Mercurial > repos > iuc > stacks_cstacks

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 21:58:49 +0000
parents 02e57ebafa9c
children
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1 <tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.0">
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2 <description>build a catalogue of loci</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="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
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10 #import re
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12 mkdir stacks_inputs stacks_outputs
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14 &&
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16 #set $samples = ""
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17 #for $input_file in $input_col
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18 #set $filename = str($input_file.element_identifier)
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19 #if not filename.endswith('.tsv')
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20 #set $filename = $filename + ".tsv"
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21 #end if
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22 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
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23 ln -s '${input_file}' 'stacks_inputs/$filename' &&
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24
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25 #if $filename.endswith('.tags.tsv')
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26 #set samples += " -s 'stacks_inputs/" + $filename[:-9] + "'"
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27 #end if
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28 #end if
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29 #end for
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31 cstacks
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32
5
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33 ## Batch description
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34 -b 1
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35
0
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36 -p \${GALAXY_SLOTS:-1}
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37
5
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38 #if $popmap
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39 -P stacks_inputs -M '$popmap'
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40 #else
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41 $samples
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42 -o stacks_outputs
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43 #end if
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44
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45 $g
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47 -n $n
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48
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49 $include_multiple
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50
5
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51 #if $gapped.use_gapped == "yes"
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52 --gapped
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53 --max_gaps $gapped.max_gaps
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54 --min_aln_len $gapped.min_aln_len
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55 #end if
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56
5
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57 2>&1 | tee cstacks.log
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58
5
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59 #if $popmap
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60 ## When using a popmap, stacks write to the input dir
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61 && mv stacks_inputs/batch_1.catalog.*.tsv stacks_outputs/
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62 #end if
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64 &&
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65
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66 stacks_summary.py --stacks-prog cstacks --res-dir stacks_outputs --logfile cstacks.log --summary stacks_outputs/summary.html
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67 ]]></command>
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68
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69 <inputs>
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70 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map, refmap, ustacks or pstacks)" />
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71
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72 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M" />
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73
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74 <param argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
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75
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76 <param argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample tags when building the catalog"/>
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78 <param name="include_multiple" argument="-m" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Include tags in the catalog that match to more than one entry" />
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79
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80 <conditional name="gapped">
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81 <param name="use_gapped" argument="--gapped" type="select" label="Perform gapped alignments between stacks">
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82 <option value="no" selected="true">No</option>
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83 <option value="yes">Yes</option>
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84 </param>
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85 <when value="no"/>
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86 <when value="yes">
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87 <param argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/>
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88 <param argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>
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89 </when>
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90 </conditional>
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91 </inputs>
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92
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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93 <outputs>
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94 <data format="txt" name="output_log" label="cstacks.log with ${tool.name} on ${on_string}" from_work_dir="cstacks.log" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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95
5
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96 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
620ed53d05e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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97
0
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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98 <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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99 <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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100 <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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101 </outputs>
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102
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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103 <tests>
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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104 <test>
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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105 <param name="input_col">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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106 <collection type="list">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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107 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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108 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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109 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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110 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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111 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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112 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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113 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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114 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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115 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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116 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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117 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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118 </collection>
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119 </param>
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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120
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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121 <output name="output_log">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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122 <assert_contents>
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123 <has_text text="done." />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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124 </assert_contents>
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125 </output>
5
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126 <output name="output_summary">
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127 <assert_contents>
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128 <has_text text="Stacks Statistics" />
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129 </assert_contents>
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130 </output>
0
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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131
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132 <!-- catalog -->
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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133 <output name="catalogtags">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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134 <assert_contents>
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135 <has_text text="catalog generated on" />
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136 </assert_contents>
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137 </output>
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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138 <output name="catalogsnps">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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139 <assert_contents>
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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140 <has_text text="catalog generated on" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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141 </assert_contents>
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142 </output>
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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143 <output name="catalogalleles">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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144 <assert_contents>
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145 <has_text text="catalog generated on" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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146 </assert_contents>
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147 </output>
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148 </test>
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149
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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150 <test>
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151 <param name="input_col">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
152 <collection type="list">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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153 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
154 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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155 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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156 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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157 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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158 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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159 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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160 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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161 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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162 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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163 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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164 </collection>
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165 </param>
5
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166 <param name="gapped|use_gapped" value="yes" />
0
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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167
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168 <output name="output_log">
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169 <assert_contents>
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170 <has_text text="done." />
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171 </assert_contents>
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172 </output>
5
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173 <output name="output_summary">
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174 <assert_contents>
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175 <has_text text="Stacks Statistics" />
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176 </assert_contents>
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177 </output>
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178
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179 <!-- catalog -->
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180 <output name="catalogtags">
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181 <assert_contents>
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182 <has_text text="catalog generated on" />
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183 </assert_contents>
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184 </output>
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185 <output name="catalogsnps">
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186 <assert_contents>
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187 <has_text text="catalog generated on" />
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188 </assert_contents>
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189 </output>
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190 <output name="catalogalleles">
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191 <assert_contents>
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192 <has_text text="catalog generated on" />
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193 </assert_contents>
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194 </output>
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195 </test>
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196
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197 <test>
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198 <param name="input_col">
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199 <collection type="list">
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200 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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201 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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202 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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203 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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204 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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205 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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206 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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207 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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208 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
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209 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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210 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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211 </collection>
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212 </param>
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213
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214 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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215
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216 <output name="output_log">
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217 <assert_contents>
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218 <has_text text="done." />
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219 </assert_contents>
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220 </output>
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221 <output name="output_summary">
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222 <assert_contents>
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223 <has_text text="Stacks Statistics" />
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224 </assert_contents>
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225 </output>
0
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226
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227 <!-- catalog -->
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228 <output name="catalogtags">
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229 <assert_contents>
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230 <has_text text="catalog generated on" />
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231 </assert_contents>
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232 </output>
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233 <output name="catalogsnps">
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234 <assert_contents>
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235 <has_text text="catalog generated on" />
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236 </assert_contents>
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237 </output>
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238 <output name="catalogalleles">
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239 <assert_contents>
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240 <has_text text="catalog generated on" />
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241 </assert_contents>
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242 </output>
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243 </test>
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244 </tests>
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245
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246 <help>
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247 <![CDATA[
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248 .. class:: infomark
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249
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250 **What it does**
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251
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252 A catalog can be built from any set of samples processed by the ustacks or pstacks programs. It will create a set of consensus loci, merging alleles together. In the case of a genetic cross, a catalog would be constructed from the parents of the cross to create a set of all possible alleles expected in the progeny of the cross.
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253
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254 --------
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255
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256 **Input files**
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257
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258 Output from denovo_map, refmap, ustacks or pstacks
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259
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260 **Output files**
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261
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262 - XXX.tags.tsv file:
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263
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264 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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265
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266 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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267
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268
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269 - XXX.snps.tsv file:
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270
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271 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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272
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273 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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274
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275
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276 - XXX.alleles.tsv file:
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277
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278 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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279
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280 @STACKS_INFOS@
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281 ]]>
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282 </help>
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283 <expand macro="citation" />
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284 </tool>