Mercurial > repos > iuc > stacks_sstacks

annotate stacks_sstacks.xml @ 8:45cc649c9f8a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139"
author iuc
date Tue, 22 Mar 2022 23:02:08 +0000
parents 59d244e79b8e
children ecec9bdfc46a
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1 <tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.0">
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2 <description>match stacks to a catalog</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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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 $catalog = ""
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17 #for $input_file in $input_cat
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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 = $filename + ".tsv"
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21 #end if
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22 #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
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23 ln -s '${input_file}' 'stacks_inputs/$filename' &&
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5
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25 #if $filename.endswith('.tags.tsv')
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26 #set catalog += " -c 'stacks_inputs/"+$filename[:-17] + "'"
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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 #set $samples = ""
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32 #for $input_file in $input_tags
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33 #set $filename = str($input_file.element_identifier)
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34 #if not filename.endswith('.tsv')
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35 #set $filename = $filename + ".tsv"
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36 #end if
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37 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
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38 ln -s '${input_file}' 'stacks_inputs/$filename' &&
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39
5
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40 #if $filename.endswith('.tags.tsv')
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41 #set samples += " -s 'stacks_inputs/"+$filename[:-9] + "'"
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42 #end if
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43 #end if
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44 #end for
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46 sstacks
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47
5
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48 ## Batch description
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49 -b 1
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50
0
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51 -p \${GALAXY_SLOTS:-1}
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52
5
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53 #if $popmap
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54 -P stacks_inputs -M '$popmap'
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55 #else
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56 $catalog
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57 $samples
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58 -o stacks_outputs
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59 #end if
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61 $g
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63 $check_haplo
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65 $gapped
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66
5
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67 2>&1 | tee sstacks.log
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69 #if $popmap
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70 ## When using a popmap, stacks write to the input dir
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71 && mv stacks_inputs/*matches.tsv stacks_outputs/
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72 #end if
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74 &&
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76 stacks_summary.py --stacks-prog sstacks --res-dir stacks_outputs --logfile sstacks.log --summary stacks_outputs/summary.html
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77 ]]></command>
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79 <inputs>
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80 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" />
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81 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks/pstacks" />
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82
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83 <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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84
0
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85 <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
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87 <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" />
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88
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89 <param name="gapped" argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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90 </inputs>
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91
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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92 <outputs>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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93 <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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94
5
59d244e79b8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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parents: 1
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95 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
59d244e79b8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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96
0
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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97 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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98 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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99 </collection>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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100 </outputs>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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101
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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102 <tests>
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103 <test>
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104 <param name="input_cat">
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105 <collection type="list">
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106 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
8132083ebd32 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.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
8132083ebd32 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.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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109 </collection>
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110 </param>
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111 <param name="input_tags">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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112 <collection type="list">
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113 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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114 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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115 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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116 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
8132083ebd32 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.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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118 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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119 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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120 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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121 </collection>
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122 </param>
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123
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124 <output name="output_log">
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125 <assert_contents>
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126 <has_text text="Outputing to file" />
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127 </assert_contents>
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128 </output>
5
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129 <output name="output_summary">
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130 <assert_contents>
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131 <has_text text="Stacks Statistics" />
59d244e79b8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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132 </assert_contents>
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133 </output>
0
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134
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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135 <output_collection name="matches">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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136 <element name="PopA_01.matches">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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137 <assert_contents>
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138 <has_text text="generated on " />
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139 </assert_contents>
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140 </element>
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141 </output_collection>
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142 </test>
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143
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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144 <test>
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145 <param name="input_cat">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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diff changeset
146 <collection type="list">
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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147 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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148 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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149 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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150 </collection>
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151 </param>
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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152 <param name="input_tags">
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153 <collection type="list">
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154 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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155 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
8132083ebd32 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.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
8132083ebd32 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.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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158 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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159 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
8132083ebd32 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.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
8132083ebd32 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.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
8132083ebd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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162 </collection>
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163 </param>
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164 <param name="gapped" value="true" />
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165 <param name="check_haplo" value="true" />
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166
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167 <output name="output_log">
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168 <assert_contents>
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169 <has_text text="Outputing to file" />
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170 </assert_contents>
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171 </output>
5
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172 <output name="output_summary">
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173 <assert_contents>
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174 <has_text text="Stacks Statistics" />
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175 </assert_contents>
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176 </output>
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177
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178 <output_collection name="matches">
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179 <element name="PopA_01.matches">
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180 <assert_contents>
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181 <has_text text="generated on " />
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182 </assert_contents>
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183 </element>
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184 </output_collection>
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185 </test>
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186
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187 <test>
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188 <param name="input_cat">
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189 <collection type="list">
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190 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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191 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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192 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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193 </collection>
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194 </param>
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195 <param name="input_tags">
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196 <collection type="list">
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197 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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198 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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199 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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200 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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201 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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202 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
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203 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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204 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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205 </collection>
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206 </param>
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207
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208 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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209
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210 <output name="output_log">
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211 <assert_contents>
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212 <has_text text="Outputing to file" />
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213 </assert_contents>
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214 </output>
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215 <output name="output_summary">
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216 <assert_contents>
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217 <has_text text="Stacks Statistics" />
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218 </assert_contents>
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219 </output>
0
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220
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221 <output_collection name="matches">
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222 <element name="PopA_01.matches">
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223 <assert_contents>
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224 <has_text text="generated on " />
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225 </assert_contents>
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226 </element>
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227 </output_collection>
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228 </test>
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229 </tests>
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230
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231 <help>
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232 <![CDATA[
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233 .. class:: infomark
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234
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235 **What it does**
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236
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237 Sets of stacks constructed by the ustacks or pstacks programs can be searched against a catalog produced by cstacks. In the case of a genetic map, stacks from the progeny would be matched against the catalog to determine which progeny contain which parental alleles.
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238
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239 --------
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240
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241 **Input files**
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242
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243 Output from denovo_map, refmap or cstacks/ustacks/pstacks
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244
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245 **Output files**
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246
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247 - XXX.tags.tsv file:
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248
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249 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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250
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251 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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252
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253
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254 - XXX.snps.tsv file:
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255
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256 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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257
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258 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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259
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260
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261 - XXX.alleles.tsv file:
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262
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263 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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264
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265 - XXX.matches.tsv file:
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266
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267 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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269 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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270
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271 @STACKS_INFOS@
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272 ]]>
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273 </help>
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274 <expand macro="citation" />
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275 </tool>