Mercurial > repos > iuc > stacks2_refmap

annotate stacks_refmap.xml @ 4:5e10f396979e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
author iuc
date Wed, 01 Sep 2021 11:31:54 +0000
parents 4f65e343ecdf
children 887e0991eb24
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45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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1 <tool id="stacks2_refmap" name="Stacks2: reference map" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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2 <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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6 <expand macro="requirements"/>
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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7 <expand macro="version_cmd"/>
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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8 <command detect_errors="aggressive"><![CDATA[
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9 @FASTQ_INPUT_FUNCTIONS@
1
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10 mkdir bam_inputs stacks_outputs &&
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12 #if $output_log
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13 ln -s '$output_log' stacks_outputs/ref_map.log &&
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14 #end if
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15
0
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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16 @BAM_INPUT@
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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18 ref_map.pl
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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19 --samples bam_inputs
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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20 #if str($popmap) != 'None':
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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21 --popmap '$popmap'
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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22 #end if
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23 $paired_select
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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24 -o stacks_outputs
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25 -T \${GALAXY_SLOTS:-1}
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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26 --var-alpha $model_options.var_alpha
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27 --gt-alpha $model_options.gt_alpha
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29 @EXTRACT_VCF@
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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30 ]]></command>
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31
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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32 <inputs>
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33 <expand macro="bam_input_macro"/>
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34 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map"/>
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45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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35 <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">
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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36 <option value="" selected="true">single/paired</option>
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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37 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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38 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
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39 </param>
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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40 <section name="model_options" title="Variant calling options (for gstacks)" expanded="true">
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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41 <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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42 </section>
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43 <expand macro="in_log"/>
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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44 </inputs>
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45 <outputs>
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46 <expand macro="out_log"/> <!-- pipeline also writes other logs? .. could be a collection -->
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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47 <expand macro="gstacks_outputs_macro" tooladd="(gstacks)"/>
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48 <expand macro="populations_output_light" tooladd="(populations)"/>
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49 </outputs>
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50
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51 <tests>
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52 <!-- bams as list -->
2
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53 <test expect_num_outputs="7">
0
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54 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
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55 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
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56 <param name="add_log" value="yes"/>
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57 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done."/></assert_contents></output>
0
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58 <output_collection name="gstacks_out" type="list" count="2">
2
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59 <element name="catalog.calls.vcf" file="refmap/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
3
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60 <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="diff"/>
0
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61 </output_collection>
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62 <output ftype="tabular" name="out_haplotypes" value="refmap/populations.haplotypes.tsv"/>
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63 <output ftype="tabular" name="out_hapstats" value="refmap/populations.hapstats.tsv"/>
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64 <output ftype="txt" name="out_populations_log_distribs" value="refmap/populations.log.distribs"/>
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65 <output ftype="tabular" name="out_sumstats_sum" value="refmap/populations.sumstats_summary.tsv"/>
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66 <output ftype="tabular" name="out_sumstats" value="refmap/populations.sumstats.tsv"/>
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67 </test>
2
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68 <test expect_num_outputs="7">
0
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69 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
2
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70 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
0
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71 <param name="paired_select" value="--unpaired"/>
2
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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"/>
0
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74 <assert_command>
2
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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>
2
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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>
0
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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>
45385ba40a75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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
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88 </test>
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89 </tests>
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90
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91 <help>
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92 <![CDATA[
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93 .. class:: infomark
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94
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95 **What it does**
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96
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97 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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98
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99 --------
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100
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101 **Input files**
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102
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103 - SAM, BAM
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104
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105 - Population map::
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106
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107 indv_01 1
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108 indv_02 1
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109 indv_03 1
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110 indv_04 2
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111 indv_05 2
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112 indv_06 2
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113
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114 **Output files**
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115
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116 - XXX.tags.tsv file:
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117
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118 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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119
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120 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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121
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122
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123 - XXX.snps.tsv file:
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124
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125 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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126
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127 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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128
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129
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130 - XXX.alleles.tsv file:
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131
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132 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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133
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134
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135 - XXX.matches.tsv file:
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136
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137 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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138
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139 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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140
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141
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142 - other files:
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143
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144 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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145
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146 @STACKS_INFOS@
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147 ]]>
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148 </help>
2
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149 <expand macro="citation"/>
0
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150 </tool>