Mercurial > repos > iuc > stacks2_ustacks

annotate stacks_ustacks.xml @ 0:7e5a174bc201 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 10:57:49 -0400
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7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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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11 mkdir stacks_inputs stacks_outputs
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13 &&
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15 #set $ID=1
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16 #for $sample in $input_type.fqinputs
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17 #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1")
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18 $create_links
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20 ustacks
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22 -f '$data_path'
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23 -i $ID
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24 --name $name
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25 -m $m
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26 -M $M
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27 #if $N
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28 -N $N
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29 #end if
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30 -p \${GALAXY_SLOTS:-1}
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31 -t $inputype
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32 $R
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33 $H
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34
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35 ## Assembly
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36 $assembly_options.keep_high_cov
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37 --high_cov_thres $assembly_options.high_cov_thres
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38 $assembly_options.d
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39 --max_locus_stacks $assembly_options.max_locus_stacks
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40 #if str($assembly_options.k_len)
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41 --k_len $assembly_options.k_len
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42 #end if
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43
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44 @GAP_OPTIONS@
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45
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46 ## snp_model
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47 #if str( $snp_options.select_model.model_type) == "bounded"
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48 --model_type bounded
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49 --bound_low $snp_options.select_model.bound_low
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50 --bound_high $snp_options.select_model.bound_high
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51 --alpha $snp_options.select_model.alpha
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52 #else if str( $snp_options.select_model.model_type) == "snp"
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53 --model_type snp
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54 --alpha $snp_options.select_model.alpha
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55 #else
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56 --model_type fixed
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57 --bc_err_freq $bc_err_freq
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58 #end if
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59
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60 -o stacks_outputs
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61
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62 @TEE_APPEND_LOG@
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63
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64 #set $ID=$ID+1
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65 #end for
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66 @CAT_LOG_TO_STDERR@
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67 ## If input is in gz format, stacks will output gzipped files (no option to control this)
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68 #if $inputype.startswith('gz')
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69 && gunzip stacks_outputs/*.gz
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70 #end if
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71 ]]></command>
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72
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73 <inputs>
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74 <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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75
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76 <param argument="-m" type="integer" value="3" label="Minimum depth of coverage required to create a stack"/>
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77 <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
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78 <param argument="-N" type="integer" value="" optional="true" label="Maximum distance allowed to align secondary reads to primary stacks" help="(default: M + 2)"/>
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79 <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" />
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80 <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
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81 <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True">
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82 <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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83 <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" />
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84 <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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85 <param argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/>
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86 <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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87 </section>
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88 <expand macro="gap_options"/>
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89
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90 <!-- SNP Model options -->
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91 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">
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diff changeset
92 <expand macro="snp_options_full"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
93 </section>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
94 <expand macro="in_log"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
95 </inputs>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
96
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
97 <outputs>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
98 <expand macro="out_log"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
99 <expand macro="ustacks_outputs_macro"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
100 </outputs>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
101
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
102 <tests>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
103 <!-- paired list, default options, test for file equality -->
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
104 <test>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
105 <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
iuc
parents:
diff changeset
106 <param name="input_type|fqinputs">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
107 <collection type="list:paired">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
108 <element name="PopA_01">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
109 <collection type="paired">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
110 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
111 <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
iuc
parents:
diff changeset
112 </collection>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
113 </element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
114 <element name="PopA_02">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
115 <collection type="paired">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
116 <element name="forward" 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
iuc
parents:
diff changeset
117 <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
iuc
parents:
diff changeset
118 </collection>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
119 </element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
120 </collection>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
121 </param>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
122 <param name="add_log" value="yes" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
123 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
124 <output_collection name="tabs" type="list" count="6">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
125 <element name="PopA_01.tags" ftype="tabular" file="ustacks/PopA_01.tags.tsv" lines_diff="2"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
126 <element name="PopA_01.snps" ftype="tabular" file="ustacks/PopA_01.snps.tsv" lines_diff="2"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
127 <element name="PopA_01.alleles" ftype="tabular" file="ustacks/PopA_01.alleles.tsv" lines_diff="2"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
128 <element name="PopA_02.tags" ftype="tabular" file="ustacks/PopA_02.tags.tsv" lines_diff="2"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
129 <element name="PopA_02.snps" ftype="tabular" file="ustacks/PopA_02.snps.tsv" lines_diff="2"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
130 <element name="PopA_02.alleles" ftype="tabular" file="ustacks/PopA_02.alleles.tsv" lines_diff="2"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
131 </output_collection>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
132 </test>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
133 <!-- manual selected list of elements + default args, test for file equality -->
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
134 <test>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
135 <param name="input_type|input_type_select" value="single"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
136 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
137 <param name="add_log" value="yes" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
139 <output_collection name="tabs" count="6">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
140 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
141 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
142 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
143 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
144 <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
145 <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
146 </output_collection>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
147 </test>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
148 <!-- manual selected list of elements + non-default short args, test for file presence -->
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
149 <test>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
150 <param name="input_type|input_type_select" value="single"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
151 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
152 <param name="-m" value="2" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
153 <param name="-M" value="3" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
154 <param name="-N" value="4"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
155 <param name="-R" value="-R" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
156 <param name="-H" value="-H" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
157 <param name="add_log" value="yes" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
158 <assert_command>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
159 <has_text text="-m 2" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
160 <has_text text="-M 3" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
161 <has_text text="-N 5" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
162 <has_text text="-R" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
163 <has_text text="-H" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
164 </assert_command>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
166 <output_collection name="tabs" count="6">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
167 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
168 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
169 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
170 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
171 <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
172 <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
173 </output_collection>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
174 </test>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
175 <!-- paired list, non-default model options, disabled gapped alignment, test for file presence -->
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
176 <test>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
177 <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
iuc
parents:
diff changeset
178 <param name="input_type|fqinputs">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
179 <collection type="list:paired">
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
180 <element name="PopA_01">
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181 <collection type="paired">
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182 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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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diff changeset
186 <element name="PopA_02">
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187 <collection type="paired">
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188 <element name="forward" 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
iuc
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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>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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192 </collection>
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193 </param>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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200 </conditional>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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201 <param name="gapped|use_gapped" value="no" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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202 <param name="add_log" value="yes" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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203 <assert_command>
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204 <has_text text="--model_type bounded" />
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205 <has_text text="--alpha 0.1" />
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206 <has_text text="--bound_low 0.1" />
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207 <has_text text="--bound_high 0.5" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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208 <has_text text="--bc_err_freq 0.1" />
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209 <has_text text="--disable-gapped" />
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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>
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212 <output_collection name="tabs" count="6">
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213 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
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214 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
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215 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
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216 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
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217 <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
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218 <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
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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 -->
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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222 <test>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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">
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226 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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230 <param name="assembly_options|keep_high_cov" value="--keep-high-cov"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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231 <param name="assembly_options|d" value="-d" />
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"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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233 <param name="assembly_options|max_locus_stacks" value="4" />
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"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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235 <param name="gapped|use_gapped" value="yes" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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236 <param name="gapped|max_gaps" value="3" />
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"/>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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238 <param name="add_log" value="yes" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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239 <assert_command>
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240 <has_text text="--keep_high_cov" />
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iuc
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241 <has_text text="-d" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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242 <has_text text="--high_cov_thres 2.0" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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243 <has_text text="--max_locus_stacks 4" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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244 <has_text text="--k_len 12" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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245 <has_text text="--max_gaps 3" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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246 <has_text text="--min_aln_len 3" />
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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247 </assert_command>
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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">
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250 <element name="PopA_01.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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251 <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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252 <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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253 <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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254 <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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255 <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element>
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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267
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268 --------
7e5a174bc201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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269
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270 **Input files**
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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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274 **Output files**
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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>