Mercurial > repos > matthias > stacks2_gstacks

annotate stacks_gstacks.xml @ 0:ce90584be117 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
author matthias
date Thu, 29 Nov 2018 11:52:48 -0500
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children 192f1d5f301e
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ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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1 <tool id="stacks2_gstacks" name="Stacks2: gstacks" version="@WRAPPER_VERSION@">
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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2 <description>match stacks to a catalog</description>
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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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="stdio"/>
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8 <command><![CDATA[
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9 @CLEAN_EXT@
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10
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11 mkdir bam_inputs stacks_outputs &&
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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12 #if $mode_cond.mode_select == "denovo" and not $popmap:
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13 #if $input_type.input_type_selector == 'manual':
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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14 #set count = len($input_type.input_bam)
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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15 #else
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16 #set count = len($input_type.input_bam.keys())
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17 #end if
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18 #if count == 1:
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19 #for $bam in $input_type.input_bam:
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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20 ln -s '$bam' bam_inputs/catalog.bam &&
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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21 #end for
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22 #else
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23 >&2 echo "exactly one (merged) bam file is needed in denovo mode if no population map is given" &&
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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24 exit 1 &&
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25 #end if
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26 #else
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27 @BAM_INPUT@
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28 #end if
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29
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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30 gstacks
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31
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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32 #if $mode_cond.mode_select == "denovo":
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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33 -P bam_inputs
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34 $mode_cond.ignore_pe_reads
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35 #if $mode_cond.advanced_cond.advanced_select == "yes":
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36 --kmer-length $mode_cond.advanced_cond.kmer_length
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37 --max-debruijn-reads $mode_cond.advanced_cond.max_debruijn_reads
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38 --min-kmer-cov $mode_cond.advanced_cond.min_kmer_cov
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39 #end if
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40 #else:
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41 #if $popmap
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42 -I bam_inputs
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43 #else
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44 $bamlist
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45 #end if
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46 #if $mode_cond.paired_cond.paired_select == ''
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47 $mode_cond.paired_cond.rm_unpaired_reads
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48 $mode_cond.paired_cond.rm_pcr_duplicates
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49 #else:
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50 $mode_cond.paired_cond.paired_select
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51 #end if
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52 #if $mode_cond.advanced_cond.advanced_select == "yes":
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53 --min-mapq $mode_cond.advanced_cond.min_mapq
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54 --max-clipped $mode_cond.advanced_cond.max_clipped
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55 --max-insert-len $mode_cond.advanced_cond.max_insert_len
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56 $mode_cond.advanced_cond.details
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57 --phasing-cooccurrences-thr-range $mode_cond.advanced_cond.phasing_cooccurrences_thr_min,$mode_cond.advanced_cond.phasing_cooccurrences_thr_max
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58 $mode_cond.advanced_cond.phasing_dont_prune_hets
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59 #end if
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60 #end if
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61 #if $popmap
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62 -M '$popmap'
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63 #end if
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64 -O stacks_outputs
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65 -t \${GALAXY_SLOTS:-1}
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66
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67 ##Model options:
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68 --model $model_cond.model
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69 #if $model_cond.model != "snp":
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70 --var-alpha $model_cond.var_alpha
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71 #end if
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72 --gt-alpha $model_cond.gt_alpha
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73
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74 ## annoyingly gstacks creates stacks_output/population.log
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75 ## instead of just writing to stderr as the other tools
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76 ## hence we do not use the tokens and return populations.log as log file and take the stderr
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77 && mv stacks_outputs/gstacks.log $output_log
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78
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79 ## the catalog.calls output is a gzip-ed vcf extract it
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80 ## to make it usable in Galaxy (with the downside that we
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81 ## need to gzip it again for downstream calls like populations)
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82 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
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83
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84
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85 ## TODO extract individual distributions from stacks_outputs/gstacks.log.distribs
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86 ## alternative extra tool
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87 ## for i in \$(stacks-dist-extract stacks_outputs/gstacks.log.distribs)
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88 ## do
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89 ## stacks-dist-extract stacks_outputs/gstacks.log.distribs $i > stacks_outputs/gstacks.log.\$i.tsv
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90 ## done
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91 ## TODO make optional output collection
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92 ]]></command>
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93
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94 <inputs>
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95 <expand macro="bam_input_macro"/>
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96 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" />
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97
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98 <conditional name="mode_cond">
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99 <param name="mode_select" type="select" label="Mode">
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100 <option value="denovo" selected="true">De novo mode</option>
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101 <option value="refbased">Reference-based</option>
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102 </param>
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103 <when value="denovo">
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104 <param argument="--ignore-pe-reads" name="ignore_pe_reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="ignore paired-end reads" help="ignore paired-end reads even if present in the input" />
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105 <conditional name="advanced_cond">
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106 <param name="advanced_select" type="select" label="Advanced options">
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107 <option value="no">No</option>
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108 <option value="yes">Yes</option>
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109 </param>
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110 <when value="yes">
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111 <param argument="--kmer-length" name="kmer_length" type="integer" value="31" min="2" max="31" label="kmer length for the de Bruijn graph" />
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112 <param argument="--max-debruijn-reads" name="max_debruijn_reads" type="integer" value="1000" min="1" label="maximum number of reads to use in the de Bruijn graph" />
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113 <param argument="--min-kmer-cov" name="min_kmer_cov" type="integer" value="2" label="minimum coverage to consider a kmer" />
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114 </when>
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115 <when value="no"/>
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116 </conditional>
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117 </when>
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118 <when value="refbased">
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119 <conditional name="paired_cond">
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120 <param name="paired_select" type="select" label="paired end options" help="select single/paired for single end data or to select advanced paired end options, --unpaired: treat reverse reads as if they were forward reads; --ignore-pe-reads: ignore paired-end reads even if present in the input">
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121 <option value="" selected="true">single/paired</option>
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122 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
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123 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
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124 </param>
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125 <when value="">
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126 <param argument="--rm-unpaired-reads" name="rm_unpaired_reads" type="boolean" checked="false" truevalue="--rm-unpaired-reads" falsevalue="" label="discard unpaired reads" />
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127 <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="remove read pairs of the same sample that have the same insert length" help="implies --rm-unpaired-reads" />
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128 </when>
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129 <when value="--unpaired"/>
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130 <when value="--ignore-pe-reads"/>
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131 </conditional>
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132 <conditional name="advanced_cond">
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133 <param name="advanced_select" type="select" label="Advanced options">
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134 <option value="no">No</option>
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135 <option value="yes">Yes</option>
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136 </param>
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137 <when value="yes">
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138 <param argument="--min-mapq" name="min_mapq" type="integer" value="10" min="0" max="255" label="minimum PHRED-scaled mapping quality to consider a read" />
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139 <param argument="--max-clipped" name="max_clipped" type="float" value="0.2" min="0.0" max="1.1" label="maximum soft-clipping level" help="in fraction of read length" />
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140 <param argument="--max-insert-len" name="max_insert_len" type="integer" value="1000" min="0" label="maximum allowed sequencing insert length" />
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141 <param argument="--details" type="boolean" checked="false" truevalue="--details" falsevalue="" label="write a heaview output" />
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142 <param name="phasing_cooccurrences_thr_min" type="integer" value="1" min="0" label="edge coverage min" help="(--phasing-cooccurrences-thr-range)" />
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143 <param name="phasing_cooccurrences_thr_max" type="integer" value="2" min="0" label="edge coverage max" help="range of edge coverage thresholds to iterate over when building the graph of allele cooccurrences for SNP phasing (--phasing-cooccurrences-thr-range)"/>
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144 <param argument="--phasing-dont-prune-hets" name="phasing_dont_prune_hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="don't try to ignore dubious heterozygote genotypes during phasing" />
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145 </when>
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146 <when value="no"/>
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147 </conditional>
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148 </when>
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149 </conditional>
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150
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151 <conditional name="model_cond">
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152 <param argument="--model" type="select" label="model to use to call variants and genotypes">
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153 <option value="marukilow" selected="true">marukilow</option>
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154 <option value="marukihigh">marukihigh</option>
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155 <option value="snp">snp</option>
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156 </param>
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157 <when value="marukilow">
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158 <expand macro="variant_calling_options_vg"/>
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159 </when>
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160 <when value="marukihigh">
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161 <expand macro="variant_calling_options_vg"/>
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162 </when>
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163 <when value="snp">
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164 <expand macro="variant_calling_options_g"/>
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165 </when>
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166 </conditional>
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167
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168 <expand macro="in_log"/>
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169 </inputs>
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170 <outputs>
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171 <expand macro="out_log"/>
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172 <data format="txt" name="distribs" label="${tool.name} on ${on_string} distribs" from_work_dir="gstacks.log.distribs" />
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173 <expand macro="gstacks_outputs_macro"/>
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174 </outputs>
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175
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176 <tests>
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177 <!-- denovomode, w popmap -->
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178 <test>
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179 <param name="input_type|input_type_selector" value="list"/>
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180 <param name="input_type|input_bam">
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181 <collection type="list">
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182 <element name="PopA_01.matches" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
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183 <element name="PopA_02.matches" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
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184 </collection>
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185 </param>
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186 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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187 <conditional name="mode_cond">
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188 <param name="mode_select" value="denovo"/>
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189 </conditional>
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190 <param name="add_log" value="yes" />
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191 <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="8"/>
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192 <output_collection name="gstacks_out" type="list" count="2">
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193 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.tsv" ftype="vcf" lines_diff="2"/>
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194 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
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195 </output_collection>
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196 </test>
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197 <!-- denovomode, wo popmap (allows for only one input), ignore PE, advanced, alt model -->
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198 <test>
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199 <param name="input_type|input_type_selector" value="manual"/>
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200 <param name="input_type|input_bam" value="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
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201 <conditional name="mode_cond">
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202 <param name="mode_select" value="denovo" />
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203 <param name="ignore_pe_reads" value="--ignore-pe-reads" />
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204 <conditional name="advanced_cond">
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205 <param name="advanced_select" value="yes"/>
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206 <param name="kmer_length" value="23" />
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207 <param name="max_debruijn_reads" value="666"/>
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208 <param name="min_kmer_cov" value="3" />
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209 </conditional>
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210 </conditional>
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211 <conditional name="model_cond">
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212 <param name="model" value="marukihigh"/>
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213 <param name="var_alpha" value="0.1" />
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214 <param name="gt_alpha" value="0.1" />
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215 </conditional>
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216 <param name="add_log" value="yes" />
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217 <assert_command>
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218 <has_text text="--ignore-pe-reads" />
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219 <has_text text="--rm-pcr-duplicates" />
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220 <has_text text="--kmer-length 23" />
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221 <has_text text="--max-debruijn-reads 666" />
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222 <has_text text="--min-kmer-cov 3" />
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223 <has_text text="--model marukihigh" />
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224 <has_text text="--var-alpha 0.1" />
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225 <has_text text="--gt-alpha 0.1" />
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226 </assert_command>
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227 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
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228 <output_collection name="gstacks_out" type="list" count="2"/>
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229 </test>
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230 <!-- refbased wo popmap, paired options, removing all unpaired reads results in an error -->
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231 <test expect_failure="true" expect_exit_code="1">
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232 <param name="input_type|input_type_selector" value="manual"/>
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233 <param name="input_type|input_bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
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234 <conditional name="mode_cond">
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235 <param name="mode_select" value="refbased"/>
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236 <conditional name="paired_cond">
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237 <param name="paired_select" value=""/>
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238 <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes to much of the test data and gstacks fails-->
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239 <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" />
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240 </conditional>
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241 </conditional>
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242 <param name="add_log" value="yes" />
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243 <assert_command>
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244 <has_text text="-I bam_inputs" />
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245 <not_has_text text="-B " />
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246 <has_text text="--rm-unpaired-reads" />
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247 <has_text text="--rm-pcr-duplicates" />
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248 </assert_command>
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249 </test>
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250 <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
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251 <test>
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252 <param name="input_type|input_type_selector" value="list"/>
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253 <param name="input_type|input_bam">
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254 <collection type="list">
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255 <element name="PopA_01" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
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256 <element name="PopA_02" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
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257 </collection>
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258 </param>
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259 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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260 <conditional name="mode_cond">
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261 <param name="mode_select" value="refbased"/>
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262 <conditional name="paired_cond">
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263 <param name="paired_select" value="--unpaired"/>
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264 </conditional>
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265 <conditional name="advanced_cond">
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266 <param name="advanced_select" value="yes" />
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267 <param name="min_mapq" value="23" />
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268 <param name="max_clipped" value="0.23" />
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269 <param name="max_insert_len" value="666" />
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270 <param name="details" value="--detailed"/>
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271 <param name="phasing_cooccurrences_thr_min" value="2"/>
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272 <param name="phasing_cooccurrences_thr_max" value="3"/>
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273 <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" />
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274 </conditional>
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275 </conditional>
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276 <param name="model_cond|model" value="snp"/>
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277 <param name="model_cond|gt_alpha" value="0.1" />
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278 <param name="add_log" value="yes" />
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279 <assert_command>
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280 <not_has_text text="-I bam_inputs" />
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281 <has_text text="-B " />
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282 <has_text text="--unpaired" />
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283 <has_text text="--min-mapq 23" />
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284 <has_text text="--max-clipped 0.23" />
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285 <has_text text="--max-insert-len 666" />
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286 <has_text text="--detailed" />
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287 <has_text text="--phasing-cooccurrences-thr-range 2,3" />
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288 <has_text text="--phasing-dont-prune-hets" />
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289 <has_text text="--model snp" />
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290 <has_text text="--gt-alpha 0.1" />
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291 </assert_command>
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292 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
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293 <output_collection name="gstacks_out" type="list" count="2"/>
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294 </test>
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295 <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe -->
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296 <test>
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297 <param name="input_type|input_type_selector" value="list"/>
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298 <param name="input_type|input_bam">
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299 <collection type="list">
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300 <element name="PopA_01.matches" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
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301 <element name="PopA_02.matches" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
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302 </collection>
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303 </param>
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304 <conditional name="mode_cond">
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305 <param name="mode_select" value="refbased"/>
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306 <conditional name="paired_cond">
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307 <param name="paired_select" value="--ignore-pe-reads"/>
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308 </conditional>
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309 </conditional>
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310 <param name="add_log" value="yes" />
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311 <assert_command>
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312 <has_text text="-I bam_inputs" />
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313 <not_has_text text="-B " />
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314 <has_text text="--ignore-pe-reads" />
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315 </assert_command>
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316 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
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317 <output_collection name="gstacks_out" type="list" count="2">
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318 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.tsv" ftype="vcf" lines_diff="2"/>
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319 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
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320 </output_collection>
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321 </test>
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322 </tests>
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323
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324 <help>
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325 <![CDATA[
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326 .. class:: infomark
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327
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328 **What it does**
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329
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330 For de novo analyses, this program will pull in paired-end reads, if available,
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331 assemble the paired-end contig and merge it with the single-end locus, align
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332 reads to the locus, and call SNPs.
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333
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334 For reference-aligned analyses, this program will build loci from the single
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335 and/or paired-end reads before calling SNPs. The single- and paired-end reads
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336 must be aligned and stored together in the intput BAM or SAM files and the
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337 reads must be sorted. The gstacks program will detect if single- or paired-end
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338 reads are present.
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339
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340 In either mode, gstacks is able to remove PCR duplicates if requested.
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341
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342 --------
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343
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344 **Input files**
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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345
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346 If a population map is given BAM records must be assigned to samples using BAM "reads groups"
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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347 (gstacks uses the ID/identifier and SM/sample name fields). Read groups
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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348 must be consistent if repeated different files.
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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349 Otherwise read groups are unneeded and ignored.
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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350
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351 **Output files**
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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352
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353 TODO
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354
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355 @STACKS_INFOS@
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356 ]]>
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357 </help>
ce90584be117 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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358 <expand macro="citation" />
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359 </tool>