Mercurial > repos > iuc > stacks2_sstacks

annotate stacks_sstacks.xml @ 3:cd034465d4a4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
author iuc
date Tue, 27 Apr 2021 09:36:13 +0000
parents 0b8c84a7fdb5
children 09b8edb56d80
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1 <tool id="stacks2_sstacks" name="Stacks2: sstacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>Match samples to the catalog</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="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
2
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11 trap ">&2 cat '$output_log'" err exit &&
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12 mkdir stacks_inputs stacks_outputs &&
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14 @LINK_STACKS_INPUT@
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15 @LINK_CAT_INPUT@
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17 sstacks
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19 -p \${GALAXY_SLOTS:-1}
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21 #if $popmap
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22 -P stacks_inputs
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23 -M '$popmap'
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24 #else
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25 -c stacks_inputs/
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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26 #for $sample in $samples
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27 -s 'stacks_inputs/$sample'
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28 #end for
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29 -o stacks_outputs
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30 #end if
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32 $x
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34 @GAP_OPTIONS_ONOFF@
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35 @TEE_APPEND_LOG@
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37 #if $popmap
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38 ## When using a popmap, stacks write to the input dir
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39 && mv stacks_inputs/*matches.tsv stacks_outputs/
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40 #end if
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41 ]]></command>
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43 <inputs>
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44 <expand macro="input_stacks_macro"/>
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45 <expand macro="input_cat_macro"/>
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46 <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"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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47 <param argument="-x" type="boolean" checked="true" truevalue="" falsevalue="-x" label="Verify haplotype of matching locus"/>
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48 <expand macro="gap_options_onoff"/>
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49 <expand macro="in_log"/>
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50 </inputs>
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51
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52 <outputs>
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53 <expand macro="out_log"/>
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54 <expand macro="sstacks_outputs_macro"/>
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55 </outputs>
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56
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57 <tests>
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58 <!-- test w default parameters and popmap -->
2
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59 <test expect_num_outputs="2">
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60 <param name="input_cat">
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61 <collection type="list">
2
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62 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
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63 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
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64 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
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65 </collection>
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66 </param>
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67 <param name="input_stacks">
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68 <collection type="list">
2
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69 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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70 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/>
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71 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/>
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72 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/>
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73 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/>
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74 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
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75 </collection>
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76 </param>
2
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77 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
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78 <param name="add_log" value="yes"/>
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79 <assert_command>
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80 <not_has_text text="-x"/>
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81 <not_has_text text="--disable-gapped"/>
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82 <has_text text="-M"/>
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83 </assert_command>
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84 <output name="output_log" ftype="txt" file="sstacks/sstacks.log"/>
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85 <output_collection name="matches" type="list">
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86 <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="4"/>
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87 <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="4"/>
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88 </output_collection>
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89 </test>
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90 <!-- test w default parameters -->
2
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91 <test expect_num_outputs="2">
0
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92 <param name="input_cat">
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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93 <collection type="list">
2
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94 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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95 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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96 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
0
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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97 </collection>
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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98 </param>
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99 <param name="input_stacks">
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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100 <collection type="list">
2
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101 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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102 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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103 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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104 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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105 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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106 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
0
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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107 </collection>
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108 </param>
2
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109 <param name="add_log" value="yes"/>
0
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110 <assert_command>
2
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111 <not_has_text text="-x"/>
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112 <not_has_text text="--disable-gapped"/>
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113 <not_has_text text="-M"/>
0
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114 </assert_command>
2
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115 <output name="output_log" ftype="txt"><assert_contents><has_text text="done."/></assert_contents></output>
0
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116 <output_collection name="matches" type="list" count="2">
2
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117 <element name="PopA_01.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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118 <element name="PopA_02.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
0
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119 </output_collection>
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120 </test>
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121
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122 <!-- test w non default parameters and popmap-->
2
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123 <test expect_num_outputs="1">
0
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124 <param name="input_cat">
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125 <collection type="list">
2
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126 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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127 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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128 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
0
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129 </collection>
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130 </param>
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131 <param name="input_stacks">
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132 <collection type="list">
2
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133 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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134 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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135 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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136 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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137 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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138 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
0
b7babdb3c219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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139 </collection>
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140 </param>
2
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141 <param name="gapped|use_gapped" value="yes"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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142 <param name="x" value="-x"/>
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143 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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144 <param name="add_log" value="no"/>
0
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145 <assert_command>
2
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146 <has_text text="-x"/>
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147 <not_has_text text="--disable-gapped"/>
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148 <has_text text="-M"/>
0
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149 </assert_command>
2
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150 <assert_stderr><has_text text="done."/></assert_stderr>
0
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151 <output_collection name="matches" type="list" count="2">
2
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152 <element name="PopA_01.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
0b8c84a7fdb5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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153 <element name="PopA_02.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
0
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154 </output_collection>
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155 </test>
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156 </tests>
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157
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158 <help>
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159 <![CDATA[
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160 .. class:: infomark
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161
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162 **What it does**
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163
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164 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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165
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166 --------
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167
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168 **Input files**
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169
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170 Output from denovo_map, refmap or cstacks/ustack
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171
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172 **Output files**
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173
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174 - XXX.tags.tsv file:
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175
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176 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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177
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178 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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179
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180
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181 - XXX.snps.tsv file:
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182
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183 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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184
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185 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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186
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187
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188 - XXX.alleles.tsv file:
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189
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190 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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191
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192 - XXX.matches.tsv file:
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193
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194 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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195
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196 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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197
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198 @STACKS_INFOS@
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199 ]]>
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200 </help>
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201 <expand macro="citation"/>
0
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202 </tool>