Mercurial > repos > iuc > stacks2_sstacks

annotate stacks_sstacks.xml @ 0:70d61f928d3e 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 10:53:11 -0400
parents
children 34f1233208f3
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0
70d61f928d3e 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@">
70d61f928d3e 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>
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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3 <macros>
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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4 <import>macros.xml</import>
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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5 </macros>
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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6 <expand macro="requirements"/>
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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10
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11 mkdir stacks_inputs stacks_outputs
70d61f928d3e 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 $popmap
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23 -P stacks_inputs
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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24 -M '$popmap'
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25 #else
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26 -c stacks_inputs/
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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27 #for $sample in $samples
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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28 -s 'stacks_inputs/$sample'
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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
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40 ## When using a popmap, stacks write to the input dir
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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41 && mv stacks_inputs/*matches.tsv stacks_outputs/
70d61f928d3e 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>
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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44
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45 <inputs>
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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46 <expand macro="input_stacks_macro"/>
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47 <expand macro="input_cat_macro"/>
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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" />
70d61f928d3e 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" />
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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"/>
70d61f928d3e 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">
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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95 <collection type="list">
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96 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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97 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
70d61f928d3e 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" />
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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99 </collection>
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100 </param>
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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" />
70d61f928d3e 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" />
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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105 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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106 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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107 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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" />
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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129 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
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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">
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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" />
70d61f928d3e 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" />
70d61f928d3e 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" />
70d61f928d3e 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" />
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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" />
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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.
70d61f928d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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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>