 ]]></token>
1
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99
0
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100 <xml name="lordec_inputs">
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101 <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" />
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102 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
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103 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
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104 <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
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105 </xml>
1
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106
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107 <token name="@discosnp_help@"><![CDATA[
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108 -------
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109
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110 .. class:: warningmark
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111
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112 **Input parameters**
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113
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114 -Sequences files in fasta or fastq each allele will be counted in each file individually
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115
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116 -Use collections: data list and/or data list paired
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117
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118 -Fasta sequence of a genome if case of you are willing to map the sequence extension on a reference in order to get a compliant VCF
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119
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120 -------
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121
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122 .. class:: warningmark
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123
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124 **Ouput parameters**
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125
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126 -VCF file with coordinates on the higher branch sequences or on a reference genome if provided
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127
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128 -Fasta file with sequence extensions around the SNP.
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129
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130
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131 -------
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132
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133 **Web site**
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134
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135 https://colibread.inria.fr/software/discosnp/
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136
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137 ]]></token>
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138
0
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139 <xml name="citations">
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140 <citations>
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141 <yield/>
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142 <citation type="doi">10.1186/s13742-015-0105-2</citation>
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143 </citations>
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144 </xml>
1
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145
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146 <xml name="discosnp_citation">
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147 <citation type="doi">10.1101/209965</citation>
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148 </xml>
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149
0
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150 </macros>