Mercurial > repos > iuc > medaka_consensus_pipeline
annotate medaka_consensus.xml @ 13:72b5e9dda577 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
author | iuc |
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date | Thu, 18 Nov 2021 20:01:28 +0000 |
parents | 8dfe8a52346f |
children | cb34f00cc10f |
rev | line source |
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13
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
parents:
11
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1 <tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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2 <description>Assembly polishing via neural networks</description> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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3 <macros> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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4 <import>macros.xml</import> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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5 </macros> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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6 <expand macro="requirements"/> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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7 <expand macro="version_command"/> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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8 <command detect_errors="exit_code"><![CDATA[ |
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8dfe8a52346f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
iuc
parents:
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9 ln -s '$d' 'input_assembly.fa' && |
1
551f8c9bc4cf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
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10 medaka_consensus |
551f8c9bc4cf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
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11 ## optional |
551f8c9bc4cf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
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12 -m ${m} |
551f8c9bc4cf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents:
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13 -b $b |
551f8c9bc4cf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents:
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14 -o results |
551f8c9bc4cf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents:
0
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15 -t \${GALAXY_SLOTS:-4} |
551f8c9bc4cf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents:
0
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16 ## required |
551f8c9bc4cf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents:
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17 -i '$i' |
11
8dfe8a52346f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 69eb0054f76057436094943f262a74c982d8de42"
iuc
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18 -d 'input_assembly.fa' |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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19 |
3
35666d44fe7a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
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20 2>&1 | tee '$out_log' |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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21 ]]></command> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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22 <inputs> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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23 <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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24 <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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25 <expand macro="model"/> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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26 <expand macro="b"/> |
10
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
parents:
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27 <param argument="-g" type="boolean" truevalue="-g" falsevalue="" label="Don't fill gaps in consensus with draft sequence?" checked="false" /> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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28 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="'Draft To Consensus', 'Variants' and 'Polished regions in draft coordinates' are generated using the parameter -v."> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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29 <option value="consensus" selected="true">Consensus</option> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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30 <option value="probs" selected="true">Consensus probabilities</option> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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31 <option value="calls" selected="true">Calls to draft</option> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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32 <option value="log">Log</option> |
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1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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33 <option value="gaps">Gap regions in draft</option> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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34 </param> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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35 </inputs> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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36 <outputs> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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37 <!-- standard --> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
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38 <data name="out_consensus" format="fasta" from_work_dir="results/consensus.fasta" label="${tool.name} on ${on_string}: Consensus"> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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39 <filter>'consensus' in out</filter> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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40 </data> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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41 <data name="out_probs" format="h5" from_work_dir="results/consensus_probs.hdf" label="${tool.name} on ${on_string}: Consensus probabilities"> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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42 <filter>'probs' in out</filter> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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43 </data> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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44 <data name="out_calls" format="bam" from_work_dir="results/calls_to_draft.bam" label="${tool.name} on ${on_string}: Calls to draft"> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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45 <filter>'calls' in out</filter> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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46 </data> |
10
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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47 <data name="out_gaps" format="bed" from_work_dir="results/consensus.fasta.gaps_in_draft_coords.bed" label="${tool.name} on ${on_string}: Gaps in draft"> |
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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48 <filter>'gaps' in out</filter> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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49 </data> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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50 <!-- optional --> |
1
551f8c9bc4cf
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
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51 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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52 <filter>'log' in out</filter> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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53 </data> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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54 </outputs> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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55 <tests> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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56 <!-- #1 default --> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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57 <test expect_num_outputs="3"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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58 <param name="i" value="basecalls.fastq.gz"/> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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59 <param name="d" value="assembly.fasta"/> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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60 <output name="out_consensus"> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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61 <assert_contents> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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62 <has_n_lines n="2"/> |
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63 <has_line line=">4"/> |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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64 <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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65 </assert_contents> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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66 </output> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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67 <output name="out_probs"> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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68 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
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69 <has_size value="165503" delta="100"/> |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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70 </assert_contents> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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71 </output> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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72 <output name="out_calls"> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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73 <assert_contents> |
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72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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74 <has_size value="343341" delta="100"/> |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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75 </assert_contents> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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76 </output> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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77 </test> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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78 <!-- #2 --> |
10
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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79 <test expect_num_outputs="5"> |
13
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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80 <param name="i" value="basecalls.fastq.gz"/> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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81 <param name="d" value="assembly.fasta"/> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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82 <param name="m" value="r941_min_fast_g303"/> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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83 <param name="b" value="99"/> |
10
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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84 <param name="out" value="consensus,probs,calls,log,gaps"/> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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85 <output name="out_consensus"> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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86 <assert_contents> |
10
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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87 <has_n_lines n="2"/> |
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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88 <has_line line=">4"/> <!-- Replace test --> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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89 </assert_contents> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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90 </output> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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91 <output name="out_probs"> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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92 <assert_contents> |
3
35666d44fe7a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
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93 <has_size value="166251" delta="100"/> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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94 </assert_contents> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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95 </output> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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96 <output name="out_calls"> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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97 <assert_contents> |
13
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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98 <has_size value="343340" delta="100"/> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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99 </assert_contents> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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100 </output> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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101 <output name="out_log"> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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102 <assert_contents> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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103 <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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104 </assert_contents> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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105 </output> |
10
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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106 <output name="out_gaps"> |
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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107 <assert_contents> |
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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108 <has_size value="0" delta="0"/> |
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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109 </assert_contents> |
1ca4ce7241fd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
iuc
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110 </output> |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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111 </test> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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112 </tests> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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113 <help><![CDATA[ |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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114 .. class:: infomark |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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115 |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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116 **What it does** |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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117 |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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118 @WID@ |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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119 |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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120 The *medaka_consensus* pipeline performs assembly polishing via neural networks. |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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121 |
13
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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122 ---- |
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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123 |
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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124 .. class:: infomark |
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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125 |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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126 **Input** |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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127 |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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|
128 An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required. See `Creating a Draft Assembly <https://nanoporetech.github.io/medaka/walkthrough.html#basecalling-and-draft-assembly>`_ for a detailed example of one method of obtaining these. |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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129 |
13
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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130 ---- |
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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131 |
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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132 .. class:: infomark |
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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133 |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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134 **Output** |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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135 |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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136 - Consensus polished assembly (FASTA) |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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137 - Consensus Probabilities (H5/HDF) |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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138 - Calls To Draft (BAM) |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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139 - Draft To Consensus (chain, TXT) |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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140 - Variants: VCF of changes (VCF) |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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141 - Polished: BED file of polished regions (BED) |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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142 |
13
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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143 @MODELS@ |
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
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144 |
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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|
145 ---- |
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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146 |
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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147 .. class:: infomark |
72b5e9dda577
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 52289bc7b99bfa8a3bda46cb35cea98399419dab"
iuc
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148 |
0
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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149 **References** |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
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150 |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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|
151 @REFERENCES@ |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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152 ]]></help> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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153 <expand macro="citations"/> |
ef94bace3a3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
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154 </tool> |