annotate presto_assemblepairs.xml @ 0:44c980933450 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
author iuc
date Wed, 30 May 2018 15:36:59 -0400
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44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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1 <tool id="presto_assemblepairs" name="pRESTO AssemblePairs" version="@PRESTO_VERSION@">
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2 <description>Assembles paired-end reads into a single sequence.</description>
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3
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4 <macros>
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5 <import>presto_macros.xml</import>
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6 <xml name="align-params">
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7 <param argument="--alpha" type="float" value="1e-05" label="Alpha" help="Significance threshold for de-novo assembly."/>
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8 <param argument="--maxerror" type="float" value="0.3" label="Max Error" help="Maximum error rate for de novo assembly."/>
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9 <param argument="--minlen" type="integer" value="8" label="Minimum Length" help="Minimum sequence length to scan for overlap."/>
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10 <param argument="--maxlen" type="integer" value="1000" label="Maximum Length" help="Maximum sequence length to scan for overlap."/>
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11 <param argument="--scanrev" type="boolean" value="false" truevalue="--scanrev" falsevalue="" label="Scan past the end of the tail sequence in de novo assembly to allow the head sequence to overhang the end of the tail sequence."/>
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12 </xml>
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13
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14 <xml name="reference-params">
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15 <param argument="-r" type="data" format="fasta" label="Reference sequence FASTA file."/>
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16 <param argument="--minident" type="float" value="0.5" label="Minimum Identity" help="Minimum identical fraction between assembled sequence and reference."/>
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17 <param argument="--evalue" type="float" value="1e-05" label="E-Value" help="Minimum E-value for reference alignment for both the read sequences."/>
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18 <param argument="--maxhits" type="integer" value="100" label="Max Hits" help="Maximum number of hits in the reference sequence to examine per assembled sequence."/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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19 <param argument="--fill" type="boolean" value="false" truevalue="--fill" falsevalue="" label="Fill With Reference" help="For read pairs with a gap between them, fill with reference sequence instead of Ns."/>
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20 <param argument="--aligner" type="select" value="blastn" label="Aligner" help="Aligner to use to align reads to reference.">
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21 <option value="blastn">Blast</option>
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22 <option value="usearch">USearch</option>
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23 </param>
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24 </xml>
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25 </macros>
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26
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27 <expand macro="requirements"/>
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28
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29 <version_command>AssemblePairs.py --version</version_command>
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30 <command detect_errors="exit_code"><![CDATA[
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31 ln -s '$r1_in' r1.fastq &&
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32 ln -s '$r2_in' r2.fastq &&
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33 #if $varExists('cc.r')
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34 ln -s '$cc.r' reference.fasta &&
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35 #end if
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36 AssemblePairs.py $cc.command
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37 --nproc "\${GALAXY_SLOTS:-1}"
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38 -1 r1.fastq
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39 -2 r2.fastq
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40 --coord $coord
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41 #if $rc
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42 --rc '$rc'
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43 #end if
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44 #if $r1_annotations
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45 --1f $r1_annotations
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46 #end if
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47 #if $r2_annotations
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48 --2f $r2_annotations
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49 #end if
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50
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51 #if $cc.command == "join"
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52 --gap '$cc.gap'
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53 #end if
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54
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55 #if $cc.command == "align" or $cc.command == "sequential"
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56 --alpha '$cc.alpha'
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57 --maxerror '$cc.maxerror'
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58 --minlen '$cc.minlen'
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59 --maxlen '$cc.maxlen'
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60 $cc.scanrev
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61 #end if
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62
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63 #if $cc.command == "reference" or $cc.command == "sequential"
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64 -r reference.fasta
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65 --minident '$cc.minident'
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66 --evalue '$cc.evalue'
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67 --maxhits '$cc.maxhits'
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68 --aligner '$cc.aligner'
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69 $cc.fill
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70 #end if
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71
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72 --outdir=.
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73 --outname=tmp
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74 #if $capture_log
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75 --log '$log_out'
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76 #end if
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77 ]]></command>
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78 <inputs>
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79 <param argument="-1" name="r1_in" type="data" format="fastq" label="Read 1 FASTQ file"/>
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80 <param argument="-2" name="r2_in" type="data" format="fastq" label="Read 2 FASTQ file"/>
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81 <param argument="--rc" type="select" label="Reverse Complement" value="" help="Reverse complement neither, R1, R2 or both reads before assembly.">
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82 <option value="">Neither</option>
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83 <option value="head">Read 1 Only</option>
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84 <option value="tail">Read 2 Only</option>
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85 <option value="both">R1 and R2</option>
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86 </param>
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87 <param argument="--1f" name="r1_annotations" type="text" optional="true" label="R1 Fields To Copy" help="Annotation fields to copy from R1 into the output.">
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
88 <expand macro="text-regex-validator"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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diff changeset
89 </param>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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diff changeset
90 <param argument="--2f" name="r2_annotations" type="text" optional="true" label="R2 Fields To Copy" help="Annotation fields to copy from R2 into the output.">
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
91 <expand macro="text-regex-validator"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
92 </param>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
93
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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94 <conditional name="cc">
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
95 <param name="command" type="select" label="Command" value="sequential">
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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96 <option value="align">Assemble pairs by aligning ends (align)</option>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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97 <option value="join">Assemble pairs by concatenating ends (join)</option>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
98 <option value="reference">Assemble pairs by aligning reads against a reference (reference)</option>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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99 <option value="sequential">Attempt assembly via alignment, then reference guided assembly (sequential)</option>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
100 </param>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
101 <when value="align">
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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102 <expand macro="align-params"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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103 </when>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
104 <when value="join">
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
105 <param argument="--gap" type="integer" value="0" label="Gap Size" help="Number of N characters to place between joined Ns."/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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diff changeset
106 </when>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
107 <when value="reference">
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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108 <expand macro="reference-params"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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109 </when>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
110 <when value="sequential">
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
111 <expand macro="align-params"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
112 <expand macro="reference-params"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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113 </when>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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114 </conditional>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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115
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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116 <expand macro="presto-coord-param"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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117 <expand macro="presto-log-param"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
118 </inputs>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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119
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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120 <outputs>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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121 <data name="fastq_out" format="fastq" from_work_dir="tmp_assemble-pass.fastq"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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122 <expand macro="presto-log-output"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
123 </outputs>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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124
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iuc
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diff changeset
125 <tests>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
126 <test>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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127 <param name="command" value="join"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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128 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
129 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
130 <param name="coord" value="presto"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
131 <param name="rc" value="tail"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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132 <param name="r1_annotations" value="CONSCOUNT"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
133 <param name="r2_annotations" value="PRCONS CONSCOUNT"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
134 <param name="gap" value="10"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
135 <output name="fastq_out" file="presto_assemblepairs_test_join_out.fastq" sort="true"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
136 </test>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
137
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
138 <test>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
139 <param name="command" value="align"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
140 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
141 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
142 <param name="coord" value="presto"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
143 <param name="rc" value="tail"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
144 <param name="r1_annotations" value="CONSCOUNT"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
145 <param name="r2_annotations" value="PRCONS CONSCOUNT"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
146 <param name="scanrev" value="true"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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147 <output name="fastq_out" file="presto_assemblepairs_test_align_out.fastq" sort="true"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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148 </test>
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iuc
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149
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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diff changeset
150 <test>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
151 <param name="command" value="reference"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
152 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
153 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
154 <param name="coord" value="presto"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
155 <param name="rc" value="tail"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
156 <param name="r1_annotations" value="CONSCOUNT"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
157 <param name="r2_annotations" value="PRCONS CONSCOUNT"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
158 <param name="r" value="reference_repertoire.fasta"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
159 <param name="aligner" value="blastn"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
160 <output name="fastq_out" file="presto_assemblepairs_test_reference_out.fastq" sort="true"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
161 </test>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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162
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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diff changeset
163 <test>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
164 <param name="command" value="sequential"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
165 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
166 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
167 <param name="coord" value="presto"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
168 <param name="rc" value="tail"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
169 <param name="r1_annotations" value="CONSCOUNT"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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diff changeset
170 <param name="r2_annotations" value="PRCONS CONSCOUNT"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
171 <param name="scanrev" value="true"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
172 <param name="r" value="reference_repertoire.fasta"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff changeset
173 <param name="aligner" value="blastn"/>
44c980933450 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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174 <output name="fastq_out" file="presto_assemblepairs_test_sequential_out.fastq" sort="true"/>
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175 </test>
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176 </tests>
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177
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178 <help><![CDATA[
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179 Assembles paired-end reads into a single sequence.
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180
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181 See the `pRESTO online help <@PRESTO_URL_BASE@/AssemblePairs.html>`_ for more information.
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182
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183 @HELP_NOTE@
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184 ]]></help>
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185 <expand macro="citations" />
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186 </tool>