disco: disco.xml annotate

annotate disco.xml @ 0:3c16cb5b2b5b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666

author	iuc
date	Fri, 03 Nov 2017 15:44:00 -0400
parents
children	56b0772e3379

rev	line source
0 3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	1 <tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.0">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	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 iuc parents: diff changeset	3 <macros>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	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 iuc parents: diff changeset	5 <xml name="assembly_params">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	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 iuc parents: diff changeset	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 parents: diff changeset	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 parents: diff changeset	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 iuc parents: diff changeset	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 iuc parents: diff changeset	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 iuc parents: diff changeset	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 iuc parents: diff changeset	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 iuc parents: diff changeset	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 iuc parents: diff changeset	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 iuc parents: diff changeset	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 iuc parents: diff changeset	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 iuc parents: diff changeset	18 </xml>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	19 </macros>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	20 <requirements>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	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 iuc parents: diff changeset	22 </requirements>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	23 <version_command>runDisco.sh --version</version_command>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	24 <command detect_errors="exit_code"><![CDATA[
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	25 runDisco.sh
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	26 -n \${GALAXY_SLOTS:-4}
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	27 -m \${DISCO_MAX_MEMORY:-4}
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	28 -d .
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	29 -o disco
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	30 #if $input.library_type == "single"
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	31 -inS '$input.inS'
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	32 #else
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	33 #if $input.paired_input.type == "separated"
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	34 -in1 '$input.paired_input.in1'
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	35 -in2 '$input.paired_input.in2'
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	36 #else
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	37 -inP '$input.paired_input.inP'
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	38 #end if
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	39 #end if
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	40 $obg
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	41 $osg
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	42 -p '$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	43 -p2 '$second_assembly_iteration_params'
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	44 -p3 '$third_assembly_iteration_params'
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	45 ]]></command>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	46 <configfiles>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	47 <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	48 <![CDATA[
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	49 MinOverlap4BuildGraph = $MinOverlap4BuildGraph
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	50 PrintContigs = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	51 PrintScaffolds = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	52 PrintUnused = $PrintUnused
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	53 PrintGFA = $PrintGFA
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	54 PrintGFA2 = $PrintGFA2
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	55 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	56 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	57 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	58 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	59 minNonUniquePEsupport = $first_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	60 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	61 minEdgeLengthToBeNotDeadEnd = $first_assembly_iter_param.minEdgeLengthToBeNotDeadEnd
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	62 minFoldToBeShortBranch = $first_assembly_iter_param.minFoldToBeShortBranch
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	63 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	64 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	65 minReadsCountInEdgeToBe1MinFlow = $first_assembly_iter_param.minReadsCountInEdgeToBe1MinFlow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	66 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	67 ]]></configfile>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	68 <configfile name="second_assembly_iteration_params">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	69 <![CDATA[
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	70 MinOverlap4BuildGraph = $MinOverlap4BuildGraph
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	71 PrintContigs = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	72 PrintScaffolds = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	73 PrintUnused = $PrintUnused
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	74 PrintGFA = $PrintGFA
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	75 PrintGFA2 = $PrintGFA2
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	76 minSequenceLengthTobePrinted = $second_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	77 MinOverlap4SimplifyGraph = $second_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	78 minOverlapDifference4ClipBranches = $second_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	79 minUniquePEsupport = $second_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	80 minNonUniquePEsupport = $second_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	81 minReadsCountInEdgeToBeNotDeadEnd = $second_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	82 minEdgeLengthToBeNotDeadEnd = $second_assembly_iter_param.minEdgeLengthToBeNotDeadEnd
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	83 minFoldToBeShortBranch = $second_assembly_iter_param.minFoldToBeShortBranch
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	84 minReadsCountToHave0Flow = $second_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	85 minEdgeLengthToHave0Flow = $second_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	86 minReadsCountInEdgeToBe1MinFlow = $second_assembly_iter_param.minReadsCountInEdgeToBe1MinFlow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	87 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	88 ]]></configfile>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	89 <configfile name="third_assembly_iteration_params">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	90 <![CDATA[
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	91 MinOverlap4BuildGraph = $MinOverlap4BuildGraph
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	92 PrintContigs = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	93 PrintScaffolds = true
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	94 PrintUnused = $PrintUnused
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	95 PrintGFA = $PrintGFA
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	96 PrintGFA2 = $PrintGFA2
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	97 minSequenceLengthTobePrinted = $third_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	98 MinOverlap4SimplifyGraph = $third_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	99 minOverlapDifference4ClipBranches = $third_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	100 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	101 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	102 minReadsCountInEdgeToBeNotDeadEnd = $third_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	103 minEdgeLengthToBeNotDeadEnd = $third_assembly_iter_param.minEdgeLengthToBeNotDeadEnd
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	104 minFoldToBeShortBranch = $third_assembly_iter_param.minFoldToBeShortBranch
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	105 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: diff changeset	106 minEdgeLengthToHave0Flow = $third_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	107 minReadsCountInEdgeToBe1MinFlow = $third_assembly_iter_param.minReadsCountInEdgeToBe1MinFlow
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	108 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	109 ]]></configfile>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	110 </configfiles>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	111 <inputs>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	112 <conditional name="input">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	113 <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 iuc parents: diff changeset	114 <option value="single">Single-end reads</option>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	115 <option value="paired">Paired-end reads</option>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	116 </param>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	117 <when value="single">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	118 <param argument="-inS" type="data" format="fastq,fasta" multiple="true" label="Single-read files"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	119 </when>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	120 <when value="paired">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	121 <conditional name="paired_input">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	122 <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 iuc parents: diff changeset	123 <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 parents: diff changeset	124 <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 iuc parents: diff changeset	125 </param>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	126 <when value="separated">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	127 <param argument="-in1" type="data" format="fastq,fasta" label="Forward read file" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	128 <param argument="-in2" type="data" format="fastq,fasta" label="Reverse read file" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	129 </when>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	130 <when value="interleaved">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	131 <param argument="-inP" type="data" format="fastq,fasta" multiple="true" label="Interleaved paired-read files" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	132 </when>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	133 </conditional>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	134 </when>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	135 </conditional>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	136 <param argument="-obg" type="boolean" truevalue="-obg" falsevalue="" checked="false" label="Only build overlap graph?"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	137 <param argument="-osg" type="boolean" truevalue="-osg" falsevalue="" checked="false" label="Only simplify existing overlap graph?"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	138 <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"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	139 <param name="log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log file?"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	140 <param argument="PrintScaffolds" type="boolean" truevalue="true" falsevalue="false" label="Print scaffolds?"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	141 <param argument="PrintUnused" type="boolean" truevalue="true" falsevalue="false" label="Print unused reads?"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	142 <param argument="PrintGFA" type="boolean" truevalue="true" falsevalue="false" label="Print GFA graph format?"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	143 <param argument="PrintGFA2" type="boolean" truevalue="true" falsevalue="false" label="Print GFA2 graph format?"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	144 <section name="first_assembly_iter_param" title="Parameters for 1st assembly iteration" expanded="False">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	145 <expand macro="assembly_params"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	146 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	147 <section name="second_assembly_iter_param" title="Parameters for 2nd assembly iteration" expanded="False">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	148 <expand macro="assembly_params"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	149 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	150 <section name="third_assembly_iter_param" title="Parameters for 3rd assembly iteration" expanded="False">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	151 <expand macro="assembly_params"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	152 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	153 </inputs>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	154 <outputs>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	155 <data format="txt" name="log" from_work_dir="disco.log" label="${tool.name} on ${on_string}: Log file">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	156 <filter>log</filter>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	157 </data>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	158 <data format="fasta" name="contigs" from_work_dir="disco_contigsFinalCombined.fasta" label="${tool.name} on ${on_string}: Contigs"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	159 <data format="fasta" name="scaffolds" from_work_dir="disco_scaffoldsFinalCombined.fasta" label="${tool.name} on ${on_string}: Scaffolds"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	160 <collection name="unused_reads" type="list" label="${tool.name} on ${on_string}: Unused reads">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	161 <filter>PrintUnused</filter>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	162 <discover_datasets pattern="disco_0_Unused(?P<designation>.+)\.fasta" format="fasta" directory="assembly" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	163 </collection>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	164 <collection name="gfa_graphs" type="list" label="${tool.name} on ${on_string}: GFA graph">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	165 <filter>PrintGFA</filter>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	166 <discover_datasets pattern="disco_Graph_(?P<designation>.+)\.gfa" format="txt" directory="assembly" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	167 </collection>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	168 <collection name="gfa2_graphs" type="list" label="${tool.name} on ${on_string}: GFA2 graph">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	169 <filter>PrintGFA2</filter>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	170 <discover_datasets pattern="disco_Graph_(?P<designation>.+)\.gfa2" format="txt" directory="assembly" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	171 </collection>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	172 </outputs>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	173 <tests>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	174 <test>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	175 <conditional name="input">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	176 <param name="library_type" value="paired"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	177 <conditional name="paired_input">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	178 <param name="type" value="separated"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	179 <param name="in1" value="ecoli_1K_1.fq"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	180 <param name="in2" value="ecoli_1K_2.fq"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	181 </conditional>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	182 </conditional>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	183 <param name="obg" value=""/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	184 <param name="osg" value=""/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	185 <param name="MinOverlap4BuildGraph" value="20"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	186 <param name="log" value="true"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	187 <param name="PrintUnused" value="true"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	188 <param name="PrintGFA" value="true"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	189 <param name="PrintGFA2" value="true"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	190 <section name="first_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	191 <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	192 <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	193 <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	194 <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	195 <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	196 <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	197 <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	198 <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	199 <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	200 <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	201 <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	202 <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	203 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	204 <section name="second_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	205 <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	206 <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	207 <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	208 <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	209 <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	210 <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	211 <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	212 <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	213 <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	214 <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	215 <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	216 <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	217 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	218 <section name="third_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	219 <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	220 <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	221 <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	222 <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	223 <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	224 <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	225 <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	226 <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	227 <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	228 <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	229 <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	230 <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	231 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	232 <output name="log">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	233 <assert_contents>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	234 <has_text text="Software: Disco Assembler" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	235 <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 parents: diff changeset	236 <has_text text="2054 reads streamed from this read file" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	237 <has_text text="Graph simplification" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	238 </assert_contents>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	239 </output>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	240 <output name="contigs" value="test1_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 parents: diff changeset	241 <output name="scaffolds" value="test1_scaffolds.fasta" compare="sim_size" delta="5"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	242 <output_collection name="unused_reads" type="list">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	243 <element name="PairedReads1">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	244 <assert_contents>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	245 <has_text text="EAS20_8_6_1_9_1972/1" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	246 <has_text text="EAS20_8_6_10_415_709/1" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	247 <has_text text="EAS20_8_6_36_1124_470/1" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	248 <has_text text="EAS20_8_6_100_1637_1332/1" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	249 </assert_contents>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	250 </element>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	251 <element name="PairedReads2">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	252 <assert_contents>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	253 <has_text text="EAS20_8_6_1_9_1972/2" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	254 <has_text text="EAS20_8_6_10_415_709/2" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	255 <has_text text="EAS20_8_6_36_1124_470/2" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	256 <has_text text="EAS20_8_6_100_1637_1332/2" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	257 </assert_contents>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	258 </element>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	259 </output_collection>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	260 <output_collection name="gfa_graphs" type="list">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	261 <element name="1" file="test1_graph_1.gfa" compare="sim_size" delta="6000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	262 </output_collection>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	263 <output_collection name="gfa2_graphs" type="list">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	264 <element name="1" file="test1_graph_1.gfa2" compare="sim_size" delta="6000"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	265 </output_collection>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	266 </test>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	267 <test>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	268 <conditional name="input">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	269 <param name="library_type" value="paired"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	270 <conditional name="paired_input">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	271 <param name="type" value="interleaved"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	272 <param name="inP" value="ecoli_1K_interleaved.fq,ecoli_1K_interleaved.fq"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	273 </conditional>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	274 </conditional>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	275 <param name="obg" value=""/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	276 <param name="osg" value=""/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	277 <param name="MinOverlap4BuildGraph" value="20"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	278 <param name="log" value="true"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	279 <param name="PrintUnused" value="false"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	280 <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	281 <param name="PrintGFA2" value="false"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	282 <section name="first_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	283 <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	284 <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	285 <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	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	296 <section name="second_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	310 <section name="third_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	311 <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	312 <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	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	324 <output name="log">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	325 <assert_contents>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	326 <has_text text="Software: Disco Assembler" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	327 <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 parents: diff changeset	328 <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 iuc parents: diff changeset	329 <has_text text="Graph simplification" />
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	330 </assert_contents>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	331 </output>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	332 <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 parents: diff changeset	333 <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 iuc parents: diff changeset	334 </test>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	335 <test>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	336 <conditional name="input">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	337 <param name="library_type" value="single"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	338 <param name="inS" value="ecoli_1K_1.fq"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	339 </conditional>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	340 <param name="obg" value=""/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	341 <param name="osg" value=""/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	342 <param name="MinOverlap4BuildGraph" value="20"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	343 <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	344 <param name="PrintUnused" value="false"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	345 <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	346 <param name="PrintGFA2" value="false"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	347 <section name="first_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	348 <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	349 <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	350 <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	351 <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	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 <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	359 <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	360 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	361 <section name="second_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	362 <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	363 <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	364 <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	365 <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	366 <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	367 <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	368 <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	369 <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	370 <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	371 <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	372 <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	373 <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	374 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	375 <section name="third_assembly_iter_param">
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	376 <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	377 <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	378 <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	379 <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	380 <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	381 <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	382 <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	383 <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	384 <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	385 <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	386 <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	387 <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	388 </section>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	389 <output name="contigs" value="test3_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 parents: diff changeset	390 <output name="scaffolds" value="test3_scaffolds.fasta" compare="sim_size" delta="5"/>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	391 </test>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	392 </tests>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	393 <help><![CDATA[
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	394 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.
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	395
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	396 The detailed user manual of the assembler and how to use it to acheive best results is provided here: 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.
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	397 ]]></help>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	398 <citations>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	399 </citations>
3c16cb5b2b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit c1327b5793477da611684e92e0ce4635370c7666 iuc parents: diff changeset	400 </tool>

Mercurial > repos > iuc > disco

annotate disco.xml @ 0:3c16cb5b2b5b draft