Mercurial > repos > iuc > unicycler
annotate unicycler.xml @ 9:def4cbdf745d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
| author | iuc |
|---|---|
| date | Sat, 24 Sep 2022 21:13:30 +0000 |
| parents | f9973e8f6f22 |
| children | 906f76188535 |
| rev | line source |
|---|---|
|
9
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> |
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2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
2 <macros> |
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9
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
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3 <token name="@TOOL_VERSION@">0.5.0</token> |
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def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
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4 <token name="@VERSION_SUFFIX@">0</token> |
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2
6710edf12bac
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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5 </macros> |
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9
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
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6 <xrefs> |
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def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
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7 <xref type="bio.tools">unicycler</xref> |
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def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
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8 </xrefs> |
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7
e3f1860582ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
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9 <edam_topics> |
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e3f1860582ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
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10 <edam_topic>topic_0196</edam_topic> |
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e3f1860582ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
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11 </edam_topics> |
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e3f1860582ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
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12 <edam_operations> |
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e3f1860582ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
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13 <edam_operation>operation_0525</edam_operation> |
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e3f1860582ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
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14 </edam_operations> |
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0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
15 <requirements> |
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9
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
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16 <requirement type="package" version="@TOOL_VERSION@">unicycler</requirement> |
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def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
17 <requirement type="package" version="1.15.1">samtools</requirement> |
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0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
18 </requirements> |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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19 <command detect_errors="exit_code"><![CDATA[ |
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2
6710edf12bac
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 ## Preparing files |
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6710edf12bac
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 #if str( $paired_unpaired.fastq_input_selector ) == "paired" |
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6710edf12bac
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 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger') |
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6710edf12bac
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 #set fq1 = "fq1.fastq" |
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6710edf12bac
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 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz') |
|
6710edf12bac
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.gz" |
|
6710edf12bac
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 #end if |
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6710edf12bac
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 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger') |
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6710edf12bac
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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28 #set fq2 = "fq2.fastq" |
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6710edf12bac
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 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz') |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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30 #set fq2 = "fq2.fastq.gz" |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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31 #end if |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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32 ln -s '${paired_unpaired.fastq_input1}' $fq1 && |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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33 ln -s '${paired_unpaired.fastq_input2}' $fq2 && |
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6710edf12bac
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 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" |
|
6710edf12bac
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 #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger') |
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6710edf12bac
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 #set fq1 = "fq1.fastq" |
|
6710edf12bac
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 #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz') |
|
6710edf12bac
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 fq1 = "fq1.fastq.gz" |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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39 #end if |
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2
6710edf12bac
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 #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger') |
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6710edf12bac
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 #set fq2 = "fq2.fastq" |
|
6710edf12bac
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 #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz') |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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43 #set fq2 = "fq2.fastq.gz" |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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44 #end if |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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45 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 && |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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46 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 && |
|
6710edf12bac
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 str( $paired_unpaired.fastq_input_selector ) == "single" |
|
6710edf12bac
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 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger') |
|
6710edf12bac
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 #set fq = "fq.fastq" |
|
6710edf12bac
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 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz') |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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51 #set fq = "fq.fastq.gz" |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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52 #end if |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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53 ln -s '${paired_unpaired.fastq_input1}' '$fq' && |
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6710edf12bac
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 #end if |
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6710edf12bac
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 #if $long |
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6710edf12bac
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 #if $long.is_of_type('fastqsanger') |
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6710edf12bac
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 #set lr = "lr.fastq" |
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6710edf12bac
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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58 #elif $long.is_of_type('fastqsanger.gz') |
|
6710edf12bac
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 #set lr = "lr.fastq.gz" |
|
6710edf12bac
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 #elif $long.is_of_type('fasta') |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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61 #set lr = "lr.fasta" |
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0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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62 #end if |
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2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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63 ln -s '${long}' '$lr' && |
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6710edf12bac
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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64 #end if |
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6710edf12bac
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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65 ## Running Unicycler |
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6710edf12bac
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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66 unicycler -t "\${GALAXY_SLOTS:-4}" |
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6710edf12bac
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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67 -o ./ |
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6710edf12bac
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 --verbosity 3 |
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4
608d1d0ba3a8
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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69 #if str( $paired_unpaired.fastq_input_selector ) == "paired" |
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2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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70 -1 '$fq1' |
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6710edf12bac
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 -2 '$fq2' |
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4
608d1d0ba3a8
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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72 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" |
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608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
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73 -1 '$fq1' |
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608d1d0ba3a8
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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74 -2 '$fq2' |
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608d1d0ba3a8
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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75 #elif str( $paired_unpaired.fastq_input_selector ) == "single" |
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2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
76 -s '$fq' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
77 #end if |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
78 #if $long |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
79 -l $lr |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
80 #end if |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
81 ## General Unicycler Options section |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
82 ## ---------------------------------------------------------- |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
83 --mode '$mode' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
84 --min_fasta_length '$min_fasta_length' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
85 --linear_seqs '$linear_seqs' |
|
4
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
86 #if str($min_anchor_seg_len) != '' |
|
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
87 --min_anchor_seg_len '$min_anchor_seg_len' |
|
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
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diff
changeset
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88 #end if |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
89 ## Spades Options section |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
90 ## ---------------------------------------------------------- |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
91 --min_kmer_frac '$spades.min_kmer_frac' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
92 --max_kmer_frac '$spades.max_kmer_frac' |
|
4
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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diff
changeset
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93 #if str($spades.kmers) != '' |
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608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
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diff
changeset
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94 --kmers '$spades.kmers' |
|
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
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diff
changeset
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95 #end if |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
96 --kmer_count '$spades.kmer_count' |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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97 --depth_filter '$spades.depth_filter' |
|
7
e3f1860582ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
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diff
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98 #if $spades.largest_component |
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e3f1860582ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
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99 --largest_component |
|
e3f1860582ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
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diff
changeset
|
100 #end if |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
101 ## Rotation Options section |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
changeset
|
102 ## ---------------------------------------------------------- |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
changeset
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103 $rotation.no_rotate |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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104 #if $rotation.start_genes |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
105 --start_genes '$rotation.start_genes' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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106 #end if |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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107 --start_gene_id '$rotation.start_gene_id' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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108 --start_gene_cov '$rotation.start_gene_cov' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
changeset
|
109 ## Graph cleaning Options sdection |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
110 ## ---------------------------------------------------------- |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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111 --min_component_size '$graph_clean.min_component_size' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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112 --min_dead_end_size '$graph_clean.min_dead_end_size' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
changeset
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113 ## Long Read Alignment Options |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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114 ## ---------------------------------------------------------- |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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changeset
|
115 #if $lr_align.contamination |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
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116 --contamination '$lr_align.contamination' |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
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117 #end if |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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118 --scores '${lr_align.scores}' |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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119 #if str($lr_align.low_score) != '' |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
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120 --low_score '$lr_align.low_score' |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
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121 #end if |
|
9
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
changeset
|
122 $lr_align.no_simple_bridges |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
changeset
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123 --keep $keep |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
changeset
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124 #if $keep != '0' |
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def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
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125 && mkdir 'spades_graphs' |
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def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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126 && mv 00*gfa './spades_graphs/' |
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def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
changeset
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127 #end if |
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def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
changeset
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128 #if $keep == '2' and $long |
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def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
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129 && samtools view -@ "\${GALAXY_SLOTS:-4}" -u 'read_alignment/long_read_alignments.sam' | samtools sort -@ "\${GALAXY_SLOTS:-4}" -o 'read_alignment/long_read_alignments.bam' |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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130 #end if |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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131 ]]></command> |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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132 <inputs> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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133 <conditional name="paired_unpaired"> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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134 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data"> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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135 <option selected="True" value="paired">Paired</option> |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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136 <option value="paired_collection">Paired Collection</option> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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137 <option value="single">Single</option> |
|
4
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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138 <option value="none">None</option> |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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|
139 </param> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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140 <when value="paired"> |
|
6
d1ac6363b63b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
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141 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz" |
|
d1ac6363b63b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
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142 label="Select first set of reads" help="Specify dataset with forward reads"/> |
|
d1ac6363b63b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
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143 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz" |
|
d1ac6363b63b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
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144 label="Select second set of reads" help="Specify dataset with reverse reads"/> |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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145 </when> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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146 <when value="paired_collection"> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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147 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" /> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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148 </when> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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149 <when value="single"> |
|
6
d1ac6363b63b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
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diff
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150 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" |
|
d1ac6363b63b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
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151 label="Select unpaired reads" help="Specify dataset with unpaired reads"/> |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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152 </when> |
|
4
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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153 <when value="none"> |
|
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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154 </when> |
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0
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155 </conditional> |
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156 <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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157 <param argument="--mode" type="select" label="Select Bridging mode"> |
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158 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option> |
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159 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option> |
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160 <option value="bold">Bold (longest contigs, higher misassembly rate)</option> |
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161 </param> |
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162 <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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163 <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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164 <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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165 <section name="spades" expanded="False" title="SPAdes options" |
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166 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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167 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2" |
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168 label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/> |
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169 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95" |
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170 label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/> |
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171 <param argument="--kmers" type="text" value="" optional="true" label="Exact k-mers to use for SPAdes assembly, comma-separated"> |
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172 <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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173 </param> |
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174 <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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175 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25" |
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176 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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177 <param argument="--largest_component" type="boolean" checked="false" |
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178 label="Only keep the largest connected component of the assembly graph"/> |
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179 </section> |
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180 <section name="rotation" expanded="false" title="Rotation options" |
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181 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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182 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue="" |
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183 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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184 <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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185 <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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186 <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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187 </section> |
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188 <section name="graph_clean" expanded="false" title="Graph cleaning options" |
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189 help="These options control the removal of small leftover sequences after bridging is complete."> |
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190 <param argument="--min_component_size" type="integer" min="0" value="1000" |
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191 label="Unbridged graph components smaller than this size will be removed from the final graph" /> |
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192 <param argument="--min_dead_end_size" type="integer" min="0" value="1000" |
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193 label="Graph dead ends smaller than this size will be removed from the final graph"/> |
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194 </section> |
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195 <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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196 <param argument="--contamination" optional="true" type="data" format="fasta" |
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197 label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." /> |
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198 <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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199 <param argument="--low_score" optional="true" type="integer" value="" |
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200 label="Score threshold - alignments below this are considered poor" help="default = set automatically"/> |
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201 <param argument="--no_simple_bridges" type="boolean" truevalue="--no_simple_bridges" falsevalue="" checked="false" label="Simple long-read bridging" help="Default: No" /> |
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202 </section> |
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203 <param argument="--keep" type="select" label="Outputs to keep" help="Level of file retention. Default: 1"> |
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204 <option value="0">0: only keep final files</option> |
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205 <option value="1" selected="true">1: save graphs at main checkpoints</option> |
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206 <option value="2">2: also keep SAM</option> |
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207 </param> |
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208 </inputs> |
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209 <outputs> |
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210 <data name="assembly_graph" format="gfa1" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> |
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211 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> |
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212 <collection name="spades_collection" type="list" label="${tool.name} on ${on_string}: SPAdes graphs"> |
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213 <discover_datasets pattern="__designation_and_ext__" format="gfa1" directory="spades_graphs"/> |
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214 <filter>keep != "0"</filter> |
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215 </collection> |
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216 <data name="bam_file" format="bam" from_work_dir="read_alignment/long_read_alignments.bam" label="${tool.name} on ${on_string}: Long read alignments BAM"> |
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217 <filter>keep == "2" and long</filter> |
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218 </data> |
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219 </outputs> |
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220 <tests> |
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221 <test expect_num_outputs="2"> |
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222 <conditional name="paired_unpaired"> |
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223 <param name="fastq_input_selector" value="paired" /> |
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224 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
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225 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
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226 </conditional> |
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227 <param name="mode" value="normal" /> |
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228 <param name="min_fasta_length" value="100"/> |
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229 <param name="linear_seqs" value="0"/> |
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230 <section name="spades"> |
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231 <param name="min_kmer_frac" value="0.2"/> |
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232 <param name="max_kmer_frac" value="0.95"/> |
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233 <param name="kmer_count" value="10"/> |
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234 <param name="depth_filter" value="0.25"/> |
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235 </section> |
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236 <section name="rotation"> |
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237 <param name="no_rotate" value=""/> |
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238 <param name="start_gene_id" value="90"/> |
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239 <param name="start_gene_cov" value="95"/> |
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240 </section> |
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241 <section name="graph_clean"> |
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242 <param name="min_component_size" value="1000"/> |
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243 <param name="min_dead_end_size" value="1000"/> |
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244 </section> |
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245 <section name="lr_align"> |
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246 <param name="scores" value="3,-6,-5,-2"/> |
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247 </section> |
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248 <param name="keep" value="0"/> |
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249 <output name="assembly_graph" ftype="gfa1"> |
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250 <assert_contents> |
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251 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
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252 </assert_contents> |
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253 </output> |
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254 <output name="assembly" ftype="fasta"> |
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255 <assert_contents> |
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256 <has_text text="length=5386" /> |
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257 </assert_contents> |
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258 </output> |
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259 </test> |
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260 <!-- |
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261 Following test corresponds to the command: |
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262 |
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263 unicycler -t "${GALAXY_SLOTS:-8}" -o ./ - -verbose 3 - -pilon_path `pilon - -jar_dir` \ |
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264 -1 test-data/phix_f.fq.gz -2 test-data/phix_r.fq.gz -l test-data/onp.fa \ |
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265 - -mode 'normal' - -no_correct |
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266 |
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267 This command causes a segfault with the current version of unicycler on bioconda for Linux |
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268 during the minimap step (which seems to be compiled C code). A gist of the log can be found |
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269 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb. |
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270 --> |
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271 <test expect_num_outputs="2"> |
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272 <conditional name="paired_unpaired"> |
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273 <param name="fastq_input_selector" value="paired" /> |
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274 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger.gz" /> |
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275 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger.gz" /> |
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276 </conditional> |
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277 <param name="long" value="onp.fa" ftype="fasta" /> |
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278 <param name="mode" value="normal" /> |
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279 <param name="min_fasta_length" value="100"/> |
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280 <param name="linear_seqs" value="0"/> |
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281 <section name="spades"> |
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282 <param name="min_kmer_frac" value="0.2"/> |
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283 <param name="max_kmer_frac" value="0.95"/> |
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284 <param name="kmer_count" value="10"/> |
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285 <param name="depth_filter" value="0.25"/> |
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286 </section> |
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287 <section name="rotation"> |
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288 <param name="no_rotate" value=""/> |
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289 <param name="start_gene_id" value="90"/> |
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290 <param name="start_gene_cov" value="95"/> |
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291 </section> |
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292 <section name="graph_clean"> |
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293 <param name="min_component_size" value="1000"/> |
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294 <param name="min_dead_end_size" value="1000"/> |
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295 </section> |
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296 <section name="lr_align"> |
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297 <param name="scores" value="3,-6,-5,-2"/> |
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298 </section> |
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299 <param name="keep" value="0"/> |
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300 <output name="assembly_graph" ftype="gfa1"> |
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301 <assert_contents> |
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302 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
303 </assert_contents> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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changeset
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304 </output> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
305 <output name="assembly" ftype="fasta"> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
306 <assert_contents> |
|
6710edf12bac
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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307 <has_text text="length=5386" /> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
308 </assert_contents> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
309 </output> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
310 </test> |
|
9
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
311 <test expect_num_outputs="2"> |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
312 <conditional name="paired_unpaired"> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
313 <param name="fastq_input_selector" value="paired_collection"/> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
314 <param name="fastq_input1"> |
|
6710edf12bac
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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315 <collection type="paired"> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
316 <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
317 <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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318 </collection> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
319 </param> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
320 </conditional> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
321 <param name="mode" value="normal" /> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
322 <param name="min_fasta_length" value="100"/> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
323 <param name="linear_seqs" value="0"/> |
|
6710edf12bac
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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324 <section name="spades"> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
325 <param name="min_kmer_frac" value="0.2"/> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
326 <param name="max_kmer_frac" value="0.95"/> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
327 <param name="kmer_count" value="10"/> |
|
6710edf12bac
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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328 <param name="depth_filter" value="0.25"/> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
329 </section> |
|
6710edf12bac
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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330 <section name="rotation"> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
331 <param name="no_rotate" value=""/> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
332 <param name="start_gene_id" value="90"/> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
333 <param name="start_gene_cov" value="95"/> |
|
6710edf12bac
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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334 </section> |
|
6710edf12bac
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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335 <section name="graph_clean"> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
336 <param name="min_component_size" value="1000"/> |
|
6710edf12bac
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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337 <param name="min_dead_end_size" value="1000"/> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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338 </section> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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339 <section name="lr_align"> |
|
6710edf12bac
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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340 <param name="scores" value="3,-6,-5,-2"/> |
|
6710edf12bac
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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341 </section> |
|
9
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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342 <param name="keep" value="0"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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343 <output name="assembly_graph" ftype="gfa1"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
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344 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
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345 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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346 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
changeset
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347 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
changeset
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348 <output name="assembly" ftype="fasta"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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349 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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350 <has_text text="length=5386" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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351 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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352 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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353 </test> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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354 <test expect_num_outputs="2"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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355 <conditional name="paired_unpaired"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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356 <param name="fastq_input_selector" value="none"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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357 </conditional> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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358 <param name="min_anchor_seg_len" value="10"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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359 <section name="spades"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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360 <param name="kmers" value="21,23"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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361 </section> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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362 <param name="long" value="only_long.fasta" ftype="fasta" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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363 <param name="keep" value="0"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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364 <output name="assembly_graph" ftype="gfa1"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
|
365 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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366 <has_text text="S" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
|
367 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
368 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
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369 <output name="assembly" ftype="fasta"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
370 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
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371 <has_text text=">1" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
|
372 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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373 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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374 </test> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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375 <!-- Test keep value = 1 --> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
376 <test expect_num_outputs="3"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
377 <conditional name="paired_unpaired"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
378 <param name="fastq_input_selector" value="paired" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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379 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
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380 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
381 </conditional> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
382 <param name="mode" value="normal" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
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383 <param name="keep" value="1"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
384 <output name="assembly_graph" ftype="gfa1"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
385 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
386 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
387 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
388 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
389 <output name="assembly" ftype="fasta"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
390 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
391 <has_text text="length=5386" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
392 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
393 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
394 <output_collection name="spades_collection" type="list" count="14"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
395 <element name="001_spades_graph_k027"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
396 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
397 <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
398 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
399 </element> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
400 </output_collection> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
401 </test> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
402 <!-- Test keep value = 2 --> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
403 <test expect_num_outputs="4"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
404 <conditional name="paired_unpaired"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
405 <param name="fastq_input_selector" value="paired" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
406 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
407 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
408 </conditional> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
409 <param name="long" value="onp.fa" ftype="fasta" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
410 <param name="mode" value="normal" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
411 <param name="keep" value="2"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
412 <output name="assembly_graph" ftype="gfa1"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
413 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
414 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
415 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
416 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
417 <output name="assembly" ftype="fasta"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
418 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
419 <has_text text="length=5386" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
420 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
421 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
422 <output_collection name="spades_collection" type="list" count="14"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
423 <element name="001_spades_graph_k027"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
424 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
425 <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
426 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
427 </element> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
428 </output_collection> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
429 <output name="bam_file" ftype="bam"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
430 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
431 <has_size value="2084" delta="100"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
432 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
433 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
434 </test> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
435 <!-- Test no simple bridges option --> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
436 <test expect_num_outputs="2"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
437 <conditional name="paired_unpaired"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
438 <param name="fastq_input_selector" value="paired" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
439 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
440 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
441 </conditional> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
442 <param name="long" value="onp.fa" ftype="fasta" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
443 <param name="mode" value="normal" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
444 <param name="keep" value="0"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
445 <section name="lr_align"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
446 <param name="no_simple_bridges" value="true"/> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
447 </section> |
|
8
f9973e8f6f22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
448 <output name="assembly_graph" ftype="gfa1"> |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
449 <assert_contents> |
|
8
f9973e8f6f22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
450 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
451 </assert_contents> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
452 </output> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
453 <output name="assembly" ftype="fasta"> |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
454 <assert_contents> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
455 <has_text text="length=5386" /> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
456 </assert_contents> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
457 </output> |
|
9
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
458 <assert_command> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
459 <has_text text="--no_simple_bridges" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
460 </assert_command> |
|
4
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
461 </test> |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
462 </tests> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
463 <help><![CDATA[ |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
464 |
|
15a21071f0a2
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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465 **Unicycler** |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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466 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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467 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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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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468 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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469 .. _`Ryan Wick`: https://github.com/rrwick |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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470 .. _`github page`: https://github.com/rrwick/Unicycler |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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471 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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472 ----- |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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473 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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474 **Input data** |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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475 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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476 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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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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477 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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478 .. _`Sanger encoding`: https://en.wikipedia.org/wiki/FASTQ_format#Quality |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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479 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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480 The input options 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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481 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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482 -1 SHORT1, --short1 SHORT1 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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483 FASTQ file of short reads (first reads in each pair) |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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484 -2 SHORT2, --short2 SHORT2 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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485 FASTQ file of short reads (second reads in each pair) |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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486 -s SHORT_UNPAIRED, --short_unpaired SHORT_UNPAIRED |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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487 FASTQ file of unpaired short reads |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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488 -l LONG, --long LONG |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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489 FASTQ or FASTA file of long reads, if all reads are available at start. |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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490 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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491 ----- |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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492 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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493 **Bridging mode** |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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494 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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495 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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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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496 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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497 .. _`description of modes`: https://github.com/rrwick/Unicycler#conservative-normal-and-bold |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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498 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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499 The available modes are:: |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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500 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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501 --mode {conservative,normal,bold} |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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502 Bridging mode (default: normal) |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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503 conservative = smaller contigs, lowest misassembly rate |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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504 normal = moderate contig size and misassembly rate |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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505 bold = longest contigs, higher misassembly rate |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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506 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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507 ---- |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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508 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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509 **Skip SPAdes error correction step** |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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510 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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511 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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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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512 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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513 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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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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514 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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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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515 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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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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516 4. Solid *k*-mers are derived from cluster centers and are assumed to be *error free*. |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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517 5. Solid *k*-mers are mapped back to the reads and used to correct them. |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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518 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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519 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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15a21071f0a2
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520 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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521 .. _`BayesHammer`: https://goo.gl/1iGkMe |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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522 .. _`Hamming graph`: https://en.wikipedia.org/wiki/Hamming_graph |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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523 .. _`Hamming distance`: https://en.wikipedia.org/wiki/Hamming_distance |
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15a21071f0a2
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524 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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525 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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526 ----- |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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527 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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528 **Do not rotate completed replicons to start at a standard gene** |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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529 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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530 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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15a21071f0a2
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531 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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532 The following option turns rotation on and off:: |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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533 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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534 --no_rotate |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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535 Do not rotate completed replicons |
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15a21071f0a2
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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536 to start at a standard gene |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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537 (default: completed replicons are rotated) |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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538 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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539 **Do not use Pilon to polish the final assembly** |
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15a21071f0a2
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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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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changeset
|
541 `Pilon`_ is a tool for improving overall quality of draft assemblies and finding variation among strains. Unicycler uses it for assembly *polishing*. |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
542 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
543 The following option turns pilon part of Unicycler pipeline on and off:: |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
544 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
545 --no_pilon |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
546 Do not use Pilon to polish the |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
547 final assembly (default: Pilon is used) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
548 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
549 .. _`Pilon`: https://github.com/broadinstitute/pilon/wiki |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
550 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
551 ------ |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
552 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
553 **Expected number of linear sequences** |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
554 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
555 If you expect your sample to contain linear (non circular) sequences, set this option:: |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
556 |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
557 --linear_seqs EXPECTED_LINEAR_SEQS |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
558 The expected number of linear (i.e. non-circular) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
559 sequences in the underlying sequence |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
560 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
561 ---- |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
562 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
563 **SPAdes options** |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
564 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
565 This section provides control of SPAdes options:: |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
566 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
567 --min_kmer_frac MIN_KMER_FRAC |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
568 Lowest k-mer size for SPAdes assembly, |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
569 expressed as a fraction of the read length |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
570 (default: 0.2) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
571 --max_kmer_frac MAX_KMER_FRAC |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
572 Highest k-mer size for SPAdes assembly, |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
573 expressed as a fraction of the read length |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
574 (default: 0.95) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
575 --kmer_count KMER_COUNT |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
576 Number of k-mer steps to use in |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
577 SPAdes assembly (default: 10) |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
578 --depth_filter DEPTH_FILTER |
|
4
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
579 Filter out contigs lower than this fraction |
|
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
580 of the chromosomal depth, if doing so does |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
581 not result in graph dead ends (default: 0.25) |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
582 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
583 ---- |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
584 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
585 **Rotation options** |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
586 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
587 Unicycler attempts to rotate circular assemblies to make sure that they begin at a consistent starting gene. The following parameters control assembly rotation:: |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
588 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
589 --start_genes START_GENES |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
590 FASTA file of genes for start point |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
591 of rotated replicons |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
592 (default: start_genes.fasta) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
593 --start_gene_id START_GENE_ID |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
594 The minimum required BLAST percent identity |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
595 for a start gene search |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
596 (default: 90.0) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
597 --start_gene_cov START_GENE_COV |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
598 The minimum required BLAST percent coverage |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
599 for a start gene search |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
600 (default: 95.0) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
601 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
602 ----- |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
603 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
604 **Graph cleaning options** |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
605 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
606 These options control the removal of small leftover sequences after bridging is complete:: |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
607 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
608 --min_component_size MIN_COMPONENT_SIZE |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
609 Unbridged graph components smaller |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
610 than this size (bp) will be removed |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
611 from the final graph (default: 1000) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
612 --min_dead_end_size MIN_DEAD_END_SIZE |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
613 Graph dead ends smaller than this size (bp) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
614 will be removed from the final graph |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
615 (default: 1000) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
616 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
617 ----- |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
618 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
619 **Long read alignment options** |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
620 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
621 These options control the alignment of long reads to the assembly graph:: |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
622 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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623 --contamination CONTAMINATION |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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624 FASTA file of known contamination in long reads |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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625 --scores SCORES |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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626 Comma-delimited string of alignment scores: |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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627 match, mismatch, gap open, gap extend |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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628 (default: 3,-6,-5,-2) |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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629 --low_score LOW_SCORE |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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630 Score threshold - alignments below this |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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631 are considered poor |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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632 (default: set threshold automatically) |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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633 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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634 ----- |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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635 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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636 **Outputs** |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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637 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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638 Galaxy's wrapped for Unicycler produces two outputs: |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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639 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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640 * final assembly in FASTA format |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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641 * final assembly grapth in graph format |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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642 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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643 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`_. |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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644 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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645 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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646 .. _`Bandage`: https://github.com/rrwick/Bandage |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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647 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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648 |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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649 ]]></help> |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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650 <citations> |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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651 <citation type="doi">10.1101/096412</citation> |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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652 </citations> |
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15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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653 </tool> |