Mercurial > repos > iuc > stacks2_sstacks

annotate stacks_sstacks.xml @ 0:b7babdb3c219 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 11:01:59 -0400
parents
children e58e2ecb6285
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0
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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1 <tool id="stacks2_sstacks" name="Stacks2: sstacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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2 <description>Match samples to the catalog</description>
b7babdb3c219 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>
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_cmd"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 #import re
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10
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11 mkdir stacks_inputs stacks_outputs
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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12
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13 &&
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14
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15 @LINK_STACKS_INPUT@
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16 @LINK_CAT_INPUT@
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17
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18 sstacks
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19
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20 -p \${GALAXY_SLOTS:-1}
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21
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22 #if $popmap
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23 -P stacks_inputs
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24 -M '$popmap'
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25 #else
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26 -c stacks_inputs/
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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27 #for $sample in $samples
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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28 -s 'stacks_inputs/$sample'
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29 #end for
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30 -o stacks_outputs
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31 #end if
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32
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33 $x
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34
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35 @GAP_OPTIONS_ONOFF@
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36 @TEE_APPEND_LOG@
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37 @CAT_LOG_TO_STDERR@
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38
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39 #if $popmap
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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40 ## When using a popmap, stacks write to the input dir
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41 && mv stacks_inputs/*matches.tsv stacks_outputs/
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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42 #end if
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43 ]]></command>
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44
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45 <inputs>
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46 <expand macro="input_stacks_macro"/>
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47 <expand macro="input_cat_macro"/>
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48 <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" />
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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49 <param argument="-x" type="boolean" checked="true" truevalue="" falsevalue="-x" label="Verify haplotype of matching locus" />
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50 <expand macro="gap_options_onoff"/>
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51 <expand macro="in_log"/>
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52 </inputs>
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53
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54 <outputs>
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55 <expand macro="out_log"/>
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56 <expand macro="sstacks_outputs_macro"/>
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57 </outputs>
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58
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59 <tests>
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60 <!-- test w default parameters and popmap -->
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61 <test>
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62 <param name="input_cat">
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63 <collection type="list">
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64 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
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65 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
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66 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
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67 </collection>
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68 </param>
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69 <param name="input_stacks">
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70 <collection type="list">
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71 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
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72 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
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73 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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74 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
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75 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
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76 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
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77 </collection>
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78 </param>
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79 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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80 <param name="add_log" value="yes" />
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81 <assert_command>
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82 <not_has_text text="-x" />
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83 <not_has_text text="--disable-gapped" />
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84 <not_has_text text="-M" />
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85 </assert_command>
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86 <output name="output_log" ftype="txt" file="sstacks/sstacks.log"/>
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87 <output_collection name="matches" type="list">
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88 <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="2"/>
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89 <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="2"/>
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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90 </output_collection>
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91 </test>
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92 <!-- test w default parameters -->
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93 <test>
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94 <param name="input_cat">
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95 <collection type="list">
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96 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
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97 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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98 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
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99 </collection>
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100 </param>
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101 <param name="input_stacks">
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102 <collection type="list">
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103 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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104 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
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105 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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106 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
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107 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
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108 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
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109 </collection>
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110 </param>
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111 <param name="add_log" value="yes" />
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112 <assert_command>
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113 <not_has_text text="-x" />
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114 <not_has_text text="--disable-gapped" />
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115 <not_has_text text="-M" />
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116 </assert_command>
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117 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output>
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118 <output_collection name="matches" type="list" count="2">
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119 <element name="PopA_01.matches"><assert_contents><has_text text="generated on " /></assert_contents></element>
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120 <element name="PopA_02.matches"><assert_contents><has_text text="generated on " /></assert_contents></element>
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121 </output_collection>
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122 </test>
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123
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124 <!-- test w non default parameters and popmap-->
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125 <test>
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126 <param name="input_cat">
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127 <collection type="list">
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128 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
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129 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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130 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
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131 </collection>
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132 </param>
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133 <param name="input_stacks">
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134 <collection type="list">
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135 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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136 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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137 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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138 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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139 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
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140 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
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141 </collection>
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142 </param>
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143 <param name="gapped|use_gapped" value="yes" />
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144 <param name="x" value="-x" />
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145 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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146 <param name="add_log" value="yes" />
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147 <assert_command>
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148 <has_text text="-x" />
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149 <has_text text="--disable-gapped" />
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150 <has_text text="-M" />
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151 </assert_command>
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152 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output>
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153 <output_collection name="matches" type="list" count="2">
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154 <element name="PopA_01.matches"><assert_contents><has_text text="generated on " /></assert_contents></element>
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155 <element name="PopA_02.matches"><assert_contents><has_text text="generated on " /></assert_contents></element>
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156 </output_collection>
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157 </test>
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158 </tests>
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159
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160 <help>
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161 <![CDATA[
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162 .. class:: infomark
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163
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164 **What it does**
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165
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166 Sets of stacks constructed by ustacks 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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167
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168 --------
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169
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170 **Input files**
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171
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172 Output from denovo_map, refmap or cstacks/ustack
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173
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174 **Output files**
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175
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176 - XXX.tags.tsv file:
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177
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178 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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179
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180 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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181
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182
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183 - XXX.snps.tsv file:
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184
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185 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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186
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187 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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188
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189
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190 - XXX.alleles.tsv file:
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191
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192 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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193
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194 - XXX.matches.tsv file:
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195
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196 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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197
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198 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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199
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200 @STACKS_INFOS@
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201 ]]>
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202 </help>
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203 <expand macro="citation" />
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204 </tool>