Mercurial > repos > iuc > colibread_takeabreak
annotate takeabreak.xml @ 1:a018b8f663ea draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
author | iuc |
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date | Fri, 24 Nov 2017 12:49:52 -0500 |
parents | e1fdaacdabc3 |
children | b0e311ac462c |
rev | line source |
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e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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1 <?xml version='1.0' encoding='utf-8'?> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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2 <tool profile="16.0" id="takeabreak" name="TakeABreak" version="1.1.2"> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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3 <description>is a tool that can detect inversion breakpoints directly from raw NGS reads</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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4 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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5 <requirement type="package" version="1.1.2">takeabreak</requirement> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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6 </requirements> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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7 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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8 <import>macros.xml</import> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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9 </macros> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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10 <command><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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11 |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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12 ## if single reads |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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13 #if str( $input_type_option.input_type ) == "simple" |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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14 #for $input in $input_type_option.reads |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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15 #if $input |
1
a018b8f663ea
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
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16 #set $filename = os.path.basename(str($input)) + "." + $input.ext |
0
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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17 ln -sf '${input}' '${filename}' && |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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18 echo "${filename}" >> input.fof && |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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19 #end if |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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20 #end for |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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21 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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22 ## if paired reads in a list |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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23 #for $i, $list in enumerate( $input_type_option.reads_lists ) |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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24 #for $read in $list.list_reads |
1
a018b8f663ea
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
iuc
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25 #set $filename = os.path.basename(str($read)) + "." + $read.ext |
0
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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26 ln -sf '${read}' '${filename}' && |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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27 echo "${filename}" >> "indiv_${i}.fof" && |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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28 #end for |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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29 echo "indiv_${i}.fof" >> input.fof && |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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30 #end for |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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31 #end if |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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32 |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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33 TakeABreak |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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34 |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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35 -in input.fof |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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36 -kmer-size ${kmer_size} |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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37 -abundance-min '${abundance_min}' |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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38 -abundance-max ${abundance_max} |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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39 -solidity-kind ${solidity_kind} |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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40 -lct ${lct} |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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41 -max-sim ${max_sim} |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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42 -repeat ${repeat} |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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43 |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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44 ]]></command> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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45 |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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46 <inputs> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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47 <!-- Input data files --> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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48 <conditional name="input_type_option"> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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49 <param name="input_type" type="select" label="Input option"> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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50 <option value="simple">one individual = one read </option> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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51 <option value="list">one individual = several reads</option> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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52 </param> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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53 <when value="simple"> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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54 <param name='reads' argument="-in" format="fasta,fastq" type="data" multiple="true" label="Single read files" optional="True" /> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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55 </when> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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56 <when value="list"> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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57 <repeat name="reads_lists" title="Individual" min="1"> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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58 <param name='list_reads' argument="-in" format="fasta,fastq" type="data_collection" collection_type="list" multiple="true" label="Individual read files list"/> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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59 </repeat> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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60 </when> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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61 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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62 <param name="kmer_size" argument="-kmer-size" type="integer" label="Length of the k-mers" value="31" help="Set the length of used kmers" /> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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63 <param name="abundance_min" argument="-abundance-min" type="text" label="Minimal abundance threshold" value="auto" /> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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64 <param name="abundance_max" argument="-abundance-max" type="integer" label="Maximal abundance threshold" value="2147483647" /> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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65 |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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66 <param name="solidity_kind" argument="-solidity-kind" type="select" label="Way to consider a solid kmer with several input datasets" > |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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67 <option value="one">One</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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68 <option value="sum">Sum</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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69 <option value="all">All</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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70 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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71 |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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72 <param argument="-lct" type="integer" label="local complexity threshold" value="100" help="Local complexity threshold" /> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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73 <param name="max_sim" argument="-max-sim" type="integer" label="max similarity percentage" value="80" help="Inversions with a and b' (or u and v') whose longest common subsequence size is bigger than k*(this value)/100 are discarded" /> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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74 <param argument="-repeat" type="integer" label="maximal repeat size" value="8" help="Maximal repeat size at the breakpoint. Longest common suffix between a and b" /> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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75 </inputs> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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76 |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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77 <outputs> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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78 <data format="fasta" name="inversion" from_work_dir="TakeABreak_*.fasta" label="Inversions with ${tool.name} on ${on_string}"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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79 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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80 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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81 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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82 <conditional name="input_type_option"> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
parents:
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83 <param name="input_type" value="list" /> |
e1fdaacdabc3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
iuc
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84 <repeat name="reads_lists"> |
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85 <param name="list_reads"> |
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86 <collection type="list"> |
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87 <element name="example_reads" value="takeabreak/toy_example_reads.fasta" ftype="fasta"/> |
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88 <element name="example_reads_with_inv" value="takeabreak/toy_example_with_inv_reads.fasta" ftype="fasta"/> |
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89 </collection> |
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90 </param> |
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91 </repeat> |
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92 </conditional> |
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93 <output name="inversion" file="takeabreak/inversion_list.fasta"/> |
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94 </test> |
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95 <test> |
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96 <conditional name="input_type_option"> |
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97 <param name="input_type" value="simple" /> |
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98 <param name="reads" value="takeabreak/toy_example_reads.fasta,takeabreak/toy_example_with_inv_reads.fasta" /> |
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99 </conditional> |
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100 <output name="inversion" file="takeabreak/inversion.fasta"/> |
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101 </test> |
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102 </tests> |
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103 <help><![CDATA[ |
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104 |
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105 **Description** |
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106 |
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107 TakeABreak is a tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes. Its implementation has a very limited memory impact allowing its usage on common desktop computers and acceptable runtime (Illumina reads simulated at 2x40x coverage from human chromosome 22 can be treated in less than two hours, with less than 1GB of memory). |
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108 |
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109 ------- |
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110 |
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111 **Web site** |
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112 |
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113 http://colibread.inria.fr/takeabreak/ |
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114 |
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115 |
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116 ]]></help> |
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117 <expand macro="citations"> |
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118 <citation type="doi">10.1007/978-3-319-07953-0_10</citation> |
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119 </expand> |
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120 |
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121 </tool> |