Mercurial > repos > iuc > unicycler
annotate unicycler.xml @ 4:2db911a4efc5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
| author | iuc |
|---|---|
| date | Thu, 06 Sep 2018 10:59:26 -0400 |
| parents | c4eac0c7e542 |
| children | 23300b42ca18 |
| rev | line source |
|---|---|
|
3
c4eac0c7e542
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 10ded2007c3502079b28afcef4718c430755e9b8
iuc
parents:
2
diff
changeset
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1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.0"> |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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2 <macros> |
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4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
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3 <token name="@VERSION@">0.4.6</token> |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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4 </macros> |
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0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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5 <requirements> |
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4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
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6 <requirement type="package" version="@VERSION@">unicycler</requirement> |
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0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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7 </requirements> |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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8 <command detect_errors="exit_code"><![CDATA[ |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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9 ## Preparing files |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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10 #if str( $paired_unpaired.fastq_input_selector ) == "paired" |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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11 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger') |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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12 #set fq1 = "fq1.fastq" |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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13 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz') |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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14 #set fq1 = "fq1.fastq.gz" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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15 #end if |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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16 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger') |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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17 #set fq2 = "fq2.fastq" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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18 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz') |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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19 #set fq2 = "fq2.fastq.gz" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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20 #end if |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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21 ln -s '${paired_unpaired.fastq_input1}' $fq1 && |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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22 ln -s '${paired_unpaired.fastq_input2}' $fq2 && |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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23 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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24 #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger') |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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25 #set fq1 = "fq1.fastq" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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26 #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz') |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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27 #set fq1 = "fq1.fastq.gz" |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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28 #end if |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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29 #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger') |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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30 #set fq2 = "fq2.fastq" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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31 #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz') |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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32 #set fq2 = "fq2.fastq.gz" |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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33 #end if |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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34 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 && |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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35 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 && |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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36 #elif str( $paired_unpaired.fastq_input_selector ) == "single" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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37 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger') |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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38 #set fq = "fq.fastq" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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39 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz') |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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40 #set fq = "fq.fastq.gz" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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41 #end if |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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42 ln -s '${paired_unpaired.fastq_input1}' '$fq' && |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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43 #end if |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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44 #if $long |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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45 #if $long.is_of_type('fastqsanger') |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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46 #set lr = "lr.fastq" |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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47 #elif $long.is_of_type('fastqsanger.gz') |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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48 #set lr = "lr.fastq.gz" |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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49 #elif $long.is_of_type('fasta') |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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50 #set lr = "lr.fasta" |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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51 #end if |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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52 ln -s '${long}' '$lr' && |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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53 #end if |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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54 ## Get location for pilon installation |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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55 pilon=`pilon --jar_dir` && |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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56 ## Running Unicycler |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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57 unicycler -t "\${GALAXY_SLOTS:-4}" |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
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changeset
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58 -o ./ |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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59 --verbosity 3 |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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60 --pilon_path \$pilon |
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4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
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61 #if str( $paired_unpaired.fastq_input_selector ) == "paired" |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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62 -1 '$fq1' |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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63 -2 '$fq2' |
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4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
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64 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" |
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2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
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65 -1 '$fq1' |
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2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
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66 -2 '$fq2' |
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2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
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67 #elif str( $paired_unpaired.fastq_input_selector ) == "single" |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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68 -s '$fq' |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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69 #end if |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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70 #if $long |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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71 -l $lr |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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72 #end if |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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73 ## General Unicycler Options section |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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74 ## ---------------------------------------------------------- |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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75 --mode '$mode' |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
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76 --min_fasta_length '$min_fasta_length' |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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77 --linear_seqs '$linear_seqs' |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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78 #if str($min_anchor_seg_len) != '' |
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2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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79 --min_anchor_seg_len '$min_anchor_seg_len' |
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2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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80 #end if |
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2
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81 ## Spades Options section |
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82 ## ---------------------------------------------------------- |
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83 $spades.no_correct |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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84 --min_kmer_frac '$spades.min_kmer_frac' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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85 --max_kmer_frac '$spades.max_kmer_frac' |
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4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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86 #if str($spades.kmers) != '' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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87 --kmers '$spades.kmers' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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88 #end if |
|
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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89 --kmer_count '$spades.kmer_count' |
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e92675014ac9
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90 --depth_filter '$spades.depth_filter' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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91 ## Rotation Options section |
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92 ## ---------------------------------------------------------- |
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93 $rotation.no_rotate |
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94 #if $rotation.start_genes |
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95 --start_genes '$rotation.start_genes' |
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96 #end if |
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97 --start_gene_id '$rotation.start_gene_id' |
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98 --start_gene_cov '$rotation.start_gene_cov' |
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99 ## Pilon Options section |
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100 ## ---------------------------------------------------------- |
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101 $pilon.no_pilon |
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102 #if str($pilon.min_polish_size) != '' |
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103 --min_polish_size '$pilon.min_polish_size' |
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104 #end if |
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105 ## Graph cleaning Options sdection |
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106 ## ---------------------------------------------------------- |
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107 --min_component_size '$graph_clean.min_component_size' |
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108 --min_dead_end_size '$graph_clean.min_dead_end_size' |
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109 ## Long Read Alignment Options |
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110 ## ---------------------------------------------------------- |
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111 #if $lr_align.contamination |
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112 --contamination '$lr_align.contamination' |
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113 #end if |
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114 --scores '${lr_align.scores}' |
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115 #if str($lr_align.low_score) != '' |
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116 --low_score '$lr_align.low_score' |
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117 #end if |
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0
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118 ]]></command> |
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119 <inputs> |
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120 <conditional name="paired_unpaired"> |
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121 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data"> |
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122 <option selected="True" value="paired">Paired</option> |
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123 <option value="paired_collection">Paired Collection</option> |
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124 <option value="single">Single</option> |
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125 <option value="none">None</option> |
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0
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126 </param> |
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127 <when value="paired"> |
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128 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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129 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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130 </when> |
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131 <when value="paired_collection"> |
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132 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" /> |
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133 </when> |
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134 <when value="single"> |
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135 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/> |
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136 </when> |
|
4
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137 <when value="none"> |
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138 </when> |
|
0
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139 </conditional> |
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2
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140 <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/> |
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141 <param argument="--mode" type="select" label="Select Bridging mode"> |
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142 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option> |
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143 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option> |
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144 <option value="bold">Bold (longest contigs, higher misassembly rate)</option> |
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145 </param> |
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146 <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/> |
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147 <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/> |
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4
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148 <param argument="--min_anchor_seg_len" type="integer" min="0" optional="true" label="Unicycler will not use segments shorter than this as scaffolding anchors"/> |
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0
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149 <section name="spades" expanded="False" title="SPAdes options" help="Unicycler uses SPAdes to construct assembly graphs. You can modify some of the SPAdes settings here. Use this ONLY if you know what you are doing!"> |
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2
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150 <param argument="--no_correct" type="boolean" checked="false" truevalue="--no_correct" falsevalue="" label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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151 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2" label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/> |
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152 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95" label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/> |
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153 <param argument="--kmers" type="text" value="" optional="true" label="Exact k-mers to use for SPAdes assembly, comma-separated"> |
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154 <validator type="regex" message="Kmers must be comma-separated odd integers (no repitition) without space in the range of 11 to 127 (inclusive)">^(\d*[13579],)*(\d*[13579])$</validator> |
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155 </param> |
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156 <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/> |
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157 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25" label="Filter out contigs lower than this fraction of the chromosomal depth" help="It is done if does not result in graph dead ends"/> |
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158 </section> |
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159 <section name="rotation" expanded="false" title="Rotation options" help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!"> |
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160 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue="" label="Do not rotate completed replicons to start at a standard gene." help="Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence."/> |
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161 <param argument="--start_genes" optional="true" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" /> |
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162 <param argument="--start_gene_id" type="float" min="0" max="100" value="90" label="The minimum required BLAST percent identity for a start gene search"/> |
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163 <param argument="--start_gene_cov" type="float" min="0" max="100" value="95" label="The minimum required BLAST percent coverage for a start gene search"/> |
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164 </section> |
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165 <section name="pilon" title="Pilon options" expanded="false"> |
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166 <param argument="--no_pilon" type="boolean" checked="false" truevalue="--no_pilon" falsevalue="" label="Do not use Pilon to polish the final assembly." help="Unicycler uses Pilon tool for polishing final assembly."/> |
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167 <param argument="--min_polish_size" type="integer" min="0" value="1000" label="Contigs shorter than this value (bp) will not be polished using Pilon"/> |
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168 </section> |
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169 <section name="graph_clean" expanded="false" title="Graph cleaning options" help="These options control the removal of small leftover sequences after bridging is complete."> |
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170 <param argument="--min_component_size" type="integer" min="0" value="1000" label="Unbridged graph components smaller than this size will be removed from the final graph" /> |
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171 <param argument="--min_dead_end_size" type="integer" min="0" value="1000" label="Graph dead ends smaller than this size will be removed from the final graph"/> |
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172 </section> |
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173 <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph."> |
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174 <param argument="--contamination" optional="true" type="data" format="fasta" label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." /> |
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175 <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/> |
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176 <param argument="--low_score" optional="true" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/> |
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177 </section> |
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178 </inputs> |
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179 <outputs> |
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180 <data name="assembly_graph" format="txt" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> |
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181 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> |
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182 </outputs> |
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183 <tests> |
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184 <test> |
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185 <conditional name="paired_unpaired"> |
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186 <param name="fastq_input_selector" value="paired" /> |
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187 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
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188 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
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189 </conditional> |
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190 <param name="mode" value="normal" /> |
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191 <param name="min_fasta_length" value="100"/> |
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192 <param name="linear_seqs" value="0"/> |
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193 <section name="spades"> |
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194 <param name="no_correct" value="true"/> |
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195 <param name="min_kmer_frac" value="0.2"/> |
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196 <param name="max_kmer_frac" value="0.95"/> |
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197 <param name="kmer_count" value="10"/> |
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198 <param name="depth_filter" value="0.25"/> |
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199 </section> |
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200 <section name="rotation"> |
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201 <param name="no_rotate" value=""/> |
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202 <param name="start_gene_id" value="90"/> |
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203 <param name="start_gene_cov" value="95"/> |
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204 </section> |
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205 <section name="pilon"> |
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206 <param name="no_pilon" value=""/> |
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207 <param name="min_polish_size" value="1000"/> |
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208 </section> |
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209 <section name="graph_clean"> |
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210 <param name="min_component_size" value="1000"/> |
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211 <param name="min_dead_end_size" value="1000"/> |
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212 </section> |
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213 <section name="lr_align"> |
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214 <param name="scores" value="3,-6,-5,-2"/> |
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215 </section> |
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216 <output name="assembly_graph" ftype="txt"> |
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217 <assert_contents> |
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218 <has_text text="TACGGGGAAGGACGTC"/> |
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219 </assert_contents> |
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220 </output> |
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221 <output name="assembly" ftype="fasta"> |
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222 <assert_contents> |
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223 <has_text text="length=5386" /> |
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224 </assert_contents> |
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225 </output> |
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226 </test> |
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227 <!-- |
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228 Following test corresponds to the command: |
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229 |
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230 unicycler -t "${GALAXY_SLOTS:-8}" -o ./ - -verbose 3 - -pilon_path `pilon - -jar_dir` \ |
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231 -1 test-data/phix_f.fq.gz -2 test-data/phix_r.fq.gz -l test-data/onp.fa \ |
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232 - -mode 'normal' - -no_correct |
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233 |
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234 This command causes a segfault with the current version of unicycler on bioconda for Linux |
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235 during the minimap step (which seems to be compiled C code). A gist of the log can be found |
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236 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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237 --> |
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238 <test> |
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2
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239 <conditional name="paired_unpaired"> |
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240 <param name="fastq_input_selector" value="paired" /> |
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241 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger.gz" /> |
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242 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger.gz" /> |
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243 </conditional> |
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244 <param name="long" value="onp.fa" ftype="fasta" /> |
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0
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245 <param name="mode" value="normal" /> |
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2
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246 <param name="min_fasta_length" value="100"/> |
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247 <param name="linear_seqs" value="0"/> |
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248 <section name="spades"> |
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249 <param name="no_correct" value="true"/> |
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250 <param name="min_kmer_frac" value="0.2"/> |
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251 <param name="max_kmer_frac" value="0.95"/> |
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252 <param name="kmer_count" value="10"/> |
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253 <param name="depth_filter" value="0.25"/> |
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254 </section> |
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255 <section name="rotation"> |
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256 <param name="no_rotate" value=""/> |
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257 <param name="start_gene_id" value="90"/> |
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258 <param name="start_gene_cov" value="95"/> |
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259 </section> |
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260 <section name="pilon"> |
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261 <param name="no_pilon" value=""/> |
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262 <param name="min_polish_size" value="1000"/> |
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263 </section> |
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264 <section name="graph_clean"> |
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265 <param name="min_component_size" value="1000"/> |
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266 <param name="min_dead_end_size" value="1000"/> |
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267 </section> |
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268 <section name="lr_align"> |
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269 <param name="scores" value="3,-6,-5,-2"/> |
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270 </section> |
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271 <output name="assembly_graph" ftype="txt"> |
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272 <assert_contents> |
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273 <has_text text="TACGGGGAAGGACGTC" /> |
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274 </assert_contents> |
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275 </output> |
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276 <output name="assembly" ftype="fasta"> |
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277 <assert_contents> |
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278 <has_text text="length=5386" /> |
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279 </assert_contents> |
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280 </output> |
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281 </test> |
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282 <test> |
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283 <conditional name="paired_unpaired"> |
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284 <param name="fastq_input_selector" value="paired_collection"/> |
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285 <param name="fastq_input1"> |
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286 <collection type="paired"> |
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287 <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" /> |
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288 <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" /> |
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289 </collection> |
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290 </param> |
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291 </conditional> |
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292 <param name="mode" value="normal" /> |
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293 <param name="min_fasta_length" value="100"/> |
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294 <param name="linear_seqs" value="0"/> |
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295 <section name="spades"> |
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296 <param name="no_correct" value="true"/> |
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297 <param name="min_kmer_frac" value="0.2"/> |
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298 <param name="max_kmer_frac" value="0.95"/> |
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299 <param name="kmer_count" value="10"/> |
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300 <param name="depth_filter" value="0.25"/> |
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301 </section> |
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302 <section name="rotation"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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303 <param name="no_rotate" value=""/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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304 <param name="start_gene_id" value="90"/> |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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305 <param name="start_gene_cov" value="95"/> |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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306 </section> |
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307 <section name="pilon"> |
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308 <param name="no_pilon" value="true"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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309 <param name="min_polish_size" value="1000"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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310 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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311 <section name="graph_clean"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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312 <param name="min_component_size" value="1000"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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313 <param name="min_dead_end_size" value="1000"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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314 </section> |
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315 <section name="lr_align"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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316 <param name="scores" value="3,-6,-5,-2"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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317 </section> |
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318 <output name="assembly_graph" ftype="txt"> |
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319 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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320 <has_text text="TACGGGGAAGGACGTC" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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321 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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322 </output> |
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323 <output name="assembly" ftype="fasta"> |
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0
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324 <assert_contents> |
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325 <has_text text="length=5386" /> |
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326 </assert_contents> |
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327 </output> |
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328 </test> |
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4
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329 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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330 <conditional name="paired_unpaired"> |
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331 <param name="fastq_input_selector" value="none"/> |
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2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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332 </conditional> |
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333 <param name="min_anchor_seg_len" value="10"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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334 <section name="spades"> |
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335 <param name="kmers" value="21,23"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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336 </section> |
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337 <param name="long" value="only_long.fasta" ftype="fasta" /> |
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338 <output name="assembly_graph" ftype="txt"> |
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339 <assert_contents> |
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340 <has_text text="S" /> |
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341 </assert_contents> |
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342 </output> |
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343 <output name="assembly" ftype="fasta"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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344 <assert_contents> |
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345 <has_text text=">1" /> |
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346 </assert_contents> |
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347 </output> |
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348 </test> |
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0
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349 </tests> |
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350 <help><![CDATA[ |
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351 |
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352 **Unicycler** |
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353 |
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354 Unicycler is a hybrid assembly pipeline for bacterial genomes. It uses both Illumina reads and long reads (PacBio or Nanopore) to produce complete and accurate assemblies. It is written by `Ryan Wick`_ at the University of Melbourne's Centre for Systems Genomics. Much of the description below is lifted from Unicycler's `github page`_. |
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355 |
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356 .. _`Ryan Wick`: https://github.com/rrwick |
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357 .. _`github page`: https://github.com/rrwick/Unicycler |
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358 |
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359 ----- |
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360 |
|
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361 **Input data** |
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362 |
|
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363 Unicycler accepts inputs short (Illumina) reads in FASTQ format. Galaxy places additional requirement of having these in FASTQ format with `Sanger encoding`_ of quality scores. Long reads (from Oxford Nanopore or PacBio) can be either in FASTQ of FASTA form. |
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364 |
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365 .. _`Sanger encoding`: https://en.wikipedia.org/wiki/FASTQ_format#Quality |
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366 |
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367 The input options are:: |
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368 |
|
e9c1cdb9f9dc
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369 -1 SHORT1, --short1 SHORT1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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370 FASTQ file of short reads (first reads in each pair) |
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371 -2 SHORT2, --short2 SHORT2 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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372 FASTQ file of short reads (second reads in each pair) |
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373 -s SHORT_UNPAIRED, --short_unpaired SHORT_UNPAIRED |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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374 FASTQ file of unpaired short reads |
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375 -l LONG, --long LONG |
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376 FASTQ or FASTA file of long reads, if all reads are available at start. |
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377 |
|
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378 ----- |
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379 |
|
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380 **Bridging mode** |
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381 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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382 Unicycler can be run in three modes: conservative, normal (the default) and bold, set with the --mode option. Conservative mode is least likely to produce a complete assembly but has a very low risk of misassembly. Bold mode is most likely to produce a complete assembly but carries greater risk of misassembly. Normal mode is intermediate regarding both completeness and misassembly risk. See `description of modes`_ for more information. |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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383 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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384 .. _`description of modes`: https://github.com/rrwick/Unicycler#conservative-normal-and-bold |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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385 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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386 The available modes are:: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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387 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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388 --mode {conservative,normal,bold} |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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389 Bridging mode (default: normal) |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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390 conservative = smaller contigs, lowest misassembly rate |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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391 normal = moderate contig size and misassembly rate |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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392 bold = longest contigs, higher misassembly rate |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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393 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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394 ---- |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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395 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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396 **Skip SPAdes error correction step** |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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397 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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398 Sequencing data contains a substantial number of sequencing errors that manifest themselves as deviations (bulges and non-connected components) within the assembly graph. One of the ways to improve the graph even constructing it is to minimize the amount sequencing errors by performing error correction. SPAdes, which is used by Unicycler for error correction and assembly, uses `BayesHammer`_ to correct the reads. Here is a brief summary of what it does: |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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399 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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400 1. SPAdes (or rather BayesHammer) counts *k*-mers in reads and computed *k*-mer statistics that takes into account base quality values. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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401 2. `Hamming graph`_ is constructed for *k*-mers is which *k*-mers are nodes. In this graph edges connect nodes (*k*-mers) is they differ from each other by a number of nucleotides up to a certain threshold (the `Hamming distance`_). The graph is central to the error correction algorithm. |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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402 3. At this step Bayesian subclustering of the graph produced in the previous step. For each *k*-mer we now know the center of its subcluster. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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403 4. Solid *k*-mers are derived from cluster centers and are assumed to be *error free*. |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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404 5. Solid *k*-mers are mapped back to the reads and used to correct them. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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405 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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406 This step takes considerable time, so if one need to quickly evaluate assemblies this step can be skipped. However, this is not recommended if one if trying to produce a final high quality assembly. |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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407 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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408 .. _`BayesHammer`: https://goo.gl/1iGkMe |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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409 .. _`Hamming graph`: https://en.wikipedia.org/wiki/Hamming_graph |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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410 .. _`Hamming distance`: https://en.wikipedia.org/wiki/Hamming_distance |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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411 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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412 This following option turns error correction on and off:: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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413 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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414 --no_correct |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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415 Skip SPAdes error correction step |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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416 (default: conduct SPAdes error correction) |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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417 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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418 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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419 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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changeset
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420 **Do not rotate completed replicons to start at a standard gene** |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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421 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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422 Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence. |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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423 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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424 The following option turns rotation on and off:: |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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425 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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426 --no_rotate |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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427 Do not rotate completed replicons |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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428 to start at a standard gene |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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changeset
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429 (default: completed replicons are rotated) |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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430 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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431 **Do not use Pilon to polish the final assembly** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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432 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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433 `Pilon`_ is a tool for improving overall quality of draft assemblies and finding variation among strains. Unicycler uses it for assembly *polishing*. |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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434 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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435 The following option turns pilon part of Unicycler pipeline on and off:: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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436 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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437 --no_pilon |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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438 Do not use Pilon to polish the |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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439 final assembly (default: Pilon is used) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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440 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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441 .. _`Pilon`: https://github.com/broadinstitute/pilon/wiki |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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442 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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443 ------ |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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444 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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445 **Expected number of linear sequences** |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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446 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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447 If you expect your sample to contain linear (non circular) sequences, set this option:: |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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448 |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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449 --linear_seqs EXPECTED_LINEAR_SEQS |
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0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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450 The expected number of linear (i.e. non-circular) |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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451 sequences in the underlying sequence |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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452 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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453 ---- |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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454 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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455 **SPAdes options** |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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456 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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changeset
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457 This section provides control of SPAdes options:: |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
458 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
459 --min_kmer_frac MIN_KMER_FRAC |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
460 Lowest k-mer size for SPAdes assembly, |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
461 expressed as a fraction of the read length |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
462 (default: 0.2) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
463 --max_kmer_frac MAX_KMER_FRAC |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
464 Highest k-mer size for SPAdes assembly, |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
465 expressed as a fraction of the read length |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
466 (default: 0.95) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
467 --kmer_count KMER_COUNT |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
468 Number of k-mer steps to use in |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
469 SPAdes assembly (default: 10) |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
470 --depth_filter DEPTH_FILTER |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
471 Filter out contigs lower than this fraction |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
472 of the chromosomal depth, if doing so does |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
473 not result in graph dead ends (default: 0.25) |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
474 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
475 ---- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
476 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
477 **Rotation options** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
478 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
479 Unicycler attempts to rotate circular assemblies to make sure that they begin at a consistent starting gene. The following parameters control assembly rotation:: |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
480 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
481 --start_genes START_GENES |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
482 FASTA file of genes for start point |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
483 of rotated replicons |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
484 (default: start_genes.fasta) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
485 --start_gene_id START_GENE_ID |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
486 The minimum required BLAST percent identity |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
487 for a start gene search |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
488 (default: 90.0) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
489 --start_gene_cov START_GENE_COV |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
490 The minimum required BLAST percent coverage |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
491 for a start gene search |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
492 (default: 95.0) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
493 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
494 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
495 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
496 **Graph cleaning options** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
497 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
498 These options control the removal of small leftover sequences after bridging is complete:: |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
499 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
500 --min_component_size MIN_COMPONENT_SIZE |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
501 Unbridged graph components smaller |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
502 than this size (bp) will be removed |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
503 from the final graph (default: 1000) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
504 --min_dead_end_size MIN_DEAD_END_SIZE |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
505 Graph dead ends smaller than this size (bp) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
506 will be removed from the final graph |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
507 (default: 1000) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
508 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
509 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
510 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
511 **Long read alignment options** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
512 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
513 These options control the alignment of long reads to the assembly graph:: |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
514 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
515 --contamination CONTAMINATION |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
516 FASTA file of known contamination in long reads |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
517 --scores SCORES |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
518 Comma-delimited string of alignment scores: |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
519 match, mismatch, gap open, gap extend |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
520 (default: 3,-6,-5,-2) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
521 --low_score LOW_SCORE |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
522 Score threshold - alignments below this |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
523 are considered poor |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
524 (default: set threshold automatically) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
525 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
526 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
527 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
528 **Outputs** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
529 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
530 Galaxy's wrapped for Unicycler produces two outputs: |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
531 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
532 * final assembly in FASTA format |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
533 * final assembly grapth in graph format |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
534 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
535 While most will likely be interested in the FASTA dataset, the graph dataset is also quite useful and can be visualized using tools such as `Bandage`_. |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
536 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
537 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
538 .. _`Bandage`: https://github.com/rrwick/Bandage |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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539 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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540 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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541 ]]></help> |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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542 <citations> |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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543 <citation type="doi">10.1101/096412</citation> |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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544 </citations> |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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545 </tool> |