annotate stacks_gstacks.xml @ 0:d35cb34f2b85 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 10:59:14 -0400
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children 27359c6bf3e3
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0
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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1 <tool id="stacks2_gstacks" name="Stacks2: gstacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>Call variants, genotypes and haplotype</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 <requirement type="package" version="1.9">samtools</requirement>
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8 </expand>
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9 <expand macro="version_cmd"/>
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10 <command detect_errors="aggressive"><![CDATA[
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11 @FASTQ_INPUT_FUNCTIONS@
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12
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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13 mkdir bam_inputs stacks_outputs &&
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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14 #if $mode_cond.mode_select == "denovo" and not $popmap:
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15 ## since collections have no len .. yet
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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16 #try:
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17 #set count = len($input_bam)
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18 #except:
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19 #set count = len($input_bam.keys())
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20 #end try
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21 #if count == 1:
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22 #for $bam in $input_bam:
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23 ln -s '$bam' bam_inputs/catalog.bam &&
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24 #end for
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25 #else
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26 >&2 echo "exactly one (merged) bam file is needed in denovo mode if no population map is given" &&
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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27 exit 1 &&
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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28 #end if
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29 #else
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30 @BAM_INPUT@
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31 #end if
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32
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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33 gstacks
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34
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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35 #if $mode_cond.mode_select == "denovo":
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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36 -P bam_inputs
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37 $mode_cond.ignore_pe_reads
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38 #if $mode_cond.advanced_cond.advanced_select == "yes":
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39 --kmer-length $mode_cond.advanced_cond.kmer_length
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40 --max-debruijn-reads $mode_cond.advanced_cond.max_debruijn_reads
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41 --min-kmer-cov $mode_cond.advanced_cond.min_kmer_cov
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42 $mode_cond.advanced_cond.write_alignments
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43 #end if
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44 #else:
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45 #if $popmap
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46 -I bam_inputs
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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47 #else
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48 $bamlist
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49 #end if
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50 #if $mode_cond.paired_cond.paired_select == ''
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51 $mode_cond.paired_cond.rm_unpaired_reads
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52 $mode_cond.paired_cond.rm_pcr_duplicates
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53 #else:
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54 $mode_cond.paired_cond.paired_select
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55 #end if
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56 #if $mode_cond.advanced_cond.advanced_select == "yes":
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57 --min-mapq $mode_cond.advanced_cond.min_mapq
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58 --max-clipped $mode_cond.advanced_cond.max_clipped
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59 --max-insert-len $mode_cond.advanced_cond.max_insert_len
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60 $mode_cond.advanced_cond.details
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61 --phasing-cooccurrences-thr-range $mode_cond.advanced_cond.phasing_cooccurrences_thr_min,$mode_cond.advanced_cond.phasing_cooccurrences_thr_max
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62 $mode_cond.advanced_cond.phasing_dont_prune_hets
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63 #end if
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64 #end if
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65 #if $popmap
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66 -M '$popmap'
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67 #end if
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68 -O stacks_outputs
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69 -t \${GALAXY_SLOTS:-1}
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70
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71 ##Model options:
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72 --model $model_cond.model
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73 --var-alpha $model_cond.var_alpha
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74 --gt-alpha $model_cond.gt_alpha
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75
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76
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77 ## the bam files generated by gstacks (--write-alignments) are seemingly buggy
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78 ## (https://groups.google.com/d/msg/stacks-users/CazwJY1DPGA/7vuahiB2GgAJ)
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79 ## so we fix them temporarily by piping them through samtools view (disabling all
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80 ## exit codes and stderr output) this adds the samtools requirement
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81 ## for later versions where this is fixed the output bam files could just be moved
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82 ## to stacks_outputs if this is still necessary
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83 #if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments != ""
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84 #if $popmap:
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85 && for b in bam_inputs/*alns.bam; do (samtools view -b "\$b" || true) 2> /dev/null > stacks_outputs/\$(basename "\$b"); done
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86 #else
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87 && (samtools view -b bam_inputs/alignments.bam || true) 2> /dev/null > stacks_outputs/alignments.bam
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88 #end if
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89 #end if
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90
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91
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92 ## annoyingly gstacks creates stacks_output/gstacks.log
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93 ## instead of just writing to stderr as the other tools
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94 ## hence we do not use the tokens and return populations.log as log file and take the stderr
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95 #if $output_log
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96 && mv stacks_outputs/gstacks.log $output_log
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97 #end if
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98
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99 @EXTRACT_VCF@
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100
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101 ## TODO extract individual distributions from stacks_outputs/gstacks.log.distribs
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102 ## alternative extra tool
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103 ## for i in \$(stacks-dist-extract stacks_outputs/gstacks.log.distribs)
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104 ## do
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105 ## stacks-dist-extract stacks_outputs/gstacks.log.distribs $i > stacks_outputs/gstacks.log.\$i.tsv
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106 ## done
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107 ## TODO make optional output collection
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108 ]]></command>
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109
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110 <inputs>
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111 <expand macro="bam_input_macro"/>
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112 <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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113
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114 <conditional name="mode_cond">
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115 <param name="mode_select" type="select" label="Mode">
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116 <option value="denovo" selected="true">De novo mode</option>
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117 <option value="refbased">Reference-based</option>
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118 </param>
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119 <when value="denovo">
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120 <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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121 <conditional name="advanced_cond">
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122 <param name="advanced_select" type="select" label="Advanced options">
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123 <option value="no">No</option>
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124 <option value="yes">Yes</option>
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125 </param>
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126 <when value="yes">
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127 <param argument="--kmer-length" name="kmer_length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph" />
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128 <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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129 <param argument="--min-kmer-cov" name="min_kmer_cov" type="integer" value="2" label="Minimum coverage to consider a kmer" />
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130 <param argument="--write-alignments" name="write_alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/>
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131 </when>
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132 <when value="no"/>
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133 </conditional>
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134 </when>
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135 <when value="refbased">
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136 <conditional name="paired_cond">
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137 <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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138 <option value="" selected="true">single/paired</option>
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139 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
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140 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
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141 </param>
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142 <when value="">
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143 <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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144 <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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145 </when>
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146 <when value="--unpaired"/>
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147 <when value="--ignore-pe-reads"/>
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148 </conditional>
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149 <conditional name="advanced_cond">
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150 <param name="advanced_select" type="select" label="Advanced options">
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151 <option value="no">No</option>
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152 <option value="yes">Yes</option>
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153 </param>
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154 <when value="yes">
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155 <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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156 <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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157 <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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158 <param argument="--details" type="boolean" checked="false" truevalue="--details" falsevalue="" label="Write a heaview output" />
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159 <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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160 <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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161 <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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162 </when>
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163 <when value="no"/>
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164 </conditional>
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165 </when>
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166 </conditional>
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167
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168 <conditional name="model_cond">
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169 <param argument="--model" type="select" label="Model to use to call variants and genotypes">
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170 <option value="marukilow" selected="true">marukilow</option>
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171 <option value="marukihigh">marukihigh</option>
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172 <option value="snp">snp</option>
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173 </param>
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174 <when value="marukilow">
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175 <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
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176 </when>
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177 <when value="marukihigh">
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178 <expand macro="variant_calling_options_vg"/>
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179 </when>
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180 <when value="snp">
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181 <expand macro="variant_calling_options_vg"/>
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182 </when>
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183 </conditional>
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184 <param name="add_log_distribs" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log distribs output as dataset" />
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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185 <expand macro="in_log"/>
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186 </inputs>
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187 <outputs>
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188 <expand macro="out_log"/>
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189 <expand macro="gstacks_outputs_full_macro"/>
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190 </outputs>
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191
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192 <tests>
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193 <!-- denovomode, w popmap -->
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194 <test expect_num_outputs="3">
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195 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
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196 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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197 <conditional name="mode_cond">
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198 <param name="mode_select" value="denovo"/>
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199 </conditional>
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200 <param name="add_log" value="yes" />
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201 <param name="add_log_distribs" value="yes" />
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202 <output name="output_log" ftype="txt" file="gstacks/gstacks.log" lines_diff="8"/>
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203 <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size"/>
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204 <output_collection name="gstacks_out" type="list" count="2">
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205 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="2"/>
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206 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz"/>
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207 </output_collection>
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208 </test>
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209 <!-- denovomode, w popmap, write alignments -->
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210 <test expect_num_outputs="3">
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211 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
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212 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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213 <conditional name="mode_cond">
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214 <param name="mode_select" value="denovo"/>
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215 <conditional name="advanced_cond">
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216 <param name="advanced_select" value="yes"/>
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217 <param name="write_alignments" value="--write-alignments" />
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218 </conditional>
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219 </conditional>
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220 <param name="add_log" value="yes" />
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221 <assert_command>
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222 <has_text text="--write-alignments" />
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223 </assert_command>
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224 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output>
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225 <output_collection name="gstacks_out" type="list" count="2"/>
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226 <output_collection name="gstacks_alns_out" type="list" count="2">
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iuc
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227 <element name="PopA_01" file="gstacks/PopA_01.alns.bam" ftype="bam" />
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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228 <element name="PopA_02" file="gstacks/PopA_02.alns.bam" ftype="bam" />
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229 </output_collection>
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230 </test>
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231 <!-- denovomode, wo popmap (allows for only one input), ignore PE, advanced, alt model -->
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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232 <test expect_num_outputs="3">
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233 <param name="input_bam" value="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
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iuc
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234 <conditional name="mode_cond">
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235 <param name="mode_select" value="denovo" />
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236 <param name="ignore_pe_reads" value="--ignore-pe-reads" />
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iuc
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237 <conditional name="advanced_cond">
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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238 <param name="advanced_select" value="yes"/>
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239 <param name="kmer_length" value="23" />
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240 <param name="max_debruijn_reads" value="666"/>
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241 <param name="min_kmer_cov" value="3" />
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242 <param name="write_alignments" value="--write-alignments" />
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243 </conditional>
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244 </conditional>
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245 <conditional name="model_cond">
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246 <param name="model" value="marukihigh"/>
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247 <param name="var_alpha" value="0.1" />
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248 <param name="gt_alpha" value="0.1" />
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249 </conditional>
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250 <param name="add_log" value="yes" />
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251 <assert_command>
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252 <has_text text="--ignore-pe-reads" />
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253 <has_text text="--rm-pcr-duplicates" />
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254 <has_text text="--kmer-length 23" />
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255 <has_text text="--max-debruijn-reads 666" />
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256 <has_text text="--min-kmer-cov 3" />
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257 <has_text text="--write-alignments" />
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258 <has_text text="--model marukihigh" />
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259 <has_text text="--var-alpha 0.1" />
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260 <has_text text="--gt-alpha 0.1" />
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261 </assert_command>
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262 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output>
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263 <output_collection name="gstacks_out" type="list" count="2"/>
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264 <output name="gstacks_aln_out" ftype="bam" file="gstacks/alignments.bam" />
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265 </test>
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266 <!-- refbased wo popmap, paired options, removing all unpaired reads results in an error -->
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267 <test expect_failure="true" expect_exit_code="1">
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268 <param name="input_bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/>
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269 <conditional name="mode_cond">
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270 <param name="mode_select" value="refbased"/>
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271 <conditional name="paired_cond">
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272 <param name="paired_select" value=""/>
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273 <!--<param name="rm_unpaired_reads" value="\-\-rm-unpaired-reads" /> removes to much of the test data and gstacks fails-->
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274 <param name="rm_pcr_duplicates" value="--rm-pcr-duplicates" />
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275 </conditional>
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276 </conditional>
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277 <param name="add_log" value="yes" />
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278 <assert_command>
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279 <has_text text="-I bam_inputs" />
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280 <not_has_text text="-B " />
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281 <has_text text="--rm-unpaired-reads" />
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282 <has_text text="--rm-pcr-duplicates" />
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283 </assert_command>
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284 </test>
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285 <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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286 <test expect_num_outputs="2">
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287 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/>
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288 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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289 <conditional name="mode_cond">
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290 <param name="mode_select" value="refbased"/>
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291 <conditional name="paired_cond">
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292 <param name="paired_select" value="--unpaired"/>
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293 </conditional>
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294 <conditional name="advanced_cond">
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295 <param name="advanced_select" value="yes" />
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296 <param name="min_mapq" value="23" />
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297 <param name="max_clipped" value="0.23" />
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298 <param name="max_insert_len" value="666" />
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299 <param name="details" value="--detailed"/>
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300 <param name="phasing_cooccurrences_thr_min" value="2"/>
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301 <param name="phasing_cooccurrences_thr_max" value="3"/>
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302 <param name="phasing_dont_prune_hets" value="--phasing-dont-prune-hets" />
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303 </conditional>
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304 </conditional>
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305 <param name="model_cond|model" value="snp"/>
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306 <param name="model_cond|gt_alpha" value="0.1" />
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307 <param name="model_cond|var_alpha" value="0.1" />
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308 <param name="add_log" value="yes" />
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309 <assert_command>
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310 <not_has_text text="-I bam_inputs" />
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311 <has_text text="-B " />
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312 <has_text text="--unpaired" />
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iuc
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313 <has_text text="--min-mapq 23" />
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314 <has_text text="--max-clipped 0.23" />
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315 <has_text text="--max-insert-len 666" />
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316 <has_text text="--detailed" />
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317 <has_text text="--phasing-cooccurrences-thr-range 2,3" />
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318 <has_text text="--phasing-dont-prune-hets" />
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319 <has_text text="--model snp" />
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320 <has_text text="--gt-alpha 0.1" />
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321 </assert_command>
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322 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output>
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323 <output_collection name="gstacks_out" type="list" count="2"/>
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324 </test>
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325 <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe -->
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326 <test expect_num_outputs="2">
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327 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.bam,tsv2bam/PopA_02.bam"/>
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328 <conditional name="mode_cond">
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329 <param name="mode_select" value="refbased"/>
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330 <conditional name="paired_cond">
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331 <param name="paired_select" value="--ignore-pe-reads"/>
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332 </conditional>
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333 </conditional>
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334 <param name="add_log" value="yes" />
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335 <assert_command>
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336 <has_text text="-I bam_inputs" />
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337 <not_has_text text="-B " />
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338 <has_text text="--ignore-pe-reads" />
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339 </assert_command>
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340 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
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341 <output_collection name="gstacks_out" type="list" count="2"/>
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342 </test>
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343 </tests>
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344
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345 <help>
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346 <![CDATA[
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347 .. class:: infomark
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348
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349 **What it does**
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350
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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351 For de novo analyses, this program will pull in paired-end reads, if available,
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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352 assemble the paired-end contig and merge it with the single-end locus, align
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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353 reads to the locus, and call SNPs.
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354
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355 For reference-aligned analyses, this program will build loci from the single
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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356 and/or paired-end reads before calling SNPs. The single- and paired-end reads
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357 must be aligned and stored together in the intput BAM or SAM files and the
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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358 reads must be sorted. The gstacks program will detect if single- or paired-end
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359 reads are present.
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360
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361 In either mode, gstacks is able to remove PCR duplicates if requested.
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362
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363 --------
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364
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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365 **Input files**
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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366
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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367 If a population map is given BAM records must be assigned to samples using BAM "reads groups"
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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368 (gstacks uses the ID/identifier and SM/sample name fields). Read groups
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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369 must be consistent if repeated different files.
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370 Otherwise read groups are unneeded and ignored.
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371
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372 **Output files**
d35cb34f2b85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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373
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374 - Assembled contigs and variant sites
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375
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376 - Optional outputs: Read alignments and log.distribs
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377
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378 @STACKS_INFOS@
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379 ]]>
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380 </help>
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381 <expand macro="citation" />
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382 </tool>