Mercurial > repos > iuc > unicycler
annotate unicycler.xml @ 10:906f76188535 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
| author | iuc |
|---|---|
| date | Fri, 21 Oct 2022 16:02:10 +0000 |
| parents | def4cbdf745d |
| children | 2b63b5400447 |
| 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
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1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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2 <description>pipeline for bacterial genomes</description> |
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2
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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3 <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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4 <token name="@TOOL_VERSION@">0.5.0</token> |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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5 <token name="@VERSION_SUFFIX@">1</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:
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diff
changeset
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6 </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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7 <xrefs> |
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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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8 <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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9 </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:
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changeset
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10 <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:
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diff
changeset
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11 <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:
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diff
changeset
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12 </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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13 <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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14 <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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15 </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
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16 <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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17 <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
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18 <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
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19 </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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20 <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:
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changeset
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21 ## Preparing files |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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22 #set $uncompressed = ('fastqsanger','fastq') |
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906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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23 #set $compressed = ('fastqsanger.gz','fastq.gz') |
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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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24 #if str( $paired_unpaired.fastq_input_selector ) == "paired" |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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25 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed |
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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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26 #set fq1 = "fq1.fastq" |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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27 #elif $paired_unpaired.fastq_input1.file_ext in $compressed |
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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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28 #set fq1 = "fq1.fastq.gz" |
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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 #end if |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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30 #if $paired_unpaired.fastq_input2.file_ext in $uncompressed |
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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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31 #set fq2 = "fq2.fastq" |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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32 #elif $paired_unpaired.fastq_input2.file_ext in $compressed |
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2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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33 #set fq2 = "fq2.fastq.gz" |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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34 #end if |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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35 ln -s '${paired_unpaired.fastq_input1}' $fq1 && |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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36 ln -s '${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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37 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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38 #if $paired_unpaired.fastq_input1.forward.file_ext in $uncompressed |
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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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39 #set fq1 = "fq1.fastq" |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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40 #elif $paired_unpaired.fastq_input1.forward.file_ext in $compressed |
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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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41 #set fq1 = "fq1.fastq.gz" |
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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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42 #end if |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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43 #if $paired_unpaired.fastq_input1.reverse.file_ext in $uncompressed |
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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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44 #set fq2 = "fq2.fastq" |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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45 #elif $paired_unpaired.fastq_input1.reverse.file_ext in $compressed |
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2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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46 #set fq2 = "fq2.fastq.gz" |
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0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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47 #end if |
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2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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48 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 && |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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49 ln -s '${paired_unpaired.fastq_input1.reverse}' $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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50 #elif str( $paired_unpaired.fastq_input_selector ) == "single" |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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51 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed |
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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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52 #set fq = "fq.fastq" |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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53 #elif $paired_unpaired.fastq_input1.file_ext in $compressed |
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2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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54 #set fq = "fq.fastq.gz" |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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55 #end if |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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56 ln -s '${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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57 #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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58 #if $long |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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59 #if $long.file_ext in $uncompressed |
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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
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60 #set lr = "lr.fastq" |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
iuc
parents:
9
diff
changeset
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61 #elif $long.file_ext in $compressed |
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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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62 #set lr = "lr.fastq.gz" |
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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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63 #elif $long.is_of_type('fasta') |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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64 #set lr = "lr.fasta" |
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0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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65 #end if |
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2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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66 ln -s '${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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67 #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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68 ## 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:
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69 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:
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70 -o ./ |
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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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71 --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:
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72 #if str( $paired_unpaired.fastq_input_selector ) == "paired" |
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2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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73 -1 '$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
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changeset
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74 -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:
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changeset
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75 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" |
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608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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76 -1 '$fq1' |
|
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
|
77 -2 '$fq2' |
|
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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diff
changeset
|
78 #elif str( $paired_unpaired.fastq_input_selector ) == "single" |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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79 -s '$fq' |
|
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
|
80 #end if |
|
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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81 #if $long |
|
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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82 -l $lr |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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83 #end if |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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changeset
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84 ## General Unicycler Options section |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
85 ## ---------------------------------------------------------- |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
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86 --mode '$mode' |
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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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87 --min_fasta_length '$min_fasta_length' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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88 --linear_seqs '$linear_seqs' |
|
4
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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89 #if str($min_anchor_seg_len) != '' |
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608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
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90 --min_anchor_seg_len '$min_anchor_seg_len' |
|
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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91 #end if |
|
2
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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92 ## Spades 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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93 ## ---------------------------------------------------------- |
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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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94 --min_kmer_frac '$spades.min_kmer_frac' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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95 --max_kmer_frac '$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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96 #if str($spades.kmers) != '' |
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608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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97 --kmers '$spades.kmers' |
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608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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98 #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
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diff
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99 --kmer_count '$spades.kmer_count' |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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100 --depth_filter '$spades.depth_filter' |
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7
e3f1860582ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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101 #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"
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102 --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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103 #end if |
|
2
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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104 ## 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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105 ## ---------------------------------------------------------- |
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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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106 $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
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107 #if $rotation.start_genes |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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108 --start_genes '$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
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109 #end if |
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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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110 --start_gene_id '$rotation.start_gene_id' |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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111 --start_gene_cov '$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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112 ## 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
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113 ## ---------------------------------------------------------- |
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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 --min_component_size '$graph_clean.min_component_size' |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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115 --min_dead_end_size '$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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116 ## 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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117 ## ---------------------------------------------------------- |
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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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118 #if $lr_align.contamination |
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6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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119 --contamination '$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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120 #end if |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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121 --scores '${lr_align.scores}' |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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122 #if str($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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123 --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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124 #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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125 $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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126 --keep $keep |
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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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127 #if $keep != '0' |
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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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128 && mkdir 'spades_graphs' |
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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 && 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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130 #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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131 #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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132 && 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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133 #end if |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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134 ]]></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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135 <inputs> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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136 <conditional name="paired_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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137 <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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138 <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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139 <option value="paired_collection">Paired Collection</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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140 <option value="single">Single</option> |
|
4
608d1d0ba3a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
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141 <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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142 </param> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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143 <when value="paired"> |
|
10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
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144 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" |
|
6
d1ac6363b63b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
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145 label="Select first set of reads" help="Specify dataset with forward reads"/> |
|
10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
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146 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" |
|
6
d1ac6363b63b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
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147 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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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="paired_collection"> |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
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150 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" type="data_collection" collection_type="paired" label="Select a paired collection" /> |
|
0
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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151 </when> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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152 <when value="single"> |
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10
906f76188535
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
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153 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" |
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6
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154 label="Select unpaired reads" help="Specify dataset with unpaired reads"/> |
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155 </when> |
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156 <when value="none"> |
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157 </when> |
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158 </conditional> |
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159 <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta,fastq,fastq.gz" label="Select long reads. If there are no long reads, leave this empty"/> |
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160 <param argument="--mode" type="select" label="Select Bridging mode"> |
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161 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option> |
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162 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option> |
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163 <option value="bold">Bold (longest contigs, higher misassembly rate)</option> |
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164 </param> |
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165 <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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166 <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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167 <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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168 <section name="spades" expanded="False" title="SPAdes options" |
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169 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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170 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2" |
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171 label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/> |
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172 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95" |
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173 label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/> |
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174 <param argument="--kmers" type="text" value="" optional="true" label="Exact k-mers to use for SPAdes assembly, comma-separated"> |
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175 <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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176 </param> |
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177 <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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178 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25" |
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179 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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180 <param argument="--largest_component" type="boolean" checked="false" |
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181 label="Only keep the largest connected component of the assembly graph"/> |
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182 </section> |
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183 <section name="rotation" expanded="false" title="Rotation options" |
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184 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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185 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue="" |
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186 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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187 <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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188 <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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189 <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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190 </section> |
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191 <section name="graph_clean" expanded="false" title="Graph cleaning options" |
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192 help="These options control the removal of small leftover sequences after bridging is complete."> |
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193 <param argument="--min_component_size" type="integer" min="0" value="1000" |
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194 label="Unbridged graph components smaller than this size will be removed from the final graph" /> |
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195 <param argument="--min_dead_end_size" type="integer" min="0" value="1000" |
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196 label="Graph dead ends smaller than this size will be removed from the final graph"/> |
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197 </section> |
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198 <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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199 <param argument="--contamination" optional="true" type="data" format="fasta" |
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200 label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." /> |
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201 <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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202 <param argument="--low_score" optional="true" type="integer" value="" |
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203 label="Score threshold - alignments below this are considered poor" help="default = set automatically"/> |
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204 <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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205 </section> |
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206 <param argument="--keep" type="select" label="Outputs to keep" help="Level of file retention. Default: 1"> |
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207 <option value="0">0: only keep final files</option> |
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208 <option value="1" selected="true">1: save graphs at main checkpoints</option> |
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209 <option value="2">2: also keep SAM</option> |
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210 </param> |
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211 </inputs> |
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212 <outputs> |
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213 <data name="assembly_graph" format="gfa1" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> |
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214 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> |
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215 <collection name="spades_collection" type="list" label="${tool.name} on ${on_string}: SPAdes graphs"> |
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216 <discover_datasets pattern="__designation_and_ext__" format="gfa1" directory="spades_graphs"/> |
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217 <filter>keep != "0"</filter> |
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218 </collection> |
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219 <data name="bam_file" format="bam" from_work_dir="read_alignment/long_read_alignments.bam" label="${tool.name} on ${on_string}: Long read alignments BAM"> |
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220 <filter>keep == "2" and long</filter> |
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221 </data> |
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222 </outputs> |
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223 <tests> |
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224 <test expect_num_outputs="2"> |
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225 <conditional name="paired_unpaired"> |
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226 <param name="fastq_input_selector" value="paired" /> |
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227 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
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228 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
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229 </conditional> |
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230 <param name="mode" value="normal" /> |
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231 <param name="min_fasta_length" value="100"/> |
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232 <param name="linear_seqs" value="0"/> |
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233 <section name="spades"> |
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234 <param name="min_kmer_frac" value="0.2"/> |
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235 <param name="max_kmer_frac" value="0.95"/> |
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236 <param name="kmer_count" value="10"/> |
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237 <param name="depth_filter" value="0.25"/> |
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238 </section> |
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239 <section name="rotation"> |
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240 <param name="no_rotate" value=""/> |
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241 <param name="start_gene_id" value="90"/> |
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242 <param name="start_gene_cov" value="95"/> |
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243 </section> |
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244 <section name="graph_clean"> |
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245 <param name="min_component_size" value="1000"/> |
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246 <param name="min_dead_end_size" value="1000"/> |
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247 </section> |
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248 <section name="lr_align"> |
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249 <param name="scores" value="3,-6,-5,-2"/> |
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250 </section> |
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251 <param name="keep" value="0"/> |
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252 <output name="assembly_graph" ftype="gfa1"> |
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253 <assert_contents> |
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254 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
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255 </assert_contents> |
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256 </output> |
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257 <output name="assembly" ftype="fasta"> |
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258 <assert_contents> |
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259 <has_text text="length=5386" /> |
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260 </assert_contents> |
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261 </output> |
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262 </test> |
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263 <!-- |
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264 Following test corresponds to the command: |
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265 |
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266 unicycler -t "${GALAXY_SLOTS:-8}" -o ./ - -verbose 3 - -pilon_path `pilon - -jar_dir` \ |
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267 -1 test-data/phix_f.fq.gz -2 test-data/phix_r.fq.gz -l test-data/onp.fa \ |
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268 - -mode 'normal' - -no_correct |
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269 |
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270 This command causes a segfault with the current version of unicycler on bioconda for Linux |
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271 during the minimap step (which seems to be compiled C code). A gist of the log can be found |
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272 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb. |
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273 --> |
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274 <test expect_num_outputs="2"> |
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275 <conditional name="paired_unpaired"> |
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276 <param name="fastq_input_selector" value="paired" /> |
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277 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger.gz" /> |
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278 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger.gz" /> |
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279 </conditional> |
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280 <param name="long" value="onp.fa" ftype="fasta" /> |
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281 <param name="mode" value="normal" /> |
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282 <param name="min_fasta_length" value="100"/> |
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283 <param name="linear_seqs" value="0"/> |
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284 <section name="spades"> |
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285 <param name="min_kmer_frac" value="0.2"/> |
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286 <param name="max_kmer_frac" value="0.95"/> |
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287 <param name="kmer_count" value="10"/> |
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288 <param name="depth_filter" value="0.25"/> |
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289 </section> |
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290 <section name="rotation"> |
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291 <param name="no_rotate" value=""/> |
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292 <param name="start_gene_id" value="90"/> |
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293 <param name="start_gene_cov" value="95"/> |
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294 </section> |
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295 <section name="graph_clean"> |
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296 <param name="min_component_size" value="1000"/> |
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297 <param name="min_dead_end_size" value="1000"/> |
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298 </section> |
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299 <section name="lr_align"> |
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300 <param name="scores" value="3,-6,-5,-2"/> |
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301 </section> |
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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
|
302 <param name="keep" value="0"/> |
|
8
f9973e8f6f22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
303 <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
|
304 <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
|
305 <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
|
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
|
307 </output> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
308 <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
|
309 <assert_contents> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
310 <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
|
311 </assert_contents> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
312 </output> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
313 </test> |
|
9
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
314 <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
|
315 <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
|
316 <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:
1
diff
changeset
|
317 <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
|
318 <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
|
319 <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
|
320 <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:
1
diff
changeset
|
321 </collection> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
322 </param> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
323 </conditional> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
324 <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
|
325 <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
|
326 <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
|
327 <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
|
328 <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
|
329 <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
|
330 <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
|
331 <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:
1
diff
changeset
|
332 </section> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
333 <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
|
334 <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
|
335 <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
|
336 <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
|
337 </section> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
338 <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
|
339 <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
|
340 <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:
1
diff
changeset
|
341 </section> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
342 <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
|
343 <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
|
344 </section> |
|
9
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
345 <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
|
346 <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
|
347 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
348 <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
|
349 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
350 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
351 <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
|
352 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
353 <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
|
354 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
355 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
356 </test> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
357 <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
|
358 <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
|
359 <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:
8
diff
changeset
|
360 </conditional> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
361 <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:
8
diff
changeset
|
362 <section name="spades"> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
363 <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:
8
diff
changeset
|
364 </section> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
365 <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:
8
diff
changeset
|
366 <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
|
367 <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
|
368 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
369 <has_text text="S" /> |
|
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
|
371 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
372 <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
|
373 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
374 <has_text text=">1" /> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
375 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
376 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
377 </test> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
378 <!-- 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
|
379 <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
|
380 <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
|
381 <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
|
382 <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
|
383 <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
|
384 </conditional> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
385 <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
|
386 <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
|
387 <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
|
388 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
389 <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
|
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 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
392 <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
|
393 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
394 <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
|
395 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
396 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
397 <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
|
398 <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
|
399 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
400 <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
|
401 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
402 </element> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
403 </output_collection> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
404 </test> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
405 <!-- 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
|
406 <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
|
407 <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
|
408 <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
|
409 <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
|
410 <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
|
411 </conditional> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
412 <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
|
413 <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
|
414 <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
|
415 <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
|
416 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
417 <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
|
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 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
420 <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
|
421 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
422 <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
|
423 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
424 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
425 <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
|
426 <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
|
427 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
428 <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
|
429 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
430 </element> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
431 </output_collection> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
432 <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
|
433 <assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
434 <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
|
435 </assert_contents> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
436 </output> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
437 </test> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
438 <!-- 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
|
439 <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
|
440 <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
|
441 <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
|
442 <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
|
443 <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
|
444 </conditional> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
445 <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
|
446 <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
|
447 <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
|
448 <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
|
449 <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
|
450 </section> |
|
8
f9973e8f6f22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
451 <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
|
452 <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
|
453 <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
|
454 </assert_contents> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
455 </output> |
|
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
456 <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
|
457 <assert_contents> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
458 <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
|
459 </assert_contents> |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
460 </output> |
|
9
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
461 <assert_command> |
|
def4cbdf745d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
462 <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
|
463 </assert_command> |
|
4
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464 </test> |
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0
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465 </tests> |
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466 <help><![CDATA[ |
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467 |
|
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468 **Unicycler** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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469 |
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470 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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471 |
|
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472 .. _`Ryan Wick`: https://github.com/rrwick |
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473 .. _`github page`: https://github.com/rrwick/Unicycler |
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474 |
|
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475 ----- |
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476 |
|
15a21071f0a2
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477 **Input data** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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478 |
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479 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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480 |
|
15a21071f0a2
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481 .. _`Sanger encoding`: https://en.wikipedia.org/wiki/FASTQ_format#Quality |
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482 |
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483 The input options are:: |
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484 |
|
15a21071f0a2
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485 -1 SHORT1, --short1 SHORT1 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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486 FASTQ file of short reads (first reads in each pair) |
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487 -2 SHORT2, --short2 SHORT2 |
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488 FASTQ file of short reads (second reads in each pair) |
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489 -s SHORT_UNPAIRED, --short_unpaired SHORT_UNPAIRED |
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490 FASTQ file of unpaired short reads |
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491 -l LONG, --long LONG |
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492 FASTQ or FASTA file of long reads, if all reads are available at start. |
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493 |
|
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494 ----- |
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495 |
|
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496 **Bridging mode** |
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497 |
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498 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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499 |
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500 .. _`description of modes`: https://github.com/rrwick/Unicycler#conservative-normal-and-bold |
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501 |
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502 The available modes are:: |
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503 |
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504 --mode {conservative,normal,bold} |
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505 Bridging mode (default: normal) |
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506 conservative = smaller contigs, lowest misassembly rate |
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507 normal = moderate contig size and misassembly rate |
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508 bold = longest contigs, higher misassembly rate |
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509 |
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15a21071f0a2
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510 ---- |
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511 |
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512 **Skip SPAdes error correction step** |
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513 |
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514 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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515 |
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15a21071f0a2
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516 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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517 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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518 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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519 4. Solid *k*-mers are derived from cluster centers and are assumed to be *error free*. |
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520 5. Solid *k*-mers are mapped back to the reads and used to correct them. |
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521 |
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522 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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523 |
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524 .. _`BayesHammer`: https://goo.gl/1iGkMe |
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525 .. _`Hamming graph`: https://en.wikipedia.org/wiki/Hamming_graph |
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526 .. _`Hamming distance`: https://en.wikipedia.org/wiki/Hamming_distance |
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527 |
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528 |
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529 ----- |
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530 |
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15a21071f0a2
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531 **Do not rotate completed replicons to start at a standard gene** |
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15a21071f0a2
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532 |
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15a21071f0a2
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533 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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534 |
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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 The following option turns rotation on and off:: |
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536 |
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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 --no_rotate |
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15a21071f0a2
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538 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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539 to start at a standard gene |
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15a21071f0a2
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540 (default: completed replicons are rotated) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
541 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
542 **Do not use Pilon to polish the final assembly** |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
543 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
544 `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
|
545 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
546 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
|
547 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
548 --no_pilon |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
549 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
|
550 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
|
551 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
552 .. _`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
|
553 |
|
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 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
556 **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
|
557 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
558 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
|
559 |
|
2
6710edf12bac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
560 --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
|
561 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
|
562 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
|
563 |
|
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 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
566 **SPAdes options** |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
567 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
568 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
|
569 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
570 --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
|
571 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
|
572 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
|
573 (default: 0.2) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
574 --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
|
575 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
|
576 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
|
577 (default: 0.95) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
578 --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
|
579 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
|
580 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
|
581 --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
|
582 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
|
583 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
|
584 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
|
585 |
|
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 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
588 **Rotation options** |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
589 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
590 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
|
591 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
592 --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
|
593 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
|
594 of rotated replicons |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
595 (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
|
596 --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
|
597 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
|
598 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
|
599 (default: 90.0) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
600 --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
|
601 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
|
602 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
|
603 (default: 95.0) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
604 |
|
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 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
607 **Graph cleaning options** |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
608 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
609 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
|
610 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
611 --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
|
612 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
|
613 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
|
614 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
|
615 --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
|
616 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
|
617 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
|
618 (default: 1000) |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
619 |
|
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 |
|
15a21071f0a2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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622 **Long read alignment options** |
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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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623 |
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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 These options control the alignment of long reads to the assembly 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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625 |
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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 --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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627 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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628 --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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629 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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630 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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631 (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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632 --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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633 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
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634 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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635 (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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636 |
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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 |
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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 **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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640 |
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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 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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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 * 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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644 * 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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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 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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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 .. _`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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650 |
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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 |
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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 ]]></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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653 <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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654 <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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655 </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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656 </tool> |