Mercurial > repos > iuc > stacks2_ustacks

annotate stacks_ustacks.xml @ 3:cfb504394ae1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
author iuc
date Tue, 27 Apr 2021 09:30:21 +0000
parents d033e1ccb386
children d1fda11e602f
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1 <tool id="stacks2_ustacks" name="Stacks2: ustacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>Identify unique stacks</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_cmd"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 @FASTQ_INPUT_FUNCTIONS@
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10
2
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11 trap ">&2 cat '$output_log'" err exit &&
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12 mkdir stacks_inputs stacks_outputs &&
0
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14 #set $ID=1
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15 #for $sample in $input_type.fqinputs
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16 #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1")
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17 $create_links
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19 ustacks
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21 -f '$data_path'
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22 -i $ID
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23 --name $name
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24 -m $m
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25 -M $M
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26 #if $N
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27 -N $N
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28 #end if
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29 -p \${GALAXY_SLOTS:-1}
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30 -t $inputype
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31 $R
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32 $H
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33
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34 ## Assembly
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35 $assembly_options.keep_high_cov
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36 --high_cov_thres $assembly_options.high_cov_thres
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37 $assembly_options.d
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38 --max_locus_stacks $assembly_options.max_locus_stacks
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39 #if str($assembly_options.k_len)
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40 --k_len $assembly_options.k_len
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41 #end if
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43 @GAP_OPTIONS@
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44
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45 ## snp_model
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46 #if str( $snp_options.select_model.model_type) == "bounded"
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47 --model_type bounded
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48 --bound_low $snp_options.select_model.bound_low
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49 --bound_high $snp_options.select_model.bound_high
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50 --alpha $snp_options.select_model.alpha
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51 #else if str( $snp_options.select_model.model_type) == "snp"
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52 --model_type snp
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53 --alpha $snp_options.select_model.alpha
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54 #else
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55 --model_type fixed
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56 --bc_err_freq $bc_err_freq
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57 #end if
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58
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59 -o stacks_outputs
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60 @TEE_APPEND_LOG@
2
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61 &&
0
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62
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63 #set $ID=$ID+1
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64 #end for
2
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65 true
0
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66 ## If input is in gz format, stacks will output gzipped files (no option to control this)
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67 #if $inputype.startswith('gz')
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68 && gunzip stacks_outputs/*.gz
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69 #end if
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70 ]]></command>
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71
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72 <inputs>
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73 <expand macro="fastq_input" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"/>
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74
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75 <param argument="-m" type="integer" value="3" label="Minimum depth of coverage required to create a stack"/>
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76 <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
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77 <param argument="-N" type="integer" value="" optional="true" label="Maximum distance allowed to align secondary reads to primary stacks" help="(default: M + 2)"/>
2
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78 <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads"/>
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79 <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads"/>
0
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80 <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True">
2
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81 <param argument="--keep_high_cov" type="boolean" checked="false" truevalue="--keep_high_cov" falsevalue="" label="Disable the algorithm that removes highly-repetitive stacks and nearby errors. "/>
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82 <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags"/>
0
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83 <param argument="--high_cov_thres" type="float" min="0.0" value="3.0" label="Highly-repetitive stacks threshold" help="in standard deviation units"/>
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84 <param argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/>
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85 <param argument="--k_len" type="integer" value="" min="7" max="31" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/>
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86 </section>
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87 <expand macro="gap_options"/>
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88
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89 <!-- SNP Model options -->
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90 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">
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91 <expand macro="snp_options_full"/>
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92 </section>
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93 <expand macro="in_log"/>
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94 </inputs>
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95
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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96 <outputs>
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97 <expand macro="out_log"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
98 <expand macro="ustacks_outputs_macro"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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99 </outputs>
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100
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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101 <tests>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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102 <!-- paired list, default options, test for file equality -->
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
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103 <test expect_num_outputs="2">
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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104 <param name="input_type|input_type_select" value="paired"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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105 <param name="input_type|fqinputs">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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106 <collection type="list:paired">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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107 <element name="PopA_01">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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108 <collection type="paired">
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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109 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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110 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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111 </collection>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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112 </element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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113 <element name="PopA_02">
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114 <collection type="paired">
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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115 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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116 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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117 </collection>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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118 </element>
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119 </collection>
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120 </param>
2
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121 <param name="add_log" value="yes"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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122 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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123 <!-- 1st test checks for file content allowing differences in the 2 comment lines that contain date and version -->
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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124 <output_collection name="tabs" type="list" count="6">
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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125 <element name="PopA_01.tags" ftype="tabular" file="ustacks/PopA_01.tags.tsv" lines_diff="4"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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126 <element name="PopA_01.snps" ftype="tabular" file="ustacks/PopA_01.snps.tsv" lines_diff="4"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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127 <element name="PopA_01.alleles" ftype="tabular" file="ustacks/PopA_01.alleles.tsv" lines_diff="4"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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128 <element name="PopA_02.tags" ftype="tabular" file="ustacks/PopA_02.tags.tsv" lines_diff="4"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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129 <element name="PopA_02.snps" ftype="tabular" file="ustacks/PopA_02.snps.tsv" lines_diff="4"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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130 <element name="PopA_02.alleles" ftype="tabular" file="ustacks/PopA_02.alleles.tsv" lines_diff="4"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
131 </output_collection>
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132 </test>
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133 <!-- manual selected list of elements + default args, test for file equality -->
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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134 <test expect_num_outputs="2">
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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135 <param name="input_type|input_type_select" value="single"/>
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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136 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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diff changeset
137 <param name="add_log" value="yes"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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138 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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139 <output_collection name="tabs" count="6">
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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140 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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141 <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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142 <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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143 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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144 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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145 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
146 </output_collection>
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diff changeset
147 </test>
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148 <!-- manual selected list of elements + non-default short args, test for file presence -->
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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149 <test expect_num_outputs="2">
0
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150 <param name="input_type|input_type_select" value="single"/>
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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diff changeset
151 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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diff changeset
152 <param name="m" value="2"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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153 <param name="M" value="3"/>
1
21d2aa544835 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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parents: 0
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154 <param name="N" value="4"/>
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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diff changeset
155 <param name="R" value="-R"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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diff changeset
156 <param name="H" value="-H"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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diff changeset
157 <param name="add_log" value="yes"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
158 <assert_command>
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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159 <has_text text="-m 2"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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160 <has_text text="-M 3"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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161 <has_text text="-N 4"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
diff changeset
162 <has_text text="-R"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
diff changeset
163 <has_text text="-H"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
164 </assert_command>
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165 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
166 <output_collection name="tabs" count="6">
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
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167 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
168 <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
diff changeset
169 <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
diff changeset
170 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
diff changeset
171 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
172 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
0
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173 </output_collection>
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174 </test>
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175 <!-- paired list, non-default model options, disabled gapped alignment, test for file presence -->
2
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176 <test expect_num_outputs="2">
0
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177 <param name="input_type|input_type_select" value="paired"/>
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178 <param name="input_type|fqinputs">
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179 <collection type="list:paired">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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180 <element name="PopA_01">
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181 <collection type="paired">
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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182 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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183 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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184 </collection>
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185 </element>
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186 <element name="PopA_02">
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187 <collection type="paired">
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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188 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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189 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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190 </collection>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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191 </element>
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192 </collection>
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193 </param>
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194 <conditional name="select_model">
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195 <param name="model_type" value="snp"/>
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196 <param name="alpha" value="0.1"/>
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197 <param name="bound_low" value="0.1"/>
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198 <param name="bound_high" value="0.5"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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199 <param name="bc_err_freq" value="0.1"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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200 </conditional>
2
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201 <param name="gapped|use_gapped" value="no"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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202 <param name="add_log" value="yes"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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203 <assert_command>
2
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204 <has_text text="--model_type snp"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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205 <has_text text="--alpha 0.1"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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206 <not_has_text text="--bound_low 0.1"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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207 <not_has_text text="--bound_high 0.5"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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208 <not_has_text text="--bc_err_freq 0.1"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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209 <has_text text="--disable-gapped"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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210 </assert_command>
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211 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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212 <output_collection name="tabs" count="6">
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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213 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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214 <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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215 <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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216 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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217 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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218 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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219 </output_collection>
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220 </test>
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221 <!-- list of fwd reads, nondefault assembly and gapped alignment options, test for file presence -->
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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222 <test expect_num_outputs="2">
0
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223 <param name="input_type|input_type_select" value="paired"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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224 <param name="input_type|fqinputs">
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225 <collection type="list">
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
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226 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
227 <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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228 </collection>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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229 </param>
1
21d2aa544835 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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230 <param name="assembly_options|keep_high_cov" value="true"/>
2
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231 <param name="assembly_options|d" value="-d"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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232 <param name="assembly_options|high_cov_thres" value="2.0"/>
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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233 <param name="assembly_options|max_locus_stacks" value="4"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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234 <param name="assembly_options|k_len" value="12"/>
2
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235 <param name="gapped|use_gapped" value="yes"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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236 <param name="gapped|max_gaps" value="3"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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237 <param name="gapped|min_aln_len" value="0.7"/>
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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238 <param name="add_log" value="yes"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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239 <assert_command>
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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240 <has_text text="--keep_high_cov"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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241 <has_text text="-d"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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242 <has_text text="--high_cov_thres 2.0"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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243 <has_text text="--max_locus_stacks 4"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
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244 <has_text text="--k_len 12"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
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245 <has_text text="--max_gaps 3"/>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
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246 <has_text text="--min_aln_len 0.7"/>
0
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
247 </assert_command>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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248 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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249 <output_collection name="tabs" count="6">
2
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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250 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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251 <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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252 <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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253 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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254 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
d033e1ccb386 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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255 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
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256 </output_collection>
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257 </test>
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258 </tests>
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259
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260 <help>
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261 <![CDATA[
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262 .. class:: infomark
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263
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264 **What it does**
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265
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266 The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks. Comparing the stacks it will form a set of loci and detect SNPs at each locus using a maximum likelihood framework
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267
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268 --------
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269
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270 **Input files**
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271
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272 One or more FASTQ, FASTA files. Can be given by selecting them manually, as dataset list, or paired dataset list. Note, for the latter ustacks only uses the forward reads -- reverse reads are incorporated in tsv2bam.
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273
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274 **Output files**
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275
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276 - XXX.tags.tsv file:
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277
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278 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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279
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280 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
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281
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282
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283 - XXX.snps.tsv file:
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284
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285 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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286
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287 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
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288
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289
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290 - XXX.alleles.tsv file:
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291
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292 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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293
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294 @STACKS_INFOS@
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295 ]]>
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296 </help>
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297 <expand macro="citation"/>
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298 </tool>