Mercurial > repos > matthias > stacks2_gstacks

annotate stacks_gstacks.xml @ 2:4301ded2ea50 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
author matthias
date Tue, 18 Dec 2018 12:58:51 -0500
parents 192f1d5f301e
children 285e1f85c11a
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1 <tool id="stacks2_gstacks" name="Stacks2: gstacks" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>match stacks to a catalog</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="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 &&
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12 #if $mode_cond.mode_select == "denovo" and not $popmap:
2
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13 ## since collections have no len .. yet
4301ded2ea50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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14 #try:
4301ded2ea50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
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15 #set count = len($input_bam)
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16 #except:
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17 #set count = len($input_bam.keys())
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18 #end try
0
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19 #if count == 1:
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20 #for $bam in $input_bam:
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21 ln -s '$bam' bam_inputs/catalog.bam &&
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22 #end for
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23 #else
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24 >&2 echo "exactly one (merged) bam file is needed in denovo mode if no population map is given" &&
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25 exit 1 &&
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26 #end if
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27 #else
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28 @BAM_INPUT@
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29 #end if
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30
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31 gstacks
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32
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33 #if $mode_cond.mode_select == "denovo":
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34 -P bam_inputs
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35 $mode_cond.ignore_pe_reads
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36 #if $mode_cond.advanced_cond.advanced_select == "yes":
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37 --kmer-length $mode_cond.advanced_cond.kmer_length
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38 --max-debruijn-reads $mode_cond.advanced_cond.max_debruijn_reads
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39 --min-kmer-cov $mode_cond.advanced_cond.min_kmer_cov
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40 #end if
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41 #else:
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42 #if $popmap
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43 -I bam_inputs
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44 #else
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45 $bamlist
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46 #end if
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47 #if $mode_cond.paired_cond.paired_select == ''
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48 $mode_cond.paired_cond.rm_unpaired_reads
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49 $mode_cond.paired_cond.rm_pcr_duplicates
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50 #else:
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51 $mode_cond.paired_cond.paired_select
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52 #end if
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53 #if $mode_cond.advanced_cond.advanced_select == "yes":
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54 --min-mapq $mode_cond.advanced_cond.min_mapq
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55 --max-clipped $mode_cond.advanced_cond.max_clipped
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56 --max-insert-len $mode_cond.advanced_cond.max_insert_len
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57 $mode_cond.advanced_cond.details
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58 --phasing-cooccurrences-thr-range $mode_cond.advanced_cond.phasing_cooccurrences_thr_min,$mode_cond.advanced_cond.phasing_cooccurrences_thr_max
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59 $mode_cond.advanced_cond.phasing_dont_prune_hets
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60 #end if
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61 #end if
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62 #if $popmap
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63 -M '$popmap'
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64 #end if
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65 -O stacks_outputs
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66 -t \${GALAXY_SLOTS:-1}
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67
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68 ##Model options:
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69 --model $model_cond.model
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70 #if $model_cond.model != "snp":
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71 --var-alpha $model_cond.var_alpha
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72 #end if
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73 --gt-alpha $model_cond.gt_alpha
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74
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75 ## annoyingly gstacks creates stacks_output/population.log
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76 ## instead of just writing to stderr as the other tools
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77 ## hence we do not use the tokens and return populations.log as log file and take the stderr
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78 && mv stacks_outputs/gstacks.log $output_log
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79
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80 ## the catalog.calls output is a gzip-ed vcf extract it
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81 ## to make it usable in Galaxy (with the downside that we
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82 ## need to gzip it again for downstream calls like populations)
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83 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
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84
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85
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86 ## TODO extract individual distributions from stacks_outputs/gstacks.log.distribs
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87 ## alternative extra tool
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88 ## for i in \$(stacks-dist-extract stacks_outputs/gstacks.log.distribs)
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89 ## do
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90 ## stacks-dist-extract stacks_outputs/gstacks.log.distribs $i > stacks_outputs/gstacks.log.\$i.tsv
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91 ## done
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92 ## TODO make optional output collection
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93 ]]></command>
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94
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95 <inputs>
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96 <expand macro="bam_input_macro"/>
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97 <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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98
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99 <conditional name="mode_cond">
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100 <param name="mode_select" type="select" label="Mode">
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101 <option value="denovo" selected="true">De novo mode</option>
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102 <option value="refbased">Reference-based</option>
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103 </param>
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104 <when value="denovo">
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105 <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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106 <conditional name="advanced_cond">
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107 <param name="advanced_select" type="select" label="Advanced options">
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108 <option value="no">No</option>
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109 <option value="yes">Yes</option>
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110 </param>
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111 <when value="yes">
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112 <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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113 <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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114 <param argument="--min-kmer-cov" name="min_kmer_cov" type="integer" value="2" label="minimum coverage to consider a kmer" />
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115 </when>
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116 <when value="no"/>
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117 </conditional>
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118 </when>
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119 <when value="refbased">
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120 <conditional name="paired_cond">
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121 <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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122 <option value="" selected="true">single/paired</option>
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123 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
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124 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
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125 </param>
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126 <when value="">
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127 <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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128 <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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129 </when>
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130 <when value="--unpaired"/>
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131 <when value="--ignore-pe-reads"/>
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132 </conditional>
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133 <conditional name="advanced_cond">
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134 <param name="advanced_select" type="select" label="Advanced options">
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135 <option value="no">No</option>
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136 <option value="yes">Yes</option>
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137 </param>
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138 <when value="yes">
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139 <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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140 <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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141 <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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142 <param argument="--details" type="boolean" checked="false" truevalue="--details" falsevalue="" label="write a heaview output" />
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143 <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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144 <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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145 <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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146 </when>
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147 <when value="no"/>
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148 </conditional>
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149 </when>
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150 </conditional>
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151
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152 <conditional name="model_cond">
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153 <param argument="--model" type="select" label="model to use to call variants and genotypes">
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154 <option value="marukilow" selected="true">marukilow</option>
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155 <option value="marukihigh">marukihigh</option>
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156 <option value="snp">snp</option>
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157 </param>
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158 <when value="marukilow">
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159 <expand macro="variant_calling_options_vg"/>
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160 </when>
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161 <when value="marukihigh">
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162 <expand macro="variant_calling_options_vg"/>
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163 </when>
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164 <when value="snp">
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165 <expand macro="variant_calling_options_g"/>
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166 </when>
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167 </conditional>
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168
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169 <expand macro="in_log"/>
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170 </inputs>
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171 <outputs>
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172 <expand macro="out_log"/>
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173 <data format="txt" name="distribs" label="${tool.name} on ${on_string} distribs" from_work_dir="gstacks.log.distribs" />
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174 <expand macro="gstacks_outputs_macro"/>
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175 </outputs>
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176
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177 <tests>
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178 <!-- denovomode, w popmap -->
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179 <test>
2
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180 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
0
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181 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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182 <conditional name="mode_cond">
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183 <param name="mode_select" value="denovo"/>
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184 </conditional>
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185 <param name="add_log" value="yes" />
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186 <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="8"/>
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187 <output_collection name="gstacks_out" type="list" count="2">
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188 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.tsv" ftype="vcf" lines_diff="2"/>
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189 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
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190 </output_collection>
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191 </test>
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192 <!-- denovomode, wo popmap (allows for only one input), ignore PE, advanced, alt model -->
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193 <test>
1
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194 <param name="input_bam" value="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
0
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195 <conditional name="mode_cond">
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196 <param name="mode_select" value="denovo" />
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197 <param name="ignore_pe_reads" value="--ignore-pe-reads" />
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198 <conditional name="advanced_cond">
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199 <param name="advanced_select" value="yes"/>
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200 <param name="kmer_length" value="23" />
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201 <param name="max_debruijn_reads" value="666"/>
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202 <param name="min_kmer_cov" value="3" />
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203 </conditional>
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204 </conditional>
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205 <conditional name="model_cond">
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206 <param name="model" value="marukihigh"/>
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207 <param name="var_alpha" value="0.1" />
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208 <param name="gt_alpha" value="0.1" />
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209 </conditional>
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210 <param name="add_log" value="yes" />
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211 <assert_command>
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212 <has_text text="--ignore-pe-reads" />
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213 <has_text text="--rm-pcr-duplicates" />
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214 <has_text text="--kmer-length 23" />
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215 <has_text text="--max-debruijn-reads 666" />
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216 <has_text text="--min-kmer-cov 3" />
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217 <has_text text="--model marukihigh" />
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218 <has_text text="--var-alpha 0.1" />
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219 <has_text text="--gt-alpha 0.1" />
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220 </assert_command>
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221 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
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222 <output_collection name="gstacks_out" type="list" count="2"/>
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223 </test>
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224 <!-- refbased wo popmap, paired options, removing all unpaired reads results in an error -->
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225 <test expect_failure="true" expect_exit_code="1">
1
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226 <param name="input_bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
0
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227 <conditional name="mode_cond">
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228 <param name="mode_select" value="refbased"/>
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229 <conditional name="paired_cond">
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230 <param name="paired_select" value=""/>
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231 <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes to much of the test data and gstacks fails-->
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232 <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" />
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233 </conditional>
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234 </conditional>
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235 <param name="add_log" value="yes" />
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236 <assert_command>
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237 <has_text text="-I bam_inputs" />
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238 <not_has_text text="-B " />
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239 <has_text text="--rm-unpaired-reads" />
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240 <has_text text="--rm-pcr-duplicates" />
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241 </assert_command>
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242 </test>
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243 <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
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244 <test>
2
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245 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
0
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246 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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247 <conditional name="mode_cond">
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248 <param name="mode_select" value="refbased"/>
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249 <conditional name="paired_cond">
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250 <param name="paired_select" value="--unpaired"/>
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251 </conditional>
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252 <conditional name="advanced_cond">
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253 <param name="advanced_select" value="yes" />
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254 <param name="min_mapq" value="23" />
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255 <param name="max_clipped" value="0.23" />
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256 <param name="max_insert_len" value="666" />
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257 <param name="details" value="--detailed"/>
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258 <param name="phasing_cooccurrences_thr_min" value="2"/>
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259 <param name="phasing_cooccurrences_thr_max" value="3"/>
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260 <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" />
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261 </conditional>
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262 </conditional>
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263 <param name="model_cond|model" value="snp"/>
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264 <param name="model_cond|gt_alpha" value="0.1" />
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265 <param name="add_log" value="yes" />
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266 <assert_command>
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267 <not_has_text text="-I bam_inputs" />
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268 <has_text text="-B " />
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269 <has_text text="--unpaired" />
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270 <has_text text="--min-mapq 23" />
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271 <has_text text="--max-clipped 0.23" />
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272 <has_text text="--max-insert-len 666" />
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273 <has_text text="--detailed" />
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274 <has_text text="--phasing-cooccurrences-thr-range 2,3" />
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275 <has_text text="--phasing-dont-prune-hets" />
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276 <has_text text="--model snp" />
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277 <has_text text="--gt-alpha 0.1" />
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278 </assert_command>
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279 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
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280 <output_collection name="gstacks_out" type="list" count="2"/>
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281 </test>
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282 <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe -->
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283 <test>
2
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284 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
0
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285 <conditional name="mode_cond">
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286 <param name="mode_select" value="refbased"/>
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287 <conditional name="paired_cond">
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288 <param name="paired_select" value="--ignore-pe-reads"/>
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289 </conditional>
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290 </conditional>
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291 <param name="add_log" value="yes" />
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292 <assert_command>
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293 <has_text text="-I bam_inputs" />
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294 <not_has_text text="-B " />
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295 <has_text text="--ignore-pe-reads" />
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296 </assert_command>
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297 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
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298 <output_collection name="gstacks_out" type="list" count="2">
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299 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.tsv" ftype="vcf" lines_diff="2"/>
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300 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
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301 </output_collection>
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302 </test>
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303 </tests>
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304
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305 <help>
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306 <![CDATA[
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307 .. class:: infomark
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308
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309 **What it does**
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310
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311 For de novo analyses, this program will pull in paired-end reads, if available,
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312 assemble the paired-end contig and merge it with the single-end locus, align
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313 reads to the locus, and call SNPs.
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314
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315 For reference-aligned analyses, this program will build loci from the single
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316 and/or paired-end reads before calling SNPs. The single- and paired-end reads
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317 must be aligned and stored together in the intput BAM or SAM files and the
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318 reads must be sorted. The gstacks program will detect if single- or paired-end
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319 reads are present.
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320
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321 In either mode, gstacks is able to remove PCR duplicates if requested.
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322
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323 --------
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324
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325 **Input files**
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326
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327 If a population map is given BAM records must be assigned to samples using BAM "reads groups"
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328 (gstacks uses the ID/identifier and SM/sample name fields). Read groups
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329 must be consistent if repeated different files.
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330 Otherwise read groups are unneeded and ignored.
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331
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332 **Output files**
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333
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334 TODO
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335
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336 @STACKS_INFOS@
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337 ]]>
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338 </help>
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339 <expand macro="citation" />
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340 </tool>