Mercurial > repos > iuc > colibread_mapsembler2
annotate macros.xml @ 4:e7c5b81b3c22 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
author | iuc |
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date | Mon, 17 Aug 2020 10:40:05 -0400 |
parents | 00fd0b4274fd |
children | c5371f68db91 |
rev | line source |
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0
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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1 <macros> |
4
e7c5b81b3c22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
iuc
parents:
1
diff
changeset
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2 <token name="@DISCOSNP_VERSION@">2.5.4</token> |
e7c5b81b3c22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
iuc
parents:
1
diff
changeset
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3 |
1
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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4 <xml name="discosnp_requirements"> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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5 <requirements> |
4
e7c5b81b3c22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
iuc
parents:
1
diff
changeset
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6 <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement> |
1
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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7 </requirements> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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8 </xml> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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9 |
0
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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10 <token name="@discosnp_single_reads@"><![CDATA[ |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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11 #for $input in $input_type_options.list_reads |
1
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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12 #set $filename = os.path.basename(str($input)) + "." + $input.ext |
0
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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13 ln -sf '${input}' '${filename}' && |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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14 echo '${filename}' >> input.lst && |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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15 #end for |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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16 ]]></token> |
1
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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17 |
0
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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18 <token name="@discosnp_paired_reads@"><![CDATA[ |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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19 #for $i, $paired in enumerate( $input_type_options.list_paired_reads ) |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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20 |
1
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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21 #set $filenameFWD = os.path.basename(str($paired.forward)) + "." + $paired.forward.ext |
0
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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22 ln -sf '${paired.forward}' '${filenameFWD}' && |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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23 |
1
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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24 #set $filenameREV = os.path.basename(str($paired.reverse)) + "." + $paired.reverse.ext |
0
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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25 ln -sf '${paired.reverse}' '${filenameREV}' && |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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26 |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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27 echo '${filenameFWD}' > "paired_${i}.lst" && |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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28 echo '${filenameREV}' >> "paired_${i}.lst" && |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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29 echo "paired_${i}.lst" >> input.lst && |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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30 |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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31 #end for |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
diff
changeset
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32 ]]></token> |
1
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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33 |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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34 <xml name="discosnp_inputs"> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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35 <conditional name="input_type_options"> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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36 <param name="input_type" type="select" label="Input options"> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
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changeset
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37 <option value="single">Single end reads</option> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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38 <option value="paired">Paired end reads</option> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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39 <option value="mix">Both single and paired reads</option> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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40 </param> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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41 <when value="single"> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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42 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" /> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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43 </when> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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44 <when value="paired"> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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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" /> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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46 </when> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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47 <when value="mix"> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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48 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" /> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
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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"/> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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50 </when> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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51 </conditional> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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52 </xml> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
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53 |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
changeset
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54 <xml name="discosnp_options"> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
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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"/> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
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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"/> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
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57 <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" /> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
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58 <param argument="-k" type="integer" label="Size of kmers" value="31" /> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
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59 |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
diff
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60 <conditional name="coverage_options_type" > |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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61 <param name="coverage_options" type="select" label="Coverage option"> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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62 <option value="auto"></option> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
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63 <option value="custom"></option> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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64 </param> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
0
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65 <when value="auto" /> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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66 <when value="custom"> |
4
e7c5b81b3c22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
iuc
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67 <param argument="-c" type="text" label="Minimal coverage per read set" value="3" help="e.g. 3 / 3,5,17 / 3,auto,auto"/> |
1
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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68 </when> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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69 </conditional> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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70 |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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71 <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" /> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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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" /> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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73 |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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74 </xml> |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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75 |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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76 <token name="@discosnp_inputs@"><![CDATA[ |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
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77 -r input.lst |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
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78 -D ${D} |
00fd0b4274fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
parents:
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79 -P ${P} |
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80 ${low_complexity} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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81 -k ${k} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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82 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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83 #if str($coverage_options_type.coverage_options) == 'auto' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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84 -c auto |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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85 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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86 -c '${coverage_options_type.c}' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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87 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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88 -C ${C} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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89 -d ${d} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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90 ]]></token> |
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91 |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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92 <token name="@lordec_inputs@"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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93 -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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94 -i '${program_type_choice.i}' |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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95 -k ${program_type_choice.k} |
265fa5effd4d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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96 -s ${program_type_choice.s} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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97 ]]></token> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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98 |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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99 <xml name="lordec_inputs"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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100 <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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101 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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102 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/> |
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103 <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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104 </xml> |
1
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105 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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106 <token name="@discosnp_help@"><![CDATA[ |
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107 ------- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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108 |
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109 .. class:: warningmark |
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110 |
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111 **Input parameters** |
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112 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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113 -Sequences files in fasta or fastq each allele will be counted in each file individually |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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114 |
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115 -Use collections: data list and/or data list paired |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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116 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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117 -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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118 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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119 ------- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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120 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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121 .. class:: warningmark |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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122 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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123 **Ouput parameters** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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124 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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125 -VCF file with coordinates on the higher branch sequences or on a reference genome if provided |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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126 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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127 -Fasta file with sequence extensions around the SNP. |
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128 |
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129 |
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130 ------- |
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131 |
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132 **Web site** |
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133 |
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134 https://colibread.inria.fr/software/discosnp/ |
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135 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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136 ]]></token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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137 |
0
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138 <xml name="citations"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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139 <citations> |
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140 <yield/> |
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141 <citation type="doi">10.1186/s13742-015-0105-2</citation> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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142 </citations> |
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143 </xml> |
1
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144 |
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145 <xml name="discosnp_citation"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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146 <citation type="doi">10.1101/209965</citation> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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147 </xml> |
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148 |
0
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149 </macros> |