Mercurial > repos > iuc > stacks_cstacks

annotate stacks_cstacks.xml @ 0:e8540c860cd4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:26:00 -0400
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children 60a0f27c77fd
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0
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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1 <tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.2">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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2 <description>build a catalogue of loci</description>
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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3 <macros>
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4 <import>macros.xml</import>
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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5 </macros>
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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6 <expand macro="requirements"/>
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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7 <expand macro="stdio"/>
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8 <command><![CDATA[
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9 #import re
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10
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11 mkdir stacks_inputs stacks_outputs
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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12
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13 &&
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15 #set $samples = ""
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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16 #for $input_file in $input_col:
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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17 #set $filename = str($input_file.element_identifier)
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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18 #if not filename.endswith('.tsv'):
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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19 #set $filename = $filename + ".tsv"
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20 #end if
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21 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename):
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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22 ln -s "${input_file}" "stacks_inputs/$filename" &&
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24 #if $filename.endswith('.tags.tsv'):
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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25 #set samples += " -s \"stacks_inputs/" + $filename[:-9] + "\""
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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26 #end if
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27 #end if
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28 #end for
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29
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30 cstacks
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31
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32 -p \${GALAXY_SLOTS:-1}
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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33
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34 $samples
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35
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36 ## Batch description
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37 -b 1
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38
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39 $g
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40
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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41 -n $n
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42
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43 $include_multiple
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44
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45 #if $gapped.use_gapped:
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46 --gapped
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47 --max_gaps $gapped.max_gaps
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48 --min_aln_len $gapped.min_aln_len
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49 #end if
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50
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51 -o stacks_outputs
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52
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53 > cstacks.log 2>&1
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54 ]]></command>
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55
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56 <inputs>
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57 <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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58
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59 <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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60
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61 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample tags when building the catalog"/>
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62
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63 <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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64
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65 <conditional name="gapped">
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66 <param name="use_gapped" argument="--gapped" type="boolean" checked="false" label="Perform gapped alignments between stacks" />
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67 <when value="false"></when>
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68 <when value="true">
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69 <param name="max_gaps" argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/>
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70 <param name="min_aln_len" 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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71 </when>
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72 </conditional>
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73 </inputs>
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74
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75 <outputs>
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76 <data format="txt" name="output_log" label="cstacks.log with ${tool.name} on ${on_string}" from_work_dir="cstacks.log" />
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77
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78 <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" />
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79 <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" />
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80 <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" />
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81 </outputs>
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82
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83 <tests>
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84 <test>
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85 <param name="input_col">
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86 <collection type="list">
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87 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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88 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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diff changeset
89 <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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diff changeset
90 <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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91 <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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92 <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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93 <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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94 <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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diff changeset
95 <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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96 <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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97 <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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98 </collection>
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99 </param>
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100
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101 <output name="output_log">
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102 <assert_contents>
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103 <has_text text="done." />
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104 </assert_contents>
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105 </output>
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106
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107 <!-- catalog -->
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108 <output name="catalogtags">
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109 <assert_contents>
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110 <has_text text="catalog generated on" />
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111 </assert_contents>
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112 </output>
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113 <output name="catalogsnps">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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114 <assert_contents>
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115 <has_text text="catalog generated on" />
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116 </assert_contents>
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117 </output>
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118 <output name="catalogalleles">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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119 <assert_contents>
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120 <has_text text="catalog generated on" />
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121 </assert_contents>
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122 </output>
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123 </test>
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124
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125 <test>
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126 <param name="input_col">
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127 <collection type="list">
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128 <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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129 <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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130 <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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131 <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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132 <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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133 <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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134 <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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135 <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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136 <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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137 <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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138 <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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139 </collection>
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140 </param>
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141 <param name="gapped|use_gapped" value="true" />
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142
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143 <output name="output_log">
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144 <assert_contents>
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145 <has_text text="done." />
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146 </assert_contents>
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147 </output>
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148
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149 <!-- catalog -->
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150 <output name="catalogtags">
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151 <assert_contents>
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152 <has_text text="catalog generated on" />
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153 </assert_contents>
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154 </output>
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155 <output name="catalogsnps">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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156 <assert_contents>
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157 <has_text text="catalog generated on" />
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158 </assert_contents>
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159 </output>
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160 <output name="catalogalleles">
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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161 <assert_contents>
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162 <has_text text="catalog generated on" />
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163 </assert_contents>
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164 </output>
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165 </test>
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166 </tests>
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167
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168 <help>
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169 <![CDATA[
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170 .. class:: infomark
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171
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172 **What it does**
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173
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174 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.
e8540c860cd4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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175
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176 --------
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178 **Input files**
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180 Output from denovo_map, refmap, ustacks or pstacks
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182 **Output files**
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184 - XXX.tags.tsv file:
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186 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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188 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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191 - XXX.snps.tsv file:
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193 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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195 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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198 - XXX.alleles.tsv file:
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200 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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202 @STACKS_INFOS@
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203 ]]>
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204 </help>
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205 <expand macro="citation" />
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206 </tool>
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207