Mercurial > repos > iuc > stacks2_ustacks

annotate stacks_ustacks.xml @ 5:6df4c5bf0a91 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
author iuc
date Thu, 14 Apr 2022 09:15:59 +0000
parents 1dce9f3949c9
children cee1b75beeaf
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5
6df4c5bf0a91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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1 <tool id="stacks2_ustacks" name="Stacks2: ustacks" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
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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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13
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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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42
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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>
5
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73 <expand macro="fastq_input" multiple="true" listtype="list:paired" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"/>
0
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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">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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91 <expand macro="snp_options_full"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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92 </section>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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93 <expand macro="in_log"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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94 </inputs>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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95
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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96 <outputs>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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97 <expand macro="out_log"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
98 <expand macro="ustacks_outputs_macro"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
99 </outputs>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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100
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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101 <tests>
9eaeea3fb1bb 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
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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103 <test expect_num_outputs="2">
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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104 <param name="input_type|input_type_select" value="paired"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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105 <param name="input_type|fqinputs">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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106 <collection type="list:paired">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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107 <element name="PopA_01">
9eaeea3fb1bb 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
1dce9f3949c9 "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
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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110 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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111 </collection>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
112 </element>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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113 <element name="PopA_02">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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114 <collection type="paired">
2
1dce9f3949c9 "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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115 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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116 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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117 </collection>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
118 </element>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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119 </collection>
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120 </param>
2
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121 <param name="add_log" value="yes"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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122 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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123 <!-- 1st test checks for file content allowing differences in the 2 comment lines that contain date and version -->
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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124 <output_collection name="tabs" type="list" count="6">
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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125 <element name="PopA_01.tags" ftype="tabular" file="ustacks/PopA_01.tags.tsv" lines_diff="4"/>
1dce9f3949c9 "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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126 <element name="PopA_01.snps" ftype="tabular" file="ustacks/PopA_01.snps.tsv" lines_diff="4"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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127 <element name="PopA_01.alleles" ftype="tabular" file="ustacks/PopA_01.alleles.tsv" lines_diff="4"/>
1dce9f3949c9 "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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128 <element name="PopA_02.tags" ftype="tabular" file="ustacks/PopA_02.tags.tsv" lines_diff="4"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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129 <element name="PopA_02.snps" ftype="tabular" file="ustacks/PopA_02.snps.tsv" lines_diff="4"/>
1dce9f3949c9 "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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130 <element name="PopA_02.alleles" ftype="tabular" file="ustacks/PopA_02.alleles.tsv" lines_diff="4"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
131 </output_collection>
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diff changeset
132 </test>
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diff changeset
133 <!-- manual selected list of elements + default args, test for file equality -->
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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diff changeset
134 <test expect_num_outputs="2">
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
135 <param name="input_type|input_type_select" value="single"/>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
136 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
137 <param name="add_log" value="yes"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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138 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
139 <output_collection name="tabs" count="6">
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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140 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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141 <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
1dce9f3949c9 "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>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
143 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
1dce9f3949c9 "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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144 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
diff changeset
145 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
0
9eaeea3fb1bb 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
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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diff changeset
149 <test expect_num_outputs="2">
0
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150 <param name="input_type|input_type_select" value="single"/>
2
1dce9f3949c9 "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"/>
1dce9f3949c9 "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"/>
1dce9f3949c9 "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
aa646fe5a0b4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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154 <param name="N" value="4"/>
2
1dce9f3949c9 "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"/>
1dce9f3949c9 "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"/>
1dce9f3949c9 "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
9eaeea3fb1bb 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
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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diff changeset
159 <has_text text="-m 2"/>
1dce9f3949c9 "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"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
161 <has_text text="-N 4"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
162 <has_text text="-R"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
163 <has_text text="-H"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
164 </assert_command>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
165 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
166 <output_collection name="tabs" count="6">
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
167 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
1dce9f3949c9 "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>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
169 <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
170 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
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171 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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172 <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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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">
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180 <element name="PopA_01">
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181 <collection type="paired">
2
1dce9f3949c9 "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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182 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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183 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
9eaeea3fb1bb 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
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188 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
0
9eaeea3fb1bb 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"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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190 </collection>
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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"/>
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199 <param name="bc_err_freq" value="0.1"/>
9eaeea3fb1bb 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"/>
1dce9f3949c9 "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
9eaeea3fb1bb 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"/>
1dce9f3949c9 "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"/>
1dce9f3949c9 "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"/>
1dce9f3949c9 "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"/>
1dce9f3949c9 "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"/>
1dce9f3949c9 "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
9eaeea3fb1bb 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>
9eaeea3fb1bb 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
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213 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
1dce9f3949c9 "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>
1dce9f3949c9 "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>
1dce9f3949c9 "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>
1dce9f3949c9 "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>
1dce9f3949c9 "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
9eaeea3fb1bb 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
1dce9f3949c9 "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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iuc
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diff changeset
223 <param name="input_type|input_type_select" value="paired"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
224 <param name="input_type|fqinputs">
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225 <collection type="list">
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
diff changeset
226 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
227 <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
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228 </collection>
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229 </param>
1
aa646fe5a0b4 "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
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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231 <param name="assembly_options|d" value="-d"/>
0
9eaeea3fb1bb 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
1dce9f3949c9 "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
9eaeea3fb1bb 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
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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235 <param name="gapped|use_gapped" value="yes"/>
1dce9f3949c9 "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
9eaeea3fb1bb 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
1dce9f3949c9 "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
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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239 <assert_command>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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diff changeset
240 <has_text text="--keep_high_cov"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
241 <has_text text="-d"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
242 <has_text text="--high_cov_thres 2.0"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
243 <has_text text="--max_locus_stacks 4"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
244 <has_text text="--k_len 12"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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245 <has_text text="--max_gaps 3"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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246 <has_text text="--min_aln_len 0.7"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
247 </assert_command>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
248 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
9eaeea3fb1bb 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
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
250 <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
251 <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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252 <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
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253 <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
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254 <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>
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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>
2
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297 <expand macro="citation"/>
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298 </tool>