Mercurial > repos > iuc > disco
annotate disco.xml @ 2:dfefaf2bab95 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
author | iuc |
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date | Sun, 18 Apr 2021 17:48:28 +0000 |
parents | 6d447ebb2bf4 |
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rev | line source |
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2
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
0
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1 <tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.1" profile="20.01"> |
0
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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2 <description>to assemble metagenomics data using an overlap-layout-consensus (OLC) approach</description> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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3 <macros> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
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4 <token name="@WRAPPER_VERSION@">1.2</token> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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5 <xml name="assembly_params"> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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6 <param argument="minSequenceLengthTobePrinted" type="integer" value="1000" min="0" label="Minimum length of contigs or scaffolds to be printed"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
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7 <param argument="MinOverlap4SimplifyGraph" type="integer" value="30" min="0" label="Minimum overlap length (bp) required to keep an edge between two reads during graph simplification" help="This minimum overlap length must be equal to 30 or larger than the MinOverlap4BuildGraph above. This allows you to try different minimum overlap lengths for assembly without redoing assembly graph construction. Edges with shorter overlap length than this parameter will be ignored during graph simplification. Increase this to reduce N50 and mis-assemblies"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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8 <param argument="minOverlapDifference4ClipBranches" type="integer" value="25" min="0" label="Minimum overlap length difference (bp) to clip branches" help="If a read has multiple edges, Disco clips the branches with overlap lengths less than the largest overlap of this read by this difference or more. Increase this to reduce N50 and mis-assemblies"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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9 <param argument="minUniquePEsupport" type="integer" value="3" min="0" label="Minumum number of paired-end reads that provide unique support to merge two edges" help="Increase this to reduce N50 and mis-assemblies"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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10 <param argument="minNonUniquePEsupport" type="integer" value="0" min="0" label="Minumum number of paired-end reads that provide non-unique support to merge two edgess"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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11 <param argument="minReadsCountInEdgeToBeNotDeadEnd" type="integer" value="10" min="0" label="Minimum number of reads in an edge to be not dead-end edge"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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12 <param argument="minEdgeLengthToBeNotDeadEnd" type="integer" value="1000" min="0" label="Minimum edge length (bp) to be not dead-end edge"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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13 <param argument="minFoldToBeShortBranch" type="integer" value="5" min="0" label="Minimum fold difference between two branches' lengths to consider a branch to be short"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
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14 <param argument="minReadsCountToHave0Flow" type="integer" value="15" min="0" label="Minimum number of reads for an edge to be kept even if it has 0 flow"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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15 <param argument="minEdgeLengthToHave0Flow" type="integer" value="1500" min="0" label="Minimum edge length for an edge to be kept even if it has 0 flow"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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16 <param argument="minReadsCountInEdgeToBe1MinFlow" type="integer" value="20" min="0" label="Minimum number of reads in an edge to be assigned with 1 minimum flow"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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17 <param argument="minEdgeLengthToBe1MinFlow" type="integer" value="2000" min="0" label="Minimum edge length to be assigned with 1 minimum flow"/> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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18 </xml> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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19 </macros> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
changeset
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20 <requirements> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
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21 <requirement type="package" version="@WRAPPER_VERSION@">disco</requirement> |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff
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22 </requirements> |
2
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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23 <version_command>echo @WRAPPER_VERSION@</version_command> |
0
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
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24 <command detect_errors="exit_code"><![CDATA[ |
2
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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25 #if $input_cond.library_type == "single" |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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26 #for i, e in enumerate($input_cond.inS) |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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27 cp '$e' |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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28 #if $e.ext.endswith(".gz") |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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29 input_${i}.fastq.gz && |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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30 #else |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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31 input_${i}.fastq && |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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32 #end if |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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33 #end for |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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34 #else |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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35 #if $input_cond.paired_input.type == "separated" |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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36 #if $input_cond.paired_input.in1.ext.endswith(".gz") |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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37 cp '$input_cond.paired_input.in1' forward.fastq.gz && |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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38 cp '$input_cond.paired_input.in2' reverse.fastq.gz && |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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39 #else |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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40 cp '$input_cond.paired_input.in1' forward.fastq && |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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41 cp '$input_cond.paired_input.in2' reverse.fastq && |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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42 #end if |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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43 #else |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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44 #for i, e in enumerate($input_cond.paired_input.inP) |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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45 cp '$e' |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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46 #if $e.ext.endswith(".gz") |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents:
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47 input_${i}.fastq.gz && |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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48 #else |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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49 input_${i}.fastq && |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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50 #end if |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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51 #end for |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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52 #end if |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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53 #end if |
0
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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54 runDisco.sh |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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55 -n \${GALAXY_SLOTS:-4} |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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56 -m \${DISCO_MAX_MEMORY:-4} |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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57 -d . |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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58 -o disco |
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dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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59 #if $input_cond.library_type == "single" |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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60 -inS \$(find . -name "*fastq*" -print | tr '\n' ',' | sed 's/,$//') |
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6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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61 #else |
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dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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62 #if $input_cond.paired_input.type == "separated" |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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63 #if $input_cond.paired_input.in1.ext.endswith(".gz") |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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64 -in1 forward.fastq.gz |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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65 -in2 reverse.fastq.gz |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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66 #else |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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67 -in1 forward.fastq |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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68 -in2 reverse.fastq |
dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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69 #end if |
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6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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70 #else |
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dfefaf2bab95
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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71 -inP \$(find . -name "*fastq*" -print | tr '\n' ',' | sed 's/,$//') |
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6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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72 #end if |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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73 #end if |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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74 $obg |
6d447ebb2bf4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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75 $osg |
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76 -p '$first_assembly_iteration_params' |
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77 -p2 '$second_assembly_iteration_params' |
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78 -p3 '$third_assembly_iteration_params' |
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79 ]]></command> |
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80 <configfiles> |
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81 <configfile name="first_assembly_iteration_params"> |
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82 <![CDATA[ |
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83 MinOverlap4BuildGraph = $MinOverlap4BuildGraph |
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84 PrintContigs = true |
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85 PrintScaffolds = true |
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86 PrintUnused = $PrintUnused |
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87 PrintGFA = $PrintGFA |
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88 PrintGFA2 = $PrintGFA2 |
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89 minSequenceLengthTobePrinted = $first_assembly_iter_param.minSequenceLengthTobePrinted |
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90 MinOverlap4SimplifyGraph = $first_assembly_iter_param.MinOverlap4SimplifyGraph |
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91 minOverlapDifference4ClipBranches = $first_assembly_iter_param.minOverlapDifference4ClipBranches |
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92 minUniquePEsupport = $first_assembly_iter_param.minUniquePEsupport |
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93 minNonUniquePEsupport = $first_assembly_iter_param.minNonUniquePEsupport |
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94 minReadsCountInEdgeToBeNotDeadEnd = $first_assembly_iter_param.minReadsCountInEdgeToBeNotDeadEnd |
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95 minEdgeLengthToBeNotDeadEnd = $first_assembly_iter_param.minEdgeLengthToBeNotDeadEnd |
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96 minFoldToBeShortBranch = $first_assembly_iter_param.minFoldToBeShortBranch |
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97 minReadsCountToHave0Flow = $first_assembly_iter_param.minReadsCountToHave0Flow |
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98 minEdgeLengthToHave0Flow = $first_assembly_iter_param.minEdgeLengthToHave0Flow |
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99 minReadsCountInEdgeToBe1MinFlow = $first_assembly_iter_param.minReadsCountInEdgeToBe1MinFlow |
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100 minEdgeLengthToBe1MinFlow = $first_assembly_iter_param.minEdgeLengthToBe1MinFlow |
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101 ]]></configfile> |
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102 <configfile name="second_assembly_iteration_params"> |
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103 <![CDATA[ |
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104 MinOverlap4BuildGraph = $MinOverlap4BuildGraph |
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105 PrintContigs = true |
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106 PrintScaffolds = true |
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107 PrintUnused = $PrintUnused |
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108 PrintGFA = $PrintGFA |
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109 PrintGFA2 = $PrintGFA2 |
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110 minSequenceLengthTobePrinted = $second_assembly_iter_param.minSequenceLengthTobePrinted |
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111 MinOverlap4SimplifyGraph = $second_assembly_iter_param.MinOverlap4SimplifyGraph |
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112 minOverlapDifference4ClipBranches = $second_assembly_iter_param.minOverlapDifference4ClipBranches |
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113 minUniquePEsupport = $second_assembly_iter_param.minUniquePEsupport |
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114 minNonUniquePEsupport = $second_assembly_iter_param.minNonUniquePEsupport |
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115 minReadsCountInEdgeToBeNotDeadEnd = $second_assembly_iter_param.minReadsCountInEdgeToBeNotDeadEnd |
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116 minEdgeLengthToBeNotDeadEnd = $second_assembly_iter_param.minEdgeLengthToBeNotDeadEnd |
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117 minFoldToBeShortBranch = $second_assembly_iter_param.minFoldToBeShortBranch |
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118 minReadsCountToHave0Flow = $second_assembly_iter_param.minReadsCountToHave0Flow |
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119 minEdgeLengthToHave0Flow = $second_assembly_iter_param.minEdgeLengthToHave0Flow |
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120 minReadsCountInEdgeToBe1MinFlow = $second_assembly_iter_param.minReadsCountInEdgeToBe1MinFlow |
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121 minEdgeLengthToBe1MinFlow = $second_assembly_iter_param.minEdgeLengthToBe1MinFlow |
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122 ]]></configfile> |
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123 <configfile name="third_assembly_iteration_params"> |
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124 <![CDATA[ |
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125 MinOverlap4BuildGraph = $MinOverlap4BuildGraph |
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126 PrintContigs = true |
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127 PrintScaffolds = true |
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128 PrintUnused = $PrintUnused |
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129 PrintGFA = $PrintGFA |
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130 PrintGFA2 = $PrintGFA2 |
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131 minSequenceLengthTobePrinted = $third_assembly_iter_param.minSequenceLengthTobePrinted |
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132 MinOverlap4SimplifyGraph = $third_assembly_iter_param.MinOverlap4SimplifyGraph |
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133 minOverlapDifference4ClipBranches = $third_assembly_iter_param.minOverlapDifference4ClipBranches |
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134 minUniquePEsupport = $third_assembly_iter_param.minUniquePEsupport |
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135 minNonUniquePEsupport = $third_assembly_iter_param.minNonUniquePEsupport |
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136 minReadsCountInEdgeToBeNotDeadEnd = $third_assembly_iter_param.minReadsCountInEdgeToBeNotDeadEnd |
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137 minEdgeLengthToBeNotDeadEnd = $third_assembly_iter_param.minEdgeLengthToBeNotDeadEnd |
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138 minFoldToBeShortBranch = $third_assembly_iter_param.minFoldToBeShortBranch |
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139 minReadsCountToHave0Flow = $third_assembly_iter_param.minReadsCountToHave0Flow |
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140 minEdgeLengthToHave0Flow = $third_assembly_iter_param.minEdgeLengthToHave0Flow |
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141 minReadsCountInEdgeToBe1MinFlow = $third_assembly_iter_param.minReadsCountInEdgeToBe1MinFlow |
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142 minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow |
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143 ]]></configfile> |
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144 </configfiles> |
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145 <inputs> |
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146 <conditional name="input_cond"> |
0
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147 <param name="library_type" type="select" label="Type of library?"> |
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148 <option value="single">Single-end reads</option> |
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149 <option value="paired">Paired-end reads</option> |
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150 </param> |
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151 <when value="single"> |
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152 <param argument="-inS" type="data" format="fastq,fastq.gz,fasta" multiple="true" label="Single-read files"/> |
0
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153 </when> |
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154 <when value="paired"> |
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155 <conditional name="paired_input"> |
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156 <param name="type" type="select" label="Type of library?"> |
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157 <option value="separated">Separated forward/reverse paired-read files</option> |
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158 <option value="interleaved">Interleaved paired-read files</option> |
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159 </param> |
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160 <when value="separated"> |
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161 <param argument="-in1" type="data" format="fastq,fastq.gz,fasta" label="Forward read file" /> |
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162 <param argument="-in2" type="data" format="fastq,fastq.gz,fasta" label="Reverse read file" /> |
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163 </when> |
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164 <when value="interleaved"> |
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165 <param argument="-inP" type="data" format="fastq,fastq.gz,fasta" multiple="true" label="Interleaved paired-read files" /> |
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166 </when> |
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167 </conditional> |
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168 </when> |
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169 </conditional> |
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170 <param argument="-obg" type="boolean" truevalue="-obg" falsevalue="" checked="false" label="Only build overlap graph?"/> |
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171 <param argument="-osg" type="boolean" truevalue="-osg" falsevalue="" checked="false" label="Only simplify existing overlap graph?"/> |
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172 <param argument="MinOverlap4BuildGraph" type="integer" min="0" value="20" label="Minimum overlap length (bp) required to insert an edge between two reads during graph construction" help="Increase this to reduce N50 and mis-assemblies"/> |
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173 <param name="log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log file?"/> |
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174 <param argument="PrintScaffolds" type="boolean" truevalue="true" falsevalue="false" label="Print scaffolds?"/> |
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175 <param argument="PrintUnused" type="boolean" truevalue="true" falsevalue="false" label="Print unused reads?"/> |
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176 <param argument="PrintGFA" type="boolean" truevalue="true" falsevalue="false" label="Print GFA graph format?"/> |
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177 <param argument="PrintGFA2" type="boolean" truevalue="true" falsevalue="false" label="Print GFA2 graph format?"/> |
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178 <section name="first_assembly_iter_param" title="Parameters for 1st assembly iteration" expanded="False"> |
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179 <expand macro="assembly_params"/> |
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180 </section> |
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181 <section name="second_assembly_iter_param" title="Parameters for 2nd assembly iteration" expanded="False"> |
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182 <expand macro="assembly_params"/> |
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183 </section> |
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184 <section name="third_assembly_iter_param" title="Parameters for 3rd assembly iteration" expanded="False"> |
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185 <expand macro="assembly_params"/> |
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186 </section> |
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187 </inputs> |
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188 <outputs> |
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189 <data format="txt" name="log" from_work_dir="disco.log" label="${tool.name} on ${on_string}: Log file"> |
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190 <filter>log</filter> |
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191 </data> |
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192 <data format="fasta" name="contigs" from_work_dir="disco_contigsFinalCombined.fasta" label="${tool.name} on ${on_string}: Contigs"/> |
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193 <data format="fasta" name="scaffolds" from_work_dir="disco_scaffoldsFinalCombined.fasta" label="${tool.name} on ${on_string}: Scaffolds"/> |
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194 <collection name="unused_reads" type="list" label="${tool.name} on ${on_string}: Unused reads"> |
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195 <filter>PrintUnused</filter> |
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196 <discover_datasets pattern="disco_0_Unused(?P<designation>.+)\.fasta" format="fasta" directory="assembly" /> |
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197 </collection> |
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198 <collection name="gfa_graphs" type="list" label="${tool.name} on ${on_string}: GFA graph"> |
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199 <filter>PrintGFA</filter> |
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200 <discover_datasets pattern="disco_Graph_(?P<designation>.+)\.gfa" format="txt" directory="assembly" /> |
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201 </collection> |
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202 <collection name="gfa2_graphs" type="list" label="${tool.name} on ${on_string}: GFA2 graph"> |
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203 <filter>PrintGFA2</filter> |
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204 <discover_datasets pattern="disco_Graph_(?P<designation>.+)\.gfa2" format="txt" directory="assembly" /> |
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205 </collection> |
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206 </outputs> |
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207 <tests> |
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208 <test> |
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209 <conditional name="input_cond"> |
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210 <param name="library_type" value="paired"/> |
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211 <conditional name="paired_input"> |
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212 <param name="type" value="separated"/> |
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213 <param name="in1" value="ecoli_1K_1.fq"/> |
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214 <param name="in2" value="ecoli_1K_2.fq"/> |
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215 </conditional> |
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216 </conditional> |
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217 <param name="obg" value=""/> |
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218 <param name="osg" value=""/> |
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219 <param name="MinOverlap4BuildGraph" value="20"/> |
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220 <param name="log" value="true"/> |
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221 <param name="PrintUnused" value="true"/> |
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222 <param name="PrintGFA" value="true"/> |
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223 <param name="PrintGFA2" value="true"/> |
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224 <section name="first_assembly_iter_param"> |
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225 <param name="minSequenceLengthTobePrinted" value="1000"/> |
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226 <param name="MinOverlap4SimplifyGraph" value="30"/> |
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227 <param name="minOverlapDifference4ClipBranches" value="25"/> |
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228 <param name="minUniquePEsupport" value="3"/> |
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229 <param name="minNonUniquePEsupport" value="0"/> |
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230 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/> |
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231 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/> |
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232 <param name="minFoldToBeShortBranch" value="5"/> |
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233 <param name="minReadsCountToHave0Flow" value="15"/> |
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234 <param name="minEdgeLengthToHave0Flow" value="1500"/> |
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235 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/> |
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236 <param name="minEdgeLengthToBe1MinFlow" value="2000"/> |
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237 </section> |
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238 <section name="second_assembly_iter_param"> |
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239 <param name="minSequenceLengthTobePrinted" value="1000"/> |
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240 <param name="MinOverlap4SimplifyGraph" value="30"/> |
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241 <param name="minOverlapDifference4ClipBranches" value="25"/> |
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242 <param name="minUniquePEsupport" value="3"/> |
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243 <param name="minNonUniquePEsupport" value="0"/> |
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244 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/> |
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245 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/> |
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246 <param name="minFoldToBeShortBranch" value="5"/> |
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247 <param name="minReadsCountToHave0Flow" value="15"/> |
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248 <param name="minEdgeLengthToHave0Flow" value="1500"/> |
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249 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/> |
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250 <param name="minEdgeLengthToBe1MinFlow" value="2000"/> |
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251 </section> |
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252 <section name="third_assembly_iter_param"> |
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253 <param name="minSequenceLengthTobePrinted" value="1000"/> |
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254 <param name="MinOverlap4SimplifyGraph" value="30"/> |
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255 <param name="minOverlapDifference4ClipBranches" value="25"/> |
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256 <param name="minUniquePEsupport" value="3"/> |
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257 <param name="minNonUniquePEsupport" value="0"/> |
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258 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/> |
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259 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/> |
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260 <param name="minFoldToBeShortBranch" value="5"/> |
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261 <param name="minReadsCountToHave0Flow" value="15"/> |
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262 <param name="minEdgeLengthToHave0Flow" value="1500"/> |
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263 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/> |
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264 <param name="minEdgeLengthToBe1MinFlow" value="2000"/> |
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265 </section> |
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266 <output name="log"> |
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267 <assert_contents> |
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268 <has_text text="Software: Disco Assembler" /> |
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269 <has_text text="FIRST LOOP ITERATION 1" /> |
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270 <has_text text="2054 reads streamed from this read file" /> |
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271 <has_text text="Graph simplification" /> |
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272 </assert_contents> |
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273 </output> |
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274 <output name="contigs" value="test1_contigs.fasta" compare="sim_size" delta="5"/> |
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275 <output name="scaffolds" value="test1_scaffolds.fasta" compare="sim_size" delta="5"/> |
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276 <output_collection name="unused_reads" type="list"> |
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277 <element name="PairedReads1"> |
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278 <assert_contents> |
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279 <has_text text="EAS20_8_6_1_9_1972/1" /> |
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280 <has_text text="EAS20_8_6_10_415_709/1" /> |
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281 <has_text text="EAS20_8_6_36_1124_470/1" /> |
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282 <has_text text="EAS20_8_6_100_1637_1332/1" /> |
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283 </assert_contents> |
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284 </element> |
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285 <element name="PairedReads2"> |
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286 <assert_contents> |
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287 <has_text text="EAS20_8_6_1_9_1972/2" /> |
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288 <has_text text="EAS20_8_6_10_415_709/2" /> |
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289 <has_text text="EAS20_8_6_36_1124_470/2" /> |
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290 <has_text text="EAS20_8_6_100_1637_1332/2" /> |
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291 </assert_contents> |
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292 </element> |
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293 </output_collection> |
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294 <output_collection name="gfa_graphs" type="list"> |
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295 <element name="1" file="test1_graph_1.gfa" compare="sim_size" delta="6000"/> |
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296 </output_collection> |
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297 <output_collection name="gfa2_graphs" type="list"> |
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298 <element name="1" file="test1_graph_1.gfa2" compare="sim_size" delta="6000"/> |
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299 </output_collection> |
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300 </test> |
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301 <test> |
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302 <conditional name="input_cond"> |
0
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303 <param name="library_type" value="paired"/> |
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304 <conditional name="paired_input"> |
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305 <param name="type" value="interleaved"/> |
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306 <param name="inP" value="ecoli_1K_interleaved.fq,ecoli_1K_interleaved.fq"/> |
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307 </conditional> |
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308 </conditional> |
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309 <param name="obg" value=""/> |
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310 <param name="osg" value=""/> |
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311 <param name="MinOverlap4BuildGraph" value="20"/> |
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312 <param name="log" value="true"/> |
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313 <param name="PrintUnused" value="false"/> |
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314 <param name="PrintGFA" value="false"/> |
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315 <param name="PrintGFA2" value="false"/> |
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316 <section name="first_assembly_iter_param"> |
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317 <param name="minSequenceLengthTobePrinted" value="1000"/> |
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318 <param name="MinOverlap4SimplifyGraph" value="30"/> |
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319 <param name="minOverlapDifference4ClipBranches" value="25"/> |
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320 <param name="minUniquePEsupport" value="3"/> |
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321 <param name="minNonUniquePEsupport" value="0"/> |
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322 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/> |
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323 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/> |
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324 <param name="minFoldToBeShortBranch" value="5"/> |
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325 <param name="minReadsCountToHave0Flow" value="15"/> |
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326 <param name="minEdgeLengthToHave0Flow" value="1500"/> |
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327 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/> |
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328 <param name="minEdgeLengthToBe1MinFlow" value="2000"/> |
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329 </section> |
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330 <section name="second_assembly_iter_param"> |
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331 <param name="minSequenceLengthTobePrinted" value="1000"/> |
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332 <param name="MinOverlap4SimplifyGraph" value="30"/> |
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333 <param name="minOverlapDifference4ClipBranches" value="25"/> |
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334 <param name="minUniquePEsupport" value="3"/> |
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335 <param name="minNonUniquePEsupport" value="0"/> |
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336 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/> |
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337 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/> |
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338 <param name="minFoldToBeShortBranch" value="5"/> |
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339 <param name="minReadsCountToHave0Flow" value="15"/> |
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340 <param name="minEdgeLengthToHave0Flow" value="1500"/> |
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341 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/> |
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342 <param name="minEdgeLengthToBe1MinFlow" value="2000"/> |
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343 </section> |
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344 <section name="third_assembly_iter_param"> |
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345 <param name="minSequenceLengthTobePrinted" value="1000"/> |
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346 <param name="MinOverlap4SimplifyGraph" value="30"/> |
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347 <param name="minOverlapDifference4ClipBranches" value="25"/> |
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348 <param name="minUniquePEsupport" value="3"/> |
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349 <param name="minNonUniquePEsupport" value="0"/> |
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350 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/> |
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351 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/> |
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352 <param name="minFoldToBeShortBranch" value="5"/> |
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353 <param name="minReadsCountToHave0Flow" value="15"/> |
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354 <param name="minEdgeLengthToHave0Flow" value="1500"/> |
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355 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/> |
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356 <param name="minEdgeLengthToBe1MinFlow" value="2000"/> |
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357 </section> |
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358 <output name="log"> |
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359 <assert_contents> |
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360 <has_text text="Software: Disco Assembler" /> |
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361 <has_text text="FIRST LOOP ITERATION 1" /> |
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362 <has_text text="4108 reads streamed from this read file" /> |
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363 <has_text text="Graph simplification" /> |
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364 </assert_contents> |
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365 </output> |
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366 <output name="contigs" value="test2_contigs.fasta" compare="sim_size" delta="5"/> |
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367 <output name="scaffolds" value="test2_scaffolds.fasta" compare="sim_size" delta="5"/> |
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368 </test> |
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369 <test> |
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370 <conditional name="input_cond"> |
0
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371 <param name="library_type" value="single"/> |
2
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372 <param name="inS" value="ecoli_1K_1.fq.gz" ftype="fastq.gz"/> |
0
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373 </conditional> |
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374 <param name="obg" value=""/> |
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375 <param name="osg" value=""/> |
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376 <param name="MinOverlap4BuildGraph" value="20"/> |
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377 <param name="log" value="false"/> |
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378 <param name="PrintUnused" value="false"/> |
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379 <param name="PrintGFA" value="false"/> |
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380 <param name="PrintGFA2" value="false"/> |
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381 <section name="first_assembly_iter_param"> |
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382 <param name="minSequenceLengthTobePrinted" value="1000"/> |
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383 <param name="MinOverlap4SimplifyGraph" value="30"/> |
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384 <param name="minOverlapDifference4ClipBranches" value="25"/> |
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385 <param name="minUniquePEsupport" value="3"/> |
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386 <param name="minNonUniquePEsupport" value="0"/> |
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387 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/> |
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388 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/> |
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389 <param name="minFoldToBeShortBranch" value="5"/> |
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390 <param name="minReadsCountToHave0Flow" value="15"/> |
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391 <param name="minEdgeLengthToHave0Flow" value="1500"/> |
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392 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/> |
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393 <param name="minEdgeLengthToBe1MinFlow" value="2000"/> |
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394 </section> |
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395 <section name="second_assembly_iter_param"> |
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396 <param name="minSequenceLengthTobePrinted" value="1000"/> |
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397 <param name="MinOverlap4SimplifyGraph" value="30"/> |
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398 <param name="minOverlapDifference4ClipBranches" value="25"/> |
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399 <param name="minUniquePEsupport" value="3"/> |
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400 <param name="minNonUniquePEsupport" value="0"/> |
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401 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/> |
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402 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/> |
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403 <param name="minFoldToBeShortBranch" value="5"/> |
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404 <param name="minReadsCountToHave0Flow" value="15"/> |
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405 <param name="minEdgeLengthToHave0Flow" value="1500"/> |
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406 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/> |
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407 <param name="minEdgeLengthToBe1MinFlow" value="2000"/> |
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408 </section> |
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409 <section name="third_assembly_iter_param"> |
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410 <param name="minSequenceLengthTobePrinted" value="1000"/> |
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411 <param name="MinOverlap4SimplifyGraph" value="30"/> |
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412 <param name="minOverlapDifference4ClipBranches" value="25"/> |
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413 <param name="minUniquePEsupport" value="3"/> |
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414 <param name="minNonUniquePEsupport" value="0"/> |
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415 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/> |
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416 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/> |
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417 <param name="minFoldToBeShortBranch" value="5"/> |
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418 <param name="minReadsCountToHave0Flow" value="15"/> |
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419 <param name="minEdgeLengthToHave0Flow" value="1500"/> |
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420 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/> |
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421 <param name="minEdgeLengthToBe1MinFlow" value="2000"/> |
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422 </section> |
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423 <output name="contigs" value="test3_contigs.fasta" compare="sim_size" delta="5"/> |
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424 <output name="scaffolds" value="test3_scaffolds.fasta" compare="sim_size" delta="5"/> |
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425 </test> |
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426 </tests> |
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427 <help><![CDATA[ |
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428 DISCO is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler. Disco was developed as a scalable assembler to assemble large metagenomes from billions of Illumina sequencing reads of complex microbial communities. Disco was parallelized for computer clusters in a hybrid architecture that integrated shared-memory multi-threading, point-to-point message passing, and remote direct memory access. The assembly and scaffolding were performed using an iterative overlap graph approach. |
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429 |
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430 The detailed user manual of the assembler and how to use it to acheive best results is provided here: |
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431 http://disco.omicsbio.org/user-manual. This is a quick start guide generally for developers and testers. Users with limited experience with genome assembly are advised to use the user manual. |
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432 ]]></help> |
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433 <citations> |
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434 </citations> |
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435 </tool> |