Mercurial > repos > matthias > stacks2_refmap

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3
author matthias
date Tue, 25 Jun 2019 10:55:53 -0400
parents 60687cc87548
children
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1 <tool id="stacks2_refmap" name="Stacks2: reference map" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_cmd"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 @FASTQ_INPUT_FUNCTIONS@
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10 mkdir bam_inputs stacks_outputs&&
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11 @BAM_INPUT@
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12
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13 ref_map.pl
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14 --samples bam_inputs
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15 #if str($popmap) != 'None':
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16 --popmap '$popmap'
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17 #end if
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18 $paired_select
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19 -o stacks_outputs
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20 -T \${GALAXY_SLOTS:-1}
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21 --var-alpha $model_options.var_alpha
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22 --gt-alpha $model_options.gt_alpha
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24 @EXTRACT_VCF@
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26 #if $output_log
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27 && mv stacks_outputs/ref_map.log $output_log
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28 #end if
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29 ]]></command>
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31 <inputs>
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32 <expand macro="bam_input_macro"/>
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33 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map" />
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34 <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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35 <option value="" selected="true">single/paired</option>
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36 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
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37 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
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38 </param>
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39 <section name="model_options" title="Variant calling options (for gstacks)" expanded="true">
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40 <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
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41 </section>
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42 <expand macro="in_log"/>
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43 </inputs>
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44 <outputs>
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45 <expand macro="out_log"/> <!-- pipeline also writes other logs? .. could be a collection -->
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46 <expand macro="gstacks_outputs_macro" tooladd="(gstacks)"/>
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47 <expand macro="populations_output_light" tooladd="(populations)"/>
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48 </outputs>
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49
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50 <tests>
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51 <!-- bams as list -->
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52 <test>
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53 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
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54 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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55 <param name="add_log" value="yes" />
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56 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
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57 <output_collection name="gstacks_out" type="list" count="2">
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58 <element name="catalog.calls.vcf" file="refmap/catalog.calls.vcf" ftype="vcf" lines_diff="2"/>
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59 <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
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60 </output_collection>
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61 <output ftype="tabular" name="out_haplotypes" value="refmap/populations.haplotypes.tsv"/>
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62 <output ftype="tabular" name="out_hapstats" value="refmap/populations.hapstats.tsv"/>
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63 <output ftype="txt" name="out_populations_log_distribs" value="refmap/populations.log.distribs"/>
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64 <output ftype="tabular" name="out_sumstats_sum" value="refmap/populations.sumstats_summary.tsv"/>
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65 <output ftype="tabular" name="out_sumstats" value="refmap/populations.sumstats.tsv"/>
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66 <output ftype="tabular" name="out_sql" value="refmap/populations.markers.tsv"/>
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67 </test>
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68 <test>
3
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69 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
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70 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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71 <param name="paired_select" value="--unpaired"/>
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72 <param name="model_options|var_alpha" value="0.1" />
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73 <param name="model_options|gt_alpha" value="0.1" />
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74 <assert_command>
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75 <has_text text="--unpaired" />
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76 <has_text text="--var-alpha 0.1" />
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77 <has_text text="--gt-alpha 0.1" />
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78 </assert_command>
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79 <param name="add_log" value="yes" />
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80 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
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81 <output_collection name="gstacks_out" type="list" count="2"/>
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82 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
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83 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
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84 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
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85 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
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86 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
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87 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
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88
0
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89 </test>
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90 </tests>
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91
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92 <help>
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93 <![CDATA[
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94 .. class:: infomark
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95
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96 **What it does**
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97
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98 This program expects data that have been aligned to a reference genome, and can accept data directly from Bowtie, or from any aligner that can produce SAM format. To avoid datasets names problems, we recommand the use of the *Map with BWA for STACKS tool*. This program will execute each of the Stacks components: first, running pstacks on each of the samples specified, building loci (based on the reference alignment) and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci specified as 'parents' or 'samples' on the command line, again using alignment to match loci in the catalog. Finally, sstacks will be executed to match each sample against the catalog. The ref_map.pl program will also load the results of each stage of the analysis: individual loci, the catalog, and matches against the catalog into the database (although this can be disabled). After matching the program will build a database index to speed up access (index_radtags.pl) and enable web-based filtering.
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99
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100 --------
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101
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102 **Input files**
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103
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104 - SAM, BAM
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105
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106 - Population map::
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107
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108 indv_01 1
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109 indv_02 1
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110 indv_03 1
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111 indv_04 2
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112 indv_05 2
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113 indv_06 2
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114
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115 **Output files**
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116
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117 - XXX.tags.tsv file:
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118
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119 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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120
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121 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
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122
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123
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124 - XXX.snps.tsv file:
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125
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126 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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127
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128 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
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129
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130
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131 - XXX.alleles.tsv file:
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132
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133 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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134
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135
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136 - XXX.matches.tsv file:
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137
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138 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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139
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140 Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample.
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141
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142
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143 - other files:
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144
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145 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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146
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147 @STACKS_INFOS@
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148 ]]>
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149 </help>
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150 <expand macro="citation" />
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151 </tool>