Mercurial > repos > iuc > unicycler
annotate unicycler.xml @ 11:8f9f06995f98 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
| author | iuc |
|---|---|
| date | Tue, 19 Dec 2023 15:58:30 +0000 |
| parents | d10bdad2fd17 |
| children |
| rev | line source |
|---|---|
|
9
6e26c9afd301
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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d10bdad2fd17
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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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
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changeset
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3 <macros> |
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6e26c9afd301
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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d10bdad2fd17
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
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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6 </macros> |
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7
88c240872a65
"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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7 <edam_topics> |
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88c240872a65
"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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8 <edam_topic>topic_0196</edam_topic> |
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88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
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9 </edam_topics> |
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88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
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10 <edam_operations> |
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88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
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11 <edam_operation>operation_0525</edam_operation> |
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88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents:
6
diff
changeset
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12 </edam_operations> |
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11
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
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13 <xrefs> |
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8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
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14 <xref type="bio.tools">unicycler</xref> |
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8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
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15 </xrefs> |
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0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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16 <requirements> |
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6e26c9afd301
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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6e26c9afd301
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
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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19 </requirements> |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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20 <command detect_errors="exit_code"><![CDATA[ |
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11
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
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21 #for r in $reuse |
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8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
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22 ln -s $r.reuse_file ${r.reuse_step}.gfa && |
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8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
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23 #end for |
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8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
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24 |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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25 ## Preparing files |
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d10bdad2fd17
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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26 #set $uncompressed = ('fastqsanger','fastq') |
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d10bdad2fd17
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 #set $compressed = ('fastqsanger.gz','fastq.gz') |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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28 #if str( $paired_unpaired.fastq_input_selector ) == "paired" |
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d10bdad2fd17
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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29 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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30 #set fq1 = "fq1.fastq" |
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10
d10bdad2fd17
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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31 #elif $paired_unpaired.fastq_input1.file_ext in $compressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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32 #set fq1 = "fq1.fastq.gz" |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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33 #end if |
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d10bdad2fd17
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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34 #if $paired_unpaired.fastq_input2.file_ext in $uncompressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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35 #set fq2 = "fq2.fastq" |
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10
d10bdad2fd17
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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36 #elif $paired_unpaired.fastq_input2.file_ext in $compressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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37 #set fq2 = "fq2.fastq.gz" |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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38 #end if |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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39 ln -s '${paired_unpaired.fastq_input1}' $fq1 && |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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40 ln -s '${paired_unpaired.fastq_input2}' $fq2 && |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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41 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" |
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d10bdad2fd17
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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42 #if $paired_unpaired.fastq_input1.forward.file_ext in $uncompressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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43 #set fq1 = "fq1.fastq" |
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10
d10bdad2fd17
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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44 #elif $paired_unpaired.fastq_input1.forward.file_ext in $compressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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45 #set fq1 = "fq1.fastq.gz" |
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0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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46 #end if |
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10
d10bdad2fd17
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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47 #if $paired_unpaired.fastq_input1.reverse.file_ext in $uncompressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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48 #set fq2 = "fq2.fastq" |
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10
d10bdad2fd17
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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49 #elif $paired_unpaired.fastq_input1.reverse.file_ext in $compressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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50 #set fq2 = "fq2.fastq.gz" |
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0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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51 #end if |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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52 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 && |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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53 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 && |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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54 #elif str( $paired_unpaired.fastq_input_selector ) == "single" |
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d10bdad2fd17
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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55 #if $paired_unpaired.fastq_input1.file_ext in $uncompressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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56 #set fq = "fq.fastq" |
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10
d10bdad2fd17
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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57 #elif $paired_unpaired.fastq_input1.file_ext in $compressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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58 #set fq = "fq.fastq.gz" |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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59 #end if |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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60 ln -s '${paired_unpaired.fastq_input1}' '$fq' && |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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61 #end if |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
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62 #if $long |
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d10bdad2fd17
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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63 #if $long.file_ext in $uncompressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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64 #set lr = "lr.fastq" |
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10
d10bdad2fd17
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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65 #elif $long.file_ext in $compressed |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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66 #set lr = "lr.fastq.gz" |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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67 #elif $long.is_of_type('fasta') |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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68 #set lr = "lr.fasta" |
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0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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69 #end if |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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70 ln -s '${long}' '$lr' && |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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71 #end if |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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72 ## Running Unicycler |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
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changeset
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73 unicycler -t "\${GALAXY_SLOTS:-4}" |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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74 -o ./ |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
75 --verbosity 3 |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
76 #if str( $paired_unpaired.fastq_input_selector ) == "paired" |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
77 -1 '$fq1' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
78 -2 '$fq2' |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
79 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
80 -1 '$fq1' |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
81 -2 '$fq2' |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
82 #elif str( $paired_unpaired.fastq_input_selector ) == "single" |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
83 -s '$fq' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
84 #end if |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
85 #if $long |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
86 -l $lr |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
87 #end if |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
88 ## General Unicycler Options section |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
89 ## ---------------------------------------------------------- |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
90 --mode '$mode' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
91 --min_fasta_length '$min_fasta_length' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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92 --linear_seqs '$linear_seqs' |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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diff
changeset
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93 #if str($min_anchor_seg_len) != '' |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
94 --min_anchor_seg_len '$min_anchor_seg_len' |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
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95 #end if |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
96 ## Spades Options section |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
97 ## ---------------------------------------------------------- |
|
e92675014ac9
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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98 --min_kmer_frac '$spades.min_kmer_frac' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
|
99 --max_kmer_frac '$spades.max_kmer_frac' |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
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diff
changeset
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100 #if str($spades.kmers) != '' |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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diff
changeset
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101 --kmers '$spades.kmers' |
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2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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102 #end if |
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2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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103 --kmer_count '$spades.kmer_count' |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
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104 --depth_filter '$spades.depth_filter' |
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7
88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
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diff
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105 #if $spades.largest_component |
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88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
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106 --largest_component |
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88c240872a65
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
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diff
changeset
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107 #end if |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
changeset
|
108 ## Rotation Options section |
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e92675014ac9
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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|
109 ## ---------------------------------------------------------- |
|
e92675014ac9
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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110 $rotation.no_rotate |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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111 #if $rotation.start_genes |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
changeset
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112 --start_genes '$rotation.start_genes' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
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113 #end if |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
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114 --start_gene_id '$rotation.start_gene_id' |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
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115 --start_gene_cov '$rotation.start_gene_cov' |
|
e92675014ac9
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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116 ## Graph cleaning Options sdection |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
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|
117 ## ---------------------------------------------------------- |
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e92675014ac9
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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118 --min_component_size '$graph_clean.min_component_size' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
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119 --min_dead_end_size '$graph_clean.min_dead_end_size' |
|
e92675014ac9
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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120 ## Long Read Alignment Options |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
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121 ## ---------------------------------------------------------- |
|
e92675014ac9
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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122 #if $lr_align.contamination |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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diff
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123 --contamination '$lr_align.contamination' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
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diff
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124 #end if |
|
e92675014ac9
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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125 --scores '${lr_align.scores}' |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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126 #if str($lr_align.low_score) != '' |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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127 --low_score '$lr_align.low_score' |
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e92675014ac9
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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128 #end if |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
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129 $lr_align.no_simple_bridges |
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6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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130 --keep $keep |
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6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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131 #if $keep != '0' |
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6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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132 && mkdir 'spades_graphs' |
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6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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133 && mv 00*gfa './spades_graphs/' |
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6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
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|
134 #end if |
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6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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135 #if $keep == '2' and $long |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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136 && samtools view -@ "\${GALAXY_SLOTS:-4}" -u 'read_alignment/long_read_alignments.sam' | samtools sort -@ "\${GALAXY_SLOTS:-4}" -o 'read_alignment/long_read_alignments.bam' |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
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diff
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137 #end if |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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138 ]]></command> |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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139 <inputs> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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140 <conditional name="paired_unpaired"> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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141 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data"> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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142 <option selected="True" value="paired">Paired</option> |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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143 <option value="paired_collection">Paired Collection</option> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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144 <option value="single">Single</option> |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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145 <option value="none">None</option> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff
changeset
|
146 </param> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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147 <when value="paired"> |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
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148 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" |
|
6
0a3a602cd1e3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
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149 label="Select first set of reads" help="Specify dataset with forward reads"/> |
|
10
d10bdad2fd17
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 5f3daee2f2768cc98cf739ea417e70efbb0ce913
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150 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" |
|
6
0a3a602cd1e3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 7272906b45bad9ad1eb9bd01ee4e8936fc4c20a5
iuc
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151 label="Select second set of reads" help="Specify dataset with reverse reads"/> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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152 </when> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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153 <when value="paired_collection"> |
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154 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" type="data_collection" collection_type="paired" label="Select a paired collection" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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155 </when> |
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156 <when value="single"> |
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157 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" |
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158 label="Select unpaired reads" help="Specify dataset with unpaired reads"/> |
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159 </when> |
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160 <when value="none"> |
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161 </when> |
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162 </conditional> |
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163 <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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
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164 <param argument="--mode" type="select" label="Select Bridging mode"> |
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165 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option> |
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166 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option> |
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167 <option value="bold">Bold (longest contigs, higher misassembly rate)</option> |
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168 </param> |
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169 <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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170 <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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171 <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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172 <section name="spades" expanded="False" title="SPAdes options" |
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173 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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174 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2" |
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175 label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/> |
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176 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95" |
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177 label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/> |
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178 <param argument="--kmers" type="text" value="" optional="true" label="Exact k-mers to use for SPAdes assembly, comma-separated"> |
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179 <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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180 </param> |
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181 <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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182 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25" |
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183 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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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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184 <param argument="--largest_component" type="boolean" checked="false" |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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185 label="Only keep the largest connected component of the assembly graph"/> |
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186 </section> |
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187 <section name="rotation" expanded="false" title="Rotation options" |
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188 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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189 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue="" |
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190 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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191 <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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192 <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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193 <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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194 </section> |
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195 <section name="graph_clean" expanded="false" title="Graph cleaning options" |
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196 help="These options control the removal of small leftover sequences after bridging is complete."> |
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197 <param argument="--min_component_size" type="integer" min="0" value="1000" |
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198 label="Unbridged graph components smaller than this size will be removed from the final graph" /> |
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199 <param argument="--min_dead_end_size" type="integer" min="0" value="1000" |
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200 label="Graph dead ends smaller than this size will be removed from the final graph"/> |
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201 </section> |
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202 <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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203 <param argument="--contamination" optional="true" type="data" format="fasta" |
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204 label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." /> |
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205 <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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206 <param argument="--low_score" optional="true" type="integer" value="" |
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207 label="Score threshold - alignments below this are considered poor" help="default = set automatically"/> |
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208 <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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209 </section> |
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210 <param argument="--keep" type="select" label="Outputs to keep" help="Level of file retention. Default: 1"> |
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211 <option value="0">0: only keep final files</option> |
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212 <option value="1" selected="true">1: save graphs at main checkpoints</option> |
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213 <option value="2">2: also keep SAM</option> |
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214 </param> |
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215 <repeat name="reuse" title="Reuse checkpoint files from earlier runs" max="1" help=""> |
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216 <param name="reuse_file" type="data" optional="false" format="gfa1" label="Checkpoint file"/> |
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217 <param name="reuse_step" type="select" label="Checkpoint"> |
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218 <option value="002_depth_filter">002_depth_filter</option> |
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219 <option value="003_overlaps_removed">003_overlaps_removed</option> |
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220 <option value="004_bridges_applied">004_bridges_applied</option> |
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221 </param> |
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222 </repeat> |
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0
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223 </inputs> |
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224 <outputs> |
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225 <data name="assembly_graph" format="gfa1" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> |
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226 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> |
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227 <collection name="spades_collection" type="list" label="${tool.name} on ${on_string}: SPAdes graphs"> |
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228 <discover_datasets pattern="(?P<designation>.*)\.gfa" format="gfa1" directory="spades_graphs"/> |
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229 <filter>keep != "0"</filter> |
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230 </collection> |
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231 <data name="bam_file" format="bam" from_work_dir="read_alignment/long_read_alignments.bam" label="${tool.name} on ${on_string}: Long read alignments BAM"> |
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232 <filter>keep == "2" and long</filter> |
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233 </data> |
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234 </outputs> |
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235 <tests> |
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236 <test expect_num_outputs="2"> |
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237 <conditional name="paired_unpaired"> |
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238 <param name="fastq_input_selector" value="paired" /> |
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239 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
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240 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
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241 </conditional> |
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242 <param name="mode" value="normal" /> |
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243 <param name="min_fasta_length" value="100"/> |
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244 <param name="linear_seqs" value="0"/> |
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245 <section name="spades"> |
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246 <param name="min_kmer_frac" value="0.2"/> |
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247 <param name="max_kmer_frac" value="0.95"/> |
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248 <param name="kmer_count" value="10"/> |
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249 <param name="depth_filter" value="0.25"/> |
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250 </section> |
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251 <section name="rotation"> |
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252 <param name="no_rotate" value=""/> |
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253 <param name="start_gene_id" value="90"/> |
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254 <param name="start_gene_cov" value="95"/> |
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255 </section> |
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256 <section name="graph_clean"> |
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257 <param name="min_component_size" value="1000"/> |
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258 <param name="min_dead_end_size" value="1000"/> |
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259 </section> |
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260 <section name="lr_align"> |
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261 <param name="scores" value="3,-6,-5,-2"/> |
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262 </section> |
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263 <param name="keep" value="0"/> |
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264 <output name="assembly_graph" ftype="gfa1"> |
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265 <assert_contents> |
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266 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
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267 </assert_contents> |
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268 </output> |
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269 <output name="assembly" ftype="fasta"> |
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270 <assert_contents> |
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271 <has_text text="length=5386" /> |
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272 </assert_contents> |
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273 </output> |
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274 </test> |
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275 <!-- |
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276 Following test corresponds to the command: |
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277 |
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278 unicycler -t "${GALAXY_SLOTS:-8}" -o ./ - -verbose 3 - -pilon_path `pilon - -jar_dir` \ |
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279 -1 test-data/phix_f.fq.gz -2 test-data/phix_r.fq.gz -l test-data/onp.fa \ |
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280 - -mode 'normal' - -no_correct |
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281 |
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282 This command causes a segfault with the current version of unicycler on bioconda for Linux |
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283 during the minimap step (which seems to be compiled C code). A gist of the log can be found |
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284 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb. |
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285 --> |
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286 <test expect_num_outputs="2"> |
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287 <conditional name="paired_unpaired"> |
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288 <param name="fastq_input_selector" value="paired" /> |
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289 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger.gz" /> |
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290 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger.gz" /> |
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291 </conditional> |
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292 <param name="long" value="onp.fa" ftype="fasta" /> |
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293 <param name="mode" value="normal" /> |
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294 <param name="min_fasta_length" value="100"/> |
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295 <param name="linear_seqs" value="0"/> |
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296 <section name="spades"> |
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297 <param name="min_kmer_frac" value="0.2"/> |
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298 <param name="max_kmer_frac" value="0.95"/> |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
299 <param name="kmer_count" value="10"/> |
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e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
300 <param name="depth_filter" value="0.25"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
301 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
302 <section name="rotation"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
303 <param name="no_rotate" value=""/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
304 <param name="start_gene_id" value="90"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
305 <param name="start_gene_cov" value="95"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
306 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
307 <section name="graph_clean"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
308 <param name="min_component_size" value="1000"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
309 <param name="min_dead_end_size" value="1000"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
310 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
311 <section name="lr_align"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
312 <param name="scores" value="3,-6,-5,-2"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
313 </section> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
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diff
changeset
|
314 <param name="keep" value="0"/> |
|
8
9e3e80cc4ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
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diff
changeset
|
315 <output name="assembly_graph" ftype="gfa1"> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
316 <assert_contents> |
|
8
9e3e80cc4ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
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diff
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|
317 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
318 </assert_contents> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
319 </output> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
320 <output name="assembly" ftype="fasta"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
321 <assert_contents> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
322 <has_text text="length=5386" /> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
323 </assert_contents> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
324 </output> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
325 </test> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
326 <test expect_num_outputs="2"> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
327 <conditional name="paired_unpaired"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
328 <param name="fastq_input_selector" value="paired_collection"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
329 <param name="fastq_input1"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
330 <collection type="paired"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
331 <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
332 <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
333 </collection> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
334 </param> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
335 </conditional> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
336 <param name="mode" value="normal" /> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
337 <param name="min_fasta_length" value="100"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
338 <param name="linear_seqs" value="0"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
339 <section name="spades"> |
|
e92675014ac9
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_kmer_frac" value="0.2"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
341 <param name="max_kmer_frac" value="0.95"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
342 <param name="kmer_count" value="10"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
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343 <param name="depth_filter" value="0.25"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
344 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
345 <section name="rotation"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
346 <param name="no_rotate" value=""/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
347 <param name="start_gene_id" value="90"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
348 <param name="start_gene_cov" value="95"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
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|
349 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
350 <section name="graph_clean"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
351 <param name="min_component_size" value="1000"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
352 <param name="min_dead_end_size" value="1000"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
353 </section> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
354 <section name="lr_align"> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
355 <param name="scores" value="3,-6,-5,-2"/> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
356 </section> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
357 <param name="keep" value="0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
358 <output name="assembly_graph" ftype="gfa1"> |
|
6e26c9afd301
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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359 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
360 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
361 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
362 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
363 <output name="assembly" ftype="fasta"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
364 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
365 <has_text text="length=5386" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
366 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
367 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
368 </test> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
369 <test expect_num_outputs="2"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
370 <conditional name="paired_unpaired"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
371 <param name="fastq_input_selector" value="none"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
372 </conditional> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
373 <param name="min_anchor_seg_len" value="10"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
374 <section name="spades"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
375 <param name="kmers" value="21,23"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
376 </section> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
377 <param name="long" value="only_long.fasta" ftype="fasta" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
378 <param name="keep" value="0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
379 <output name="assembly_graph" ftype="gfa1"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
380 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
381 <has_text text="S" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
382 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
383 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
384 <output name="assembly" ftype="fasta"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
385 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
386 <has_text text=">1" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
387 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
388 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
389 </test> |
|
11
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
390 <!-- test checkpoint graph reuse |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
391 TODO more precise test and check difference to call wo reuse --> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
392 <test expect_num_outputs="2"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
393 <conditional name="paired_unpaired"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
394 <param name="fastq_input_selector" value="paired_collection"/> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
395 <param name="fastq_input1"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
396 <collection type="paired"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
397 <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
398 <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
399 </collection> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
400 </param> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
401 </conditional> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
402 <param name="long" value="only_long.fasta" ftype="fasta" /> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
403 <repeat name="reuse"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
404 <param name="reuse_file" value="phix__spades_graph.gfa1"/> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
405 <param name="reuse_step" value="002_depth_filter"/> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
406 </repeat> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
407 <param name="keep" value="0"/> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
408 <output name="assembly_graph" ftype="gfa1"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
409 <assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
410 <has_text text="S" /> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
411 </assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
412 </output> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
413 <output name="assembly" ftype="fasta"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
414 <assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
415 <has_text text=">1" /> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
416 </assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
417 </output> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
418 </test> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
419 <!-- Test keep value = 1 --> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
420 <test expect_num_outputs="3"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
421 <conditional name="paired_unpaired"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
422 <param name="fastq_input_selector" value="paired" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
423 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
424 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
425 </conditional> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
426 <param name="mode" value="normal" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
427 <param name="keep" value="1"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
428 <output name="assembly_graph" ftype="gfa1"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
429 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
430 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
431 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
432 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
433 <output name="assembly" ftype="fasta"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
434 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
435 <has_text text="length=5386" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
436 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
437 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
438 <output_collection name="spades_collection" type="list" count="14"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
439 <element name="001_spades_graph_k027"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
440 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
441 <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
442 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
443 </element> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
444 </output_collection> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
445 </test> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
446 <!-- Test keep value = 2 --> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
447 <test expect_num_outputs="4"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
448 <conditional name="paired_unpaired"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
449 <param name="fastq_input_selector" value="paired" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
450 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
451 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
452 </conditional> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
453 <param name="long" value="onp.fa" ftype="fasta" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
454 <param name="mode" value="normal" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
455 <param name="keep" value="2"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
456 <output name="assembly_graph" ftype="gfa1"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
457 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
458 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
459 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
460 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
461 <output name="assembly" ftype="fasta"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
462 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
463 <has_text text="length=5386" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
464 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
465 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
466 <output_collection name="spades_collection" type="list" count="14"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
467 <element name="001_spades_graph_k027"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
468 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
469 <has_text text="TTGAATGCCACCGGAGGCGGCTTTTTGACCGCCTCCAAAC"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
470 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
471 </element> |
|
11
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
472 <!-- there are gfa files for more k that are not tested explicily |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
473 Aim of testing these is to be sure about the names of the graphs, |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
474 since they are used for reuse. Hence if there is a change here |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
475 update reuse accordingly--> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
476 <element name="001_spades_graph_k127"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
477 <assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
478 <has_line_matching expression="^S.*"/> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
479 </assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
480 </element> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
481 <element name="002_depth_filter"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
482 <assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
483 <has_line_matching expression="^S.*"/> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
484 </assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
485 </element> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
486 <element name="003_overlaps_removed"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
487 <assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
488 <has_line_matching expression="^S.*"/> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
489 </assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
490 </element> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
491 <element name="004_bridges_applied"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
492 <assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
493 <has_line_matching expression="^S.*"/> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
494 </assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
495 </element> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
496 <element name="005_final_clean"> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
497 <assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
498 <has_line_matching expression="^S.*"/> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
499 </assert_contents> |
|
8f9f06995f98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c1cd9b717bce328b276f24d910e2e6858585b2cc
iuc
parents:
10
diff
changeset
|
500 </element> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
501 </output_collection> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
502 <output name="bam_file" ftype="bam"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
503 <assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
504 <has_size value="2084" delta="100"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
505 </assert_contents> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
506 </output> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
507 </test> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
508 <!-- Test no simple bridges option --> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
509 <test expect_num_outputs="2"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
510 <conditional name="paired_unpaired"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
511 <param name="fastq_input_selector" value="paired" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
512 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
513 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
514 </conditional> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
515 <param name="long" value="onp.fa" ftype="fasta" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
516 <param name="mode" value="normal" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
517 <param name="keep" value="0"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
518 <section name="lr_align"> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
519 <param name="no_simple_bridges" value="true"/> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
520 </section> |
|
8
9e3e80cc4ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
521 <output name="assembly_graph" ftype="gfa1"> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
522 <assert_contents> |
|
8
9e3e80cc4ad4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents:
7
diff
changeset
|
523 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
524 </assert_contents> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
525 </output> |
|
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
526 <output name="assembly" ftype="fasta"> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
527 <assert_contents> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
528 <has_text text="length=5386" /> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
529 </assert_contents> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
530 </output> |
|
9
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
531 <assert_command> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
532 <has_text text="--no_simple_bridges" /> |
|
6e26c9afd301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d95fed0458171a099928d51e363865783f89717f
iuc
parents:
8
diff
changeset
|
533 </assert_command> |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
534 </test> |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
535 </tests> |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
536 <help><![CDATA[ |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
537 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
538 **Unicycler** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
539 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
540 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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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
541 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
542 .. _`Ryan Wick`: https://github.com/rrwick |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
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543 .. _`github page`: https://github.com/rrwick/Unicycler |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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544 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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545 ----- |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
546 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff
changeset
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547 **Input data** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
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548 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
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549 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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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
550 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
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551 .. _`Sanger encoding`: https://en.wikipedia.org/wiki/FASTQ_format#Quality |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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changeset
|
552 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
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553 The input options are:: |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
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554 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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changeset
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555 -1 SHORT1, --short1 SHORT1 |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
556 FASTQ file of short reads (first reads in each pair) |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
557 -2 SHORT2, --short2 SHORT2 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
558 FASTQ file of short reads (second reads in each pair) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff
changeset
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559 -s SHORT_UNPAIRED, --short_unpaired SHORT_UNPAIRED |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
560 FASTQ file of unpaired short reads |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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561 -l LONG, --long LONG |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
562 FASTQ or FASTA file of long reads, if all reads are available at start. |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
563 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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564 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
565 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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566 **Bridging mode** |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
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567 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
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568 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. |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
569 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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570 .. _`description of modes`: https://github.com/rrwick/Unicycler#conservative-normal-and-bold |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
571 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
572 The available modes are:: |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
573 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
574 --mode {conservative,normal,bold} |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
575 Bridging mode (default: normal) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
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576 conservative = smaller contigs, lowest misassembly rate |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
577 normal = moderate contig size and misassembly rate |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
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578 bold = longest contigs, higher misassembly rate |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
|
579 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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580 ---- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
581 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
582 **Skip SPAdes error correction step** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
583 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
584 Sequencing data contains a substantial number of sequencing errors that manifest themselves as deviations (bulges and non-connected components) within the assembly graph. One of the ways to improve the graph even constructing it is to minimize the amount sequencing errors by performing error correction. SPAdes, which is used by Unicycler for error correction and assembly, uses `BayesHammer`_ to correct the reads. Here is a brief summary of what it does: |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
|
585 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
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586 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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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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587 2. `Hamming graph`_ is constructed for *k*-mers is which *k*-mers are nodes. In this graph edges connect nodes (*k*-mers) is they differ from each other by a number of nucleotides up to a certain threshold (the `Hamming distance`_). The graph is central to the error correction algorithm. |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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588 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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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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589 4. Solid *k*-mers are derived from cluster centers and are assumed to be *error free*. |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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590 5. Solid *k*-mers are mapped back to the reads and used to correct them. |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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|
591 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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592 This step takes considerable time, so if one need to quickly evaluate assemblies this step can be skipped. However, this is not recommended if one if trying to produce a final high quality assembly. |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
|
593 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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changeset
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594 .. _`BayesHammer`: https://goo.gl/1iGkMe |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff
changeset
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595 .. _`Hamming graph`: https://en.wikipedia.org/wiki/Hamming_graph |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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596 .. _`Hamming distance`: https://en.wikipedia.org/wiki/Hamming_distance |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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changeset
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597 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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598 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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changeset
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599 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
|
600 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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601 **Do not rotate completed replicons to start at a standard gene** |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
|
602 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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603 Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence. |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
|
604 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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605 The following option turns rotation on and off:: |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
|
606 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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607 --no_rotate |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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608 Do not rotate completed replicons |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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609 to start at a standard gene |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
610 (default: completed replicons are rotated) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
|
611 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
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changeset
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612 **Do not use Pilon to polish the final assembly** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
613 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
614 `Pilon`_ is a tool for improving overall quality of draft assemblies and finding variation among strains. Unicycler uses it for assembly *polishing*. |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
615 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
616 The following option turns pilon part of Unicycler pipeline on and off:: |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
617 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
618 --no_pilon |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
619 Do not use Pilon to polish the |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
620 final assembly (default: Pilon is used) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
621 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
622 .. _`Pilon`: https://github.com/broadinstitute/pilon/wiki |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
623 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
624 ------ |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
625 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
626 **Expected number of linear sequences** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
627 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
628 If you expect your sample to contain linear (non circular) sequences, set this option:: |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
629 |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
630 --linear_seqs EXPECTED_LINEAR_SEQS |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
631 The expected number of linear (i.e. non-circular) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
632 sequences in the underlying sequence |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
633 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
634 ---- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
635 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
636 **SPAdes options** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
637 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
638 This section provides control of SPAdes options:: |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
639 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
640 --min_kmer_frac MIN_KMER_FRAC |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
641 Lowest k-mer size for SPAdes assembly, |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
642 expressed as a fraction of the read length |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
643 (default: 0.2) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
644 --max_kmer_frac MAX_KMER_FRAC |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
645 Highest k-mer size for SPAdes assembly, |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
646 expressed as a fraction of the read length |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
647 (default: 0.95) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
648 --kmer_count KMER_COUNT |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
649 Number of k-mer steps to use in |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
650 SPAdes assembly (default: 10) |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
651 --depth_filter DEPTH_FILTER |
|
4
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
652 Filter out contigs lower than this fraction |
|
2db911a4efc5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents:
3
diff
changeset
|
653 of the chromosomal depth, if doing so does |
|
2
e92675014ac9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents:
1
diff
changeset
|
654 not result in graph dead ends (default: 0.25) |
|
0
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
655 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
656 ---- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
657 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
658 **Rotation options** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
659 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
660 Unicycler attempts to rotate circular assemblies to make sure that they begin at a consistent starting gene. The following parameters control assembly rotation:: |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
661 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
662 --start_genes START_GENES |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
663 FASTA file of genes for start point |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
664 of rotated replicons |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
665 (default: start_genes.fasta) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
666 --start_gene_id START_GENE_ID |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
667 The minimum required BLAST percent identity |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
668 for a start gene search |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
669 (default: 90.0) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
670 --start_gene_cov START_GENE_COV |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
671 The minimum required BLAST percent coverage |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
672 for a start gene search |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
673 (default: 95.0) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
674 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
675 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
676 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
677 **Graph cleaning options** |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
678 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
679 These options control the removal of small leftover sequences after bridging is complete:: |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
680 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
681 --min_component_size MIN_COMPONENT_SIZE |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
682 Unbridged graph components smaller |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
683 than this size (bp) will be removed |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
684 from the final graph (default: 1000) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
685 --min_dead_end_size MIN_DEAD_END_SIZE |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
686 Graph dead ends smaller than this size (bp) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
687 will be removed from the final graph |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
688 (default: 1000) |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
689 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
690 ----- |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
691 |
|
e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff
changeset
|
692 **Long read alignment options** |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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693 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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694 These options control the alignment of long reads to the assembly graph:: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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695 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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696 --contamination CONTAMINATION |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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697 FASTA file of known contamination in long reads |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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698 --scores SCORES |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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699 Comma-delimited string of alignment scores: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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700 match, mismatch, gap open, gap extend |
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e9c1cdb9f9dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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701 (default: 3,-6,-5,-2) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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702 --low_score LOW_SCORE |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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703 Score threshold - alignments below this |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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704 are considered poor |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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705 (default: set threshold automatically) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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706 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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707 ----- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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708 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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709 **Outputs** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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710 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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711 Galaxy's wrapped for Unicycler produces two outputs: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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712 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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713 * final assembly in FASTA format |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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714 * final assembly grapth in graph format |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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715 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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716 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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717 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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718 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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719 .. _`Bandage`: https://github.com/rrwick/Bandage |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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720 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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721 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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722 ]]></help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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723 <citations> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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724 <citation type="doi">10.1101/096412</citation> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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725 </citations> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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726 </tool> |