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annotate disco.xml @ 2:56b0772e3379 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
author iuc
date Sun, 18 Apr 2021 17:47:56 +0000
parents 3c16cb5b2b5b
children b6d2f5be3f88
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2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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1 <tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.1" profile="20.01">
0
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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2 <description>to assemble metagenomics data using an overlap-layout-consensus (OLC) approach</description>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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3 <macros>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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4 <token name="@WRAPPER_VERSION@">1.2</token>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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5 <xml name="assembly_params">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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6 <param argument="minSequenceLengthTobePrinted" type="integer" value="1000" min="0" label="Minimum length of contigs or scaffolds to be printed"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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18 </xml>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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19 </macros>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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20 <requirements>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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21 <requirement type="package" version="@WRAPPER_VERSION@">disco</requirement>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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22 </requirements>
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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23 <version_command>echo @WRAPPER_VERSION@</version_command>
0
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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24 <command detect_errors="exit_code"><![CDATA[
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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25 #if $input_cond.library_type == "single"
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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26 #for i, e in enumerate($input_cond.inS)
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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27 cp '$e'
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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28 #if $e.ext.endswith(".gz")
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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29 input_${i}.fastq.gz &&
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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30 #else
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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31 input_${i}.fastq &&
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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32 #end if
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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33 #end for
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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34 #else
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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35 #if $input_cond.paired_input.type == "separated"
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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36 #if $input_cond.paired_input.in1.ext.endswith(".gz")
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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37 cp '$input_cond.paired_input.in1' forward.fastq.gz &&
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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38 cp '$input_cond.paired_input.in2' reverse.fastq.gz &&
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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39 #else
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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40 cp '$input_cond.paired_input.in1' forward.fastq &&
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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41 cp '$input_cond.paired_input.in2' reverse.fastq &&
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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42 #end if
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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43 #else
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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44 #for i, e in enumerate($input_cond.paired_input.inP)
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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45 cp '$e'
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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46 #if $e.ext.endswith(".gz")
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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47 input_${i}.fastq.gz &&
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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48 #else
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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49 input_${i}.fastq &&
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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50 #end if
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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51 #end for
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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52 #end if
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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53 #end if
0
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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54 runDisco.sh
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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55 -n \${GALAXY_SLOTS:-4}
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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56 -m \${DISCO_MAX_MEMORY:-4}
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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57 -d .
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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58 -o disco
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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59 #if $input_cond.library_type == "single"
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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60 -inS \$(find . -name "*fastq*" -print | tr '\n' ',' | sed 's/,$//')
0
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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61 #else
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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62 #if $input_cond.paired_input.type == "separated"
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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63 #if $input_cond.paired_input.in1.ext.endswith(".gz")
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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64 -in1 forward.fastq.gz
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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65 -in2 reverse.fastq.gz
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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66 #else
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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67 -in1 forward.fastq
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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68 -in2 reverse.fastq
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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69 #end if
0
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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70 #else
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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71 -inP \$(find . -name "*fastq*" -print | tr '\n' ',' | sed 's/,$//')
0
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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72 #end if
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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73 #end if
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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74 $obg
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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75 $osg
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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76 -p '$first_assembly_iteration_params'
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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77 -p2 '$second_assembly_iteration_params'
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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78 -p3 '$third_assembly_iteration_params'
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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79 ]]></command>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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80 <configfiles>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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81 <configfile name="first_assembly_iteration_params">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
82 <![CDATA[
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
83 MinOverlap4BuildGraph = $MinOverlap4BuildGraph
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
84 PrintContigs = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
85 PrintScaffolds = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
86 PrintUnused = $PrintUnused
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
87 PrintGFA = $PrintGFA
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
88 PrintGFA2 = $PrintGFA2
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
89 minSequenceLengthTobePrinted = $first_assembly_iter_param.minSequenceLengthTobePrinted
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
90 MinOverlap4SimplifyGraph = $first_assembly_iter_param.MinOverlap4SimplifyGraph
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
91 minOverlapDifference4ClipBranches = $first_assembly_iter_param.minOverlapDifference4ClipBranches
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
92 minUniquePEsupport = $first_assembly_iter_param.minUniquePEsupport
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
93 minNonUniquePEsupport = $first_assembly_iter_param.minNonUniquePEsupport
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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diff changeset
94 minReadsCountInEdgeToBeNotDeadEnd = $first_assembly_iter_param.minReadsCountInEdgeToBeNotDeadEnd
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
95 minEdgeLengthToBeNotDeadEnd = $first_assembly_iter_param.minEdgeLengthToBeNotDeadEnd
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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96 minFoldToBeShortBranch = $first_assembly_iter_param.minFoldToBeShortBranch
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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diff changeset
97 minReadsCountToHave0Flow = $first_assembly_iter_param.minReadsCountToHave0Flow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
98 minEdgeLengthToHave0Flow = $first_assembly_iter_param.minEdgeLengthToHave0Flow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
99 minReadsCountInEdgeToBe1MinFlow = $first_assembly_iter_param.minReadsCountInEdgeToBe1MinFlow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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diff changeset
100 minEdgeLengthToBe1MinFlow = $first_assembly_iter_param.minEdgeLengthToBe1MinFlow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
101 ]]></configfile>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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102 <configfile name="second_assembly_iteration_params">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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103 <![CDATA[
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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104 MinOverlap4BuildGraph = $MinOverlap4BuildGraph
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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105 PrintContigs = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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106 PrintScaffolds = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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107 PrintUnused = $PrintUnused
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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108 PrintGFA = $PrintGFA
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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109 PrintGFA2 = $PrintGFA2
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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110 minSequenceLengthTobePrinted = $second_assembly_iter_param.minSequenceLengthTobePrinted
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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111 MinOverlap4SimplifyGraph = $second_assembly_iter_param.MinOverlap4SimplifyGraph
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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112 minOverlapDifference4ClipBranches = $second_assembly_iter_param.minOverlapDifference4ClipBranches
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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113 minUniquePEsupport = $second_assembly_iter_param.minUniquePEsupport
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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114 minNonUniquePEsupport = $second_assembly_iter_param.minNonUniquePEsupport
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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115 minReadsCountInEdgeToBeNotDeadEnd = $second_assembly_iter_param.minReadsCountInEdgeToBeNotDeadEnd
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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116 minEdgeLengthToBeNotDeadEnd = $second_assembly_iter_param.minEdgeLengthToBeNotDeadEnd
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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117 minFoldToBeShortBranch = $second_assembly_iter_param.minFoldToBeShortBranch
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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118 minReadsCountToHave0Flow = $second_assembly_iter_param.minReadsCountToHave0Flow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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diff changeset
119 minEdgeLengthToHave0Flow = $second_assembly_iter_param.minEdgeLengthToHave0Flow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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120 minReadsCountInEdgeToBe1MinFlow = $second_assembly_iter_param.minReadsCountInEdgeToBe1MinFlow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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121 minEdgeLengthToBe1MinFlow = $second_assembly_iter_param.minEdgeLengthToBe1MinFlow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
122 ]]></configfile>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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123 <configfile name="third_assembly_iteration_params">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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124 <![CDATA[
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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125 MinOverlap4BuildGraph = $MinOverlap4BuildGraph
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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126 PrintContigs = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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127 PrintScaffolds = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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128 PrintUnused = $PrintUnused
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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129 PrintGFA = $PrintGFA
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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130 PrintGFA2 = $PrintGFA2
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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131 minSequenceLengthTobePrinted = $third_assembly_iter_param.minSequenceLengthTobePrinted
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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132 MinOverlap4SimplifyGraph = $third_assembly_iter_param.MinOverlap4SimplifyGraph
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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133 minOverlapDifference4ClipBranches = $third_assembly_iter_param.minOverlapDifference4ClipBranches
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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134 minUniquePEsupport = $third_assembly_iter_param.minUniquePEsupport
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
135 minNonUniquePEsupport = $third_assembly_iter_param.minNonUniquePEsupport
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
136 minReadsCountInEdgeToBeNotDeadEnd = $third_assembly_iter_param.minReadsCountInEdgeToBeNotDeadEnd
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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137 minEdgeLengthToBeNotDeadEnd = $third_assembly_iter_param.minEdgeLengthToBeNotDeadEnd
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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138 minFoldToBeShortBranch = $third_assembly_iter_param.minFoldToBeShortBranch
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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139 minReadsCountToHave0Flow = $third_assembly_iter_param.minReadsCountToHave0Flow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
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140 minEdgeLengthToHave0Flow = $third_assembly_iter_param.minEdgeLengthToHave0Flow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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diff changeset
141 minReadsCountInEdgeToBe1MinFlow = $third_assembly_iter_param.minReadsCountInEdgeToBe1MinFlow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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142 minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
143 ]]></configfile>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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144 </configfiles>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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145 <inputs>
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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diff changeset
146 <conditional name="input_cond">
0
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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147 <param name="library_type" type="select" label="Type of library?">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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148 <option value="single">Single-end reads</option>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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149 <option value="paired">Paired-end reads</option>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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150 </param>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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parents:
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151 <when value="single">
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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152 <param argument="-inS" type="data" format="fastq,fastq.gz,fasta" multiple="true" label="Single-read files"/>
0
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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153 </when>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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parents:
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154 <when value="paired">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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155 <conditional name="paired_input">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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156 <param name="type" type="select" label="Type of library?">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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157 <option value="separated">Separated forward/reverse paired-read files</option>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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158 <option value="interleaved">Interleaved paired-read files</option>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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159 </param>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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parents:
diff changeset
160 <when value="separated">
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
parents: 0
diff changeset
161 <param argument="-in1" type="data" format="fastq,fastq.gz,fasta" label="Forward read file" />
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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diff changeset
162 <param argument="-in2" type="data" format="fastq,fastq.gz,fasta" label="Reverse read file" />
0
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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163 </when>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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parents:
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164 <when value="interleaved">
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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165 <param argument="-inP" type="data" format="fastq,fastq.gz,fasta" multiple="true" label="Interleaved paired-read files" />
0
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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 ${on_string}: Unused reads">
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195 <filter>PrintUnused</filter>
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196 <discover_datasets pattern="disco_0_Unused(?P&lt;designation&gt;.+)\.fasta" format="fasta" directory="assembly" />
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197 </collection>
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198 <collection name="gfa_graphs" type="list" label="${tool.name} on ${on_string}: GFA graph">
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199 <filter>PrintGFA</filter>
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200 <discover_datasets pattern="disco_Graph_(?P&lt;designation&gt;.+)\.gfa" format="txt" directory="assembly" />
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201 </collection>
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202 <collection name="gfa2_graphs" type="list" label="${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&lt;designation&gt;.+)\.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>
2
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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>
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
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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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
337 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
338 <param name="minFoldToBeShortBranch" value="5"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
339 <param name="minReadsCountToHave0Flow" value="15"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
340 <param name="minEdgeLengthToHave0Flow" value="1500"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
341 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
342 <param name="minEdgeLengthToBe1MinFlow" value="2000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
343 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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344 <section name="third_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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diff changeset
345 <param name="minSequenceLengthTobePrinted" value="1000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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346 <param name="MinOverlap4SimplifyGraph" value="30"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
347 <param name="minOverlapDifference4ClipBranches" value="25"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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diff changeset
348 <param name="minUniquePEsupport" value="3"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
349 <param name="minNonUniquePEsupport" value="0"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
350 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
351 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
352 <param name="minFoldToBeShortBranch" value="5"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
353 <param name="minReadsCountToHave0Flow" value="15"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
354 <param name="minEdgeLengthToHave0Flow" value="1500"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
355 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
356 <param name="minEdgeLengthToBe1MinFlow" value="2000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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357 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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358 <output name="log">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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359 <assert_contents>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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360 <has_text text="Software: Disco Assembler" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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361 <has_text text="FIRST LOOP ITERATION 1" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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362 <has_text text="4108 reads streamed from this read file" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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363 <has_text text="Graph simplification" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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diff changeset
364 </assert_contents>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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diff changeset
365 </output>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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366 <output name="contigs" value="test2_contigs.fasta" compare="sim_size" delta="5"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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diff changeset
367 <output name="scaffolds" value="test2_scaffolds.fasta" compare="sim_size" delta="5"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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368 </test>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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369 <test>
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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370 <conditional name="input_cond">
0
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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371 <param name="library_type" value="single"/>
2
56b0772e3379 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
iuc
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diff changeset
372 <param name="inS" value="ecoli_1K_1.fq.gz" ftype="fastq.gz"/>
0
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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373 </conditional>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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374 <param name="obg" value=""/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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375 <param name="osg" value=""/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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diff changeset
376 <param name="MinOverlap4BuildGraph" value="20"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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diff changeset
377 <param name="log" value="false"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
378 <param name="PrintUnused" value="false"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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diff changeset
379 <param name="PrintGFA" value="false"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
380 <param name="PrintGFA2" value="false"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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381 <section name="first_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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382 <param name="minSequenceLengthTobePrinted" value="1000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
383 <param name="MinOverlap4SimplifyGraph" value="30"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
384 <param name="minOverlapDifference4ClipBranches" value="25"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
385 <param name="minUniquePEsupport" value="3"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
386 <param name="minNonUniquePEsupport" value="0"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
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diff changeset
387 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
388 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
389 <param name="minFoldToBeShortBranch" value="5"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
390 <param name="minReadsCountToHave0Flow" value="15"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
391 <param name="minEdgeLengthToHave0Flow" value="1500"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
392 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
393 <param name="minEdgeLengthToBe1MinFlow" value="2000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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394 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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395 <section name="second_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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diff changeset
396 <param name="minSequenceLengthTobePrinted" value="1000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
397 <param name="MinOverlap4SimplifyGraph" value="30"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
398 <param name="minOverlapDifference4ClipBranches" value="25"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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399 <param name="minUniquePEsupport" value="3"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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parents:
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400 <param name="minNonUniquePEsupport" value="0"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
401 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
402 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
403 <param name="minFoldToBeShortBranch" value="5"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
404 <param name="minReadsCountToHave0Flow" value="15"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
405 <param name="minEdgeLengthToHave0Flow" value="1500"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
406 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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diff changeset
407 <param name="minEdgeLengthToBe1MinFlow" value="2000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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408 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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409 <section name="third_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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diff changeset
410 <param name="minSequenceLengthTobePrinted" value="1000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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diff changeset
411 <param name="MinOverlap4SimplifyGraph" value="30"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
412 <param name="minOverlapDifference4ClipBranches" value="25"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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diff changeset
413 <param name="minUniquePEsupport" value="3"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
414 <param name="minNonUniquePEsupport" value="0"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
415 <param name="minReadsCountInEdgeToBeNotDeadEnd" value="10"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
416 <param name="minEdgeLengthToBeNotDeadEnd" value="1000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
417 <param name="minFoldToBeShortBranch" value="5"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
418 <param name="minReadsCountToHave0Flow" value="15"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
iuc
parents:
diff changeset
419 <param name="minEdgeLengthToHave0Flow" value="1500"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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diff changeset
420 <param name="minReadsCountInEdgeToBe1MinFlow" value="20"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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diff changeset
421 <param name="minEdgeLengthToBe1MinFlow" value="2000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666
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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>