Mercurial > repos > iuc > unicycler

annotate unicycler.xml @ 8:f9973e8f6f22 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
author iuc
date Wed, 18 Nov 2020 20:25:42 +0000
parents e3f1860582ca
children def4cbdf745d
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rev   line source
8
f9973e8f6f22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
iuc
parents: 7
diff changeset
1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.0" profile="20.09">
2
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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2 <macros>
7
e3f1860582ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
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3 <token name="@VERSION@">0.4.8</token>
2
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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4 </macros>
7
e3f1860582ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
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5 <edam_topics>
e3f1860582ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
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6 <edam_topic>topic_0196</edam_topic>
e3f1860582ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
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7 </edam_topics>
e3f1860582ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
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8 <edam_operations>
e3f1860582ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
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9 <edam_operation>operation_0525</edam_operation>
e3f1860582ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
iuc
parents: 6
diff changeset
10 </edam_operations>
0
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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11 <requirements>
4
608d1d0ba3a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
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12 <requirement type="package" version="@VERSION@">unicycler</requirement>
0
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
13 </requirements>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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14 <command detect_errors="exit_code"><![CDATA[
2
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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15 ## Preparing files
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
16 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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17 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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18 #set fq1 = "fq1.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
19 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
20 #set fq1 = "fq1.fastq.gz"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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21 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
22 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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23 #set fq2 = "fq2.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
24 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
25 #set fq2 = "fq2.fastq.gz"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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26 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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27 ln -s '${paired_unpaired.fastq_input1}' $fq1 &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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28 ln -s '${paired_unpaired.fastq_input2}' $fq2 &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
29 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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30 #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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31 #set fq1 = "fq1.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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32 #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
33 #set fq1 = "fq1.fastq.gz"
0
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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34 #end if
2
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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35 #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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36 #set fq2 = "fq2.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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37 #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
38 #set fq2 = "fq2.fastq.gz"
0
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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39 #end if
2
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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40 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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41 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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42 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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43 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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44 #set fq = "fq.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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45 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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46 #set fq = "fq.fastq.gz"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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47 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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48 ln -s '${paired_unpaired.fastq_input1}' '$fq' &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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49 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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50 #if $long
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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51 #if $long.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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52 #set lr = "lr.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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53 #elif $long.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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54 #set lr = "lr.fastq.gz"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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55 #elif $long.is_of_type('fasta')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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56 #set lr = "lr.fasta"
0
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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57 #end if
2
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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58 ln -s '${long}' '$lr' &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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59 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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60 ## Get location for pilon installation
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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61 pilon=`pilon --jar_dir` &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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62 ## Running Unicycler
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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63 unicycler -t "\${GALAXY_SLOTS:-4}"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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64 -o ./
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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65 --verbosity 3
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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66 --pilon_path \$pilon
4
608d1d0ba3a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
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67 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
2
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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68 -1 '$fq1'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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69 -2 '$fq2'
4
608d1d0ba3a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
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70 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
608d1d0ba3a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
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71 -1 '$fq1'
608d1d0ba3a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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72 -2 '$fq2'
608d1d0ba3a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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73 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
2
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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74 -s '$fq'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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75 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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76 #if $long
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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77 -l $lr
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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78 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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79 ## General Unicycler Options section
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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80 ## ----------------------------------------------------------
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
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81 --mode '$mode'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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82 --min_fasta_length '$min_fasta_length'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
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83 --linear_seqs '$linear_seqs'
4
608d1d0ba3a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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84 #if str($min_anchor_seg_len) != ''
608d1d0ba3a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
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85 --min_anchor_seg_len '$min_anchor_seg_len'
608d1d0ba3a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
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86 #end if
2
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87 ## Spades Options section
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88 ## ----------------------------------------------------------
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89 $spades.no_correct
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90 --min_kmer_frac '$spades.min_kmer_frac'
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91 --max_kmer_frac '$spades.max_kmer_frac'
4
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92 #if str($spades.kmers) != ''
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93 --kmers '$spades.kmers'
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94 #end if
2
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95 --kmer_count '$spades.kmer_count'
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96 --depth_filter '$spades.depth_filter'
7
e3f1860582ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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97 #if $spades.largest_component
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98 --largest_component
e3f1860582ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f2e4636dbff27bc41f500f31b5500e12f0b56c8"
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99 #end if
2
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100 ## Rotation Options section
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101 ## ----------------------------------------------------------
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102 $rotation.no_rotate
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103 #if $rotation.start_genes
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104 --start_genes '$rotation.start_genes'
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105 #end if
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106 --start_gene_id '$rotation.start_gene_id'
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107 --start_gene_cov '$rotation.start_gene_cov'
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108 ## Pilon Options section
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109 ## ----------------------------------------------------------
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110 $pilon.no_pilon
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111 #if str($pilon.min_polish_size) != ''
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112 --min_polish_size '$pilon.min_polish_size'
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113 #end if
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114 ## Graph cleaning Options sdection
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115 ## ----------------------------------------------------------
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116 --min_component_size '$graph_clean.min_component_size'
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117 --min_dead_end_size '$graph_clean.min_dead_end_size'
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118 ## Long Read Alignment Options
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119 ## ----------------------------------------------------------
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120 #if $lr_align.contamination
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121 --contamination '$lr_align.contamination'
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122 #end if
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123 --scores '${lr_align.scores}'
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124 #if str($lr_align.low_score) != ''
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125 --low_score '$lr_align.low_score'
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126 #end if
0
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127 ]]></command>
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128 <inputs>
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129 <conditional name="paired_unpaired">
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130 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data">
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131 <option selected="True" value="paired">Paired</option>
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132 <option value="paired_collection">Paired Collection</option>
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133 <option value="single">Single</option>
4
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134 <option value="none">None</option>
0
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135 </param>
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136 <when value="paired">
6
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137 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz"
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138 label="Select first set of reads" help="Specify dataset with forward reads"/>
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139 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz"
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140 label="Select second set of reads" help="Specify dataset with reverse reads"/>
0
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141 </when>
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142 <when value="paired_collection">
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143 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
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144 </when>
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145 <when value="single">
6
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146 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz"
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147 label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
0
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148 </when>
4
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149 <when value="none">
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150 </when>
0
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151 </conditional>
2
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152 <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/>
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153 <param argument="--mode" type="select" label="Select Bridging mode">
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154 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option>
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155 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>
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156 <option value="bold">Bold (longest contigs, higher misassembly rate)</option>
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157 </param>
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158 <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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159 <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/>
4
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160 <param argument="--min_anchor_seg_len" type="integer" min="0" optional="true" label="Unicycler will not use segments shorter than this as scaffolding anchors"/>
6
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161 <section name="spades" expanded="False" title="SPAdes options"
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162 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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163 <param argument="--no_correct" type="boolean" checked="false" truevalue="--no_correct" falsevalue=""
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164 label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/>
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165 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2"
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166 label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
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167 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95"
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168 label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
4
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169 <param argument="--kmers" type="text" value="" optional="true" label="Exact k-mers to use for SPAdes assembly, comma-separated">
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170 <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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171 </param>
2
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172 <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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173 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25"
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174 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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175 <param argument="--largest_component" type="boolean" checked="false"
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176 label="Only keep the largest connected component of the assembly graph"/>
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177 </section>
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178 <section name="rotation" expanded="false" title="Rotation options"
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179 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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180 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue=""
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181 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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182 <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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183 <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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184 <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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185 </section>
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186 <section name="pilon" title="Pilon options" expanded="false">
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187 <param argument="--no_pilon" type="boolean" checked="false" truevalue="--no_pilon" falsevalue=""
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188 label="Do not use Pilon to polish the final assembly." help="Unicycler uses Pilon tool for polishing final assembly."/>
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189 <param argument="--min_polish_size" type="integer" min="0" value="1000" label="Contigs shorter than this value (bp) will not be polished using Pilon"/>
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190 </section>
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191 <section name="graph_clean" expanded="false" title="Graph cleaning options"
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192 help="These options control the removal of small leftover sequences after bridging is complete.">
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193 <param argument="--min_component_size" type="integer" min="0" value="1000"
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194 label="Unbridged graph components smaller than this size will be removed from the final graph" />
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195 <param argument="--min_dead_end_size" type="integer" min="0" value="1000"
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196 label="Graph dead ends smaller than this size will be removed from the final graph"/>
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197 </section>
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198 <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph.">
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199 <param argument="--contamination" optional="true" type="data" format="fasta"
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200 label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." />
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201 <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/>
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202 <param argument="--low_score" optional="true" type="integer" value=""
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203 label="Score threshold - alignments below this are considered poor" help="default = set automatically"/>
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204 </section>
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205 </inputs>
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206 <outputs>
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207 <data name="assembly_graph" format="gfa1" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
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208 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>
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209 </outputs>
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210 <tests>
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211 <test>
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212 <conditional name="paired_unpaired">
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213 <param name="fastq_input_selector" value="paired" />
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214 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
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215 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
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216 </conditional>
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217 <param name="mode" value="normal" />
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218 <param name="min_fasta_length" value="100"/>
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219 <param name="linear_seqs" value="0"/>
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220 <section name="spades">
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221 <param name="no_correct" value="true"/>
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222 <param name="min_kmer_frac" value="0.2"/>
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223 <param name="max_kmer_frac" value="0.95"/>
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224 <param name="kmer_count" value="10"/>
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225 <param name="depth_filter" value="0.25"/>
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226 </section>
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227 <section name="rotation">
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228 <param name="no_rotate" value=""/>
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229 <param name="start_gene_id" value="90"/>
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230 <param name="start_gene_cov" value="95"/>
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231 </section>
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232 <section name="pilon">
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233 <param name="no_pilon" value=""/>
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234 <param name="min_polish_size" value="1000"/>
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235 </section>
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236 <section name="graph_clean">
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237 <param name="min_component_size" value="1000"/>
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238 <param name="min_dead_end_size" value="1000"/>
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239 </section>
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240 <section name="lr_align">
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241 <param name="scores" value="3,-6,-5,-2"/>
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242 </section>
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243 <output name="assembly_graph" ftype="gfa1">
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244 <assert_contents>
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245 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/>
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246 </assert_contents>
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247 </output>
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248 <output name="assembly" ftype="fasta">
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249 <assert_contents>
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250 <has_text text="length=5386" />
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251 </assert_contents>
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252 </output>
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253 </test>
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254 <!--
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255 Following test corresponds to the command:
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256
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257 unicycler -t "${GALAXY_SLOTS:-8}" -o ./ - -verbose 3 - -pilon_path `pilon - -jar_dir` \
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258 -1 test-data/phix_f.fq.gz -2 test-data/phix_r.fq.gz -l test-data/onp.fa \
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259 - -mode 'normal' - -no_correct
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260
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261 This command causes a segfault with the current version of unicycler on bioconda for Linux
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262 during the minimap step (which seems to be compiled C code). A gist of the log can be found
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263 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb.
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264 -->
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265 <test>
2
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266 <conditional name="paired_unpaired">
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267 <param name="fastq_input_selector" value="paired" />
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268 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger.gz" />
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269 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger.gz" />
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270 </conditional>
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271 <param name="long" value="onp.fa" ftype="fasta" />
0
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272 <param name="mode" value="normal" />
2
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273 <param name="min_fasta_length" value="100"/>
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274 <param name="linear_seqs" value="0"/>
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275 <section name="spades">
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276 <param name="no_correct" value="true"/>
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277 <param name="min_kmer_frac" value="0.2"/>
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278 <param name="max_kmer_frac" value="0.95"/>
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279 <param name="kmer_count" value="10"/>
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280 <param name="depth_filter" value="0.25"/>
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281 </section>
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282 <section name="rotation">
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283 <param name="no_rotate" value=""/>
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284 <param name="start_gene_id" value="90"/>
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285 <param name="start_gene_cov" value="95"/>
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286 </section>
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287 <section name="pilon">
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288 <param name="no_pilon" value=""/>
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289 <param name="min_polish_size" value="1000"/>
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290 </section>
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291 <section name="graph_clean">
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292 <param name="min_component_size" value="1000"/>
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293 <param name="min_dead_end_size" value="1000"/>
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294 </section>
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295 <section name="lr_align">
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296 <param name="scores" value="3,-6,-5,-2"/>
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297 </section>
8
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298 <output name="assembly_graph" ftype="gfa1">
2
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299 <assert_contents>
8
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300 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/>
2
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301 </assert_contents>
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302 </output>
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303 <output name="assembly" ftype="fasta">
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304 <assert_contents>
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305 <has_text text="length=5386" />
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306 </assert_contents>
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307 </output>
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308 </test>
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309 <test>
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310 <conditional name="paired_unpaired">
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311 <param name="fastq_input_selector" value="paired_collection"/>
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312 <param name="fastq_input1">
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313 <collection type="paired">
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314 <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" />
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315 <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" />
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316 </collection>
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317 </param>
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318 </conditional>
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319 <param name="mode" value="normal" />
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320 <param name="min_fasta_length" value="100"/>
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321 <param name="linear_seqs" value="0"/>
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322 <section name="spades">
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323 <param name="no_correct" value="true"/>
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324 <param name="min_kmer_frac" value="0.2"/>
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325 <param name="max_kmer_frac" value="0.95"/>
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326 <param name="kmer_count" value="10"/>
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327 <param name="depth_filter" value="0.25"/>
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328 </section>
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329 <section name="rotation">
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330 <param name="no_rotate" value=""/>
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331 <param name="start_gene_id" value="90"/>
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332 <param name="start_gene_cov" value="95"/>
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333 </section>
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334 <section name="pilon">
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335 <param name="no_pilon" value="true"/>
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336 <param name="min_polish_size" value="1000"/>
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337 </section>
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338 <section name="graph_clean">
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339 <param name="min_component_size" value="1000"/>
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340 <param name="min_dead_end_size" value="1000"/>
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341 </section>
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342 <section name="lr_align">
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343 <param name="scores" value="3,-6,-5,-2"/>
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344 </section>
8
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345 <output name="assembly_graph" ftype="gfa1">
2
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346 <assert_contents>
8
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347 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/>
2
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348 </assert_contents>
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349 </output>
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350 <output name="assembly" ftype="fasta">
0
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351 <assert_contents>
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352 <has_text text="length=5386" />
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353 </assert_contents>
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354 </output>
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355 </test>
4
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356 <test>
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357 <conditional name="paired_unpaired">
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358 <param name="fastq_input_selector" value="none"/>
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359 </conditional>
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360 <param name="min_anchor_seg_len" value="10"/>
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361 <section name="spades">
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362 <param name="kmers" value="21,23"/>
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363 </section>
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364 <param name="long" value="only_long.fasta" ftype="fasta" />
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365 <output name="assembly_graph" ftype="gfa1">
4
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366 <assert_contents>
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367 <has_text text="S" />
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368 </assert_contents>
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369 </output>
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370 <output name="assembly" ftype="fasta">
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371 <assert_contents>
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372 <has_text text=">1" />
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373 </assert_contents>
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374 </output>
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375 </test>
0
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376 </tests>
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377 <help><![CDATA[
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378
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379 **Unicycler**
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380
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381 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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382
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383 .. _`Ryan Wick`: https://github.com/rrwick
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384 .. _`github page`: https://github.com/rrwick/Unicycler
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385
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386 -----
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387
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388 **Input data**
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389
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390 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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391
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392 .. _`Sanger encoding`: https://en.wikipedia.org/wiki/FASTQ_format#Quality
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393
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394 The input options are::
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395
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396 -1 SHORT1, --short1 SHORT1
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397 FASTQ file of short reads (first reads in each pair)
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398 -2 SHORT2, --short2 SHORT2
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399 FASTQ file of short reads (second reads in each pair)
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400 -s SHORT_UNPAIRED, --short_unpaired SHORT_UNPAIRED
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401 FASTQ file of unpaired short reads
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402 -l LONG, --long LONG
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403 FASTQ or FASTA file of long reads, if all reads are available at start.
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404
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405 -----
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406
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407 **Bridging mode**
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408
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409 Unicycler can be run in three modes: conservative, normal (the default) and bold, set with the --mode option. Conservative mode is least likely to produce a complete assembly but has a very low risk of misassembly. Bold mode is most likely to produce a complete assembly but carries greater risk of misassembly. Normal mode is intermediate regarding both completeness and misassembly risk. See `description of modes`_ for more information.
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410
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411 .. _`description of modes`: https://github.com/rrwick/Unicycler#conservative-normal-and-bold
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412
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413 The available modes are::
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414
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415 --mode {conservative,normal,bold}
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416 Bridging mode (default: normal)
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417 conservative = smaller contigs, lowest misassembly rate
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418 normal = moderate contig size and misassembly rate
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419 bold = longest contigs, higher misassembly rate
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420
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421 ----
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422
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423 **Skip SPAdes error correction step**
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424
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425 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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426
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427 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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428 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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429 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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430 4. Solid *k*-mers are derived from cluster centers and are assumed to be *error free*.
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diff changeset
431 5. Solid *k*-mers are mapped back to the reads and used to correct them.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
432
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
433 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.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
434
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
435 .. _`BayesHammer`: https://goo.gl/1iGkMe
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
436 .. _`Hamming graph`: https://en.wikipedia.org/wiki/Hamming_graph
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
437 .. _`Hamming distance`: https://en.wikipedia.org/wiki/Hamming_distance
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
438
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
439 This following option turns error correction on and off::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
440
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
441 --no_correct
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
442 Skip SPAdes error correction step
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
443 (default: conduct SPAdes error correction)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
444
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
445 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
446
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
447 **Do not rotate completed replicons to start at a standard gene**
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
448
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
449 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.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
450
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
451 The following option turns rotation on and off::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
452
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
453 --no_rotate
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
454 Do not rotate completed replicons
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
455 to start at a standard gene
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
456 (default: completed replicons are rotated)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
457
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
458 **Do not use Pilon to polish the final assembly**
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
459
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
460 `Pilon`_ is a tool for improving overall quality of draft assemblies and finding variation among strains. Unicycler uses it for assembly *polishing*.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
461
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
462 The following option turns pilon part of Unicycler pipeline on and off::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
463
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
464 --no_pilon
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
465 Do not use Pilon to polish the
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
466 final assembly (default: Pilon is used)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
467
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
468 .. _`Pilon`: https://github.com/broadinstitute/pilon/wiki
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
469
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
470 ------
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
471
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
472 **Expected number of linear sequences**
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
473
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
474 If you expect your sample to contain linear (non circular) sequences, set this option::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
475
2
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
476 --linear_seqs EXPECTED_LINEAR_SEQS
0
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
477 The expected number of linear (i.e. non-circular)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
478 sequences in the underlying sequence
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
479
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
480 ----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
481
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
482 **SPAdes options**
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
483
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
484 This section provides control of SPAdes options::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
485
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
486 --min_kmer_frac MIN_KMER_FRAC
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
487 Lowest k-mer size for SPAdes assembly,
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
488 expressed as a fraction of the read length
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
489 (default: 0.2)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
490 --max_kmer_frac MAX_KMER_FRAC
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
491 Highest k-mer size for SPAdes assembly,
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
492 expressed as a fraction of the read length
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
493 (default: 0.95)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
494 --kmer_count KMER_COUNT
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
495 Number of k-mer steps to use in
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
496 SPAdes assembly (default: 10)
2
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
497 --depth_filter DEPTH_FILTER
4
608d1d0ba3a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
498 Filter out contigs lower than this fraction
608d1d0ba3a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit c9e02d7a4de4bda4809f6c7006990901602cc3ad
iuc
parents: 3
diff changeset
499 of the chromosomal depth, if doing so does
2
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
iuc
parents: 1
diff changeset
500 not result in graph dead ends (default: 0.25)
0
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
501
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
502 ----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
503
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
504 **Rotation options**
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
505
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
506 Unicycler attempts to rotate circular assemblies to make sure that they begin at a consistent starting gene. The following parameters control assembly rotation::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
507
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
508 --start_genes START_GENES
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
509 FASTA file of genes for start point
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
510 of rotated replicons
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
511 (default: start_genes.fasta)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
512 --start_gene_id START_GENE_ID
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
513 The minimum required BLAST percent identity
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
514 for a start gene search
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
515 (default: 90.0)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
516 --start_gene_cov START_GENE_COV
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
517 The minimum required BLAST percent coverage
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
518 for a start gene search
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
519 (default: 95.0)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
520
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
521 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
522
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
523 **Graph cleaning options**
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
524
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
525 These options control the removal of small leftover sequences after bridging is complete::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
526
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
527 --min_component_size MIN_COMPONENT_SIZE
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
528 Unbridged graph components smaller
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
529 than this size (bp) will be removed
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
530 from the final graph (default: 1000)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
531 --min_dead_end_size MIN_DEAD_END_SIZE
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
532 Graph dead ends smaller than this size (bp)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
533 will be removed from the final graph
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
534 (default: 1000)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
535
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
536 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
537
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
538 **Long read alignment options**
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
539
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
540 These options control the alignment of long reads to the assembly graph::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
541
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
542 --contamination CONTAMINATION
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
543 FASTA file of known contamination in long reads
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
544 --scores SCORES
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
545 Comma-delimited string of alignment scores:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
546 match, mismatch, gap open, gap extend
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
547 (default: 3,-6,-5,-2)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
548 --low_score LOW_SCORE
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
549 Score threshold - alignments below this
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
550 are considered poor
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
551 (default: set threshold automatically)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
552
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
553 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
554
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
555 **Outputs**
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
556
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
557 Galaxy's wrapped for Unicycler produces two outputs:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
558
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
559 * final assembly in FASTA format
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
560 * final assembly grapth in graph format
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
561
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
562 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`_.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
563
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
564
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
565 .. _`Bandage`: https://github.com/rrwick/Bandage
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
566
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
567
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
568 ]]></help>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
569 <citations>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
570 <citation type="doi">10.1101/096412</citation>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
571 </citations>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
572 </tool>