Mercurial > repos > iuc > stacks2_cstacks

annotate stacks_cstacks.xml @ 0:a034f8937db6 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 10:55:17 -0400
parents
children 7b5509de8421
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0
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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1 <tool id="stacks2_cstacks" name="Stacks2: cstacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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2 <description>Generate catalog of loci</description>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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3 <macros>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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4 <import>macros.xml</import>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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5 </macros>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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6 <expand macro="requirements"/>
a034f8937db6 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"/>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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8 <command detect_errors="aggressive"><![CDATA[
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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9 #import re
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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10
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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11 mkdir stacks_inputs stacks_outputs
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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12 &&
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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13
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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14 @LINK_STACKS_INPUT@
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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15
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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16 cstacks
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17
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18 -p \${GALAXY_SLOTS:-1}
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19
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20 #if $popmap
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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21 -P stacks_inputs
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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22 -M '$popmap'
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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23 #else
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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24 #for $sample in $samples
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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25 -s 'stacks_inputs/$sample'
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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26 #end for
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27 -o stacks_outputs
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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28 #end if
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29
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30 -n $n
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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31 ## -c not implemented in Galaxy (appending can be done in Galaxy)
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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32
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33 @GAP_OPTIONS@
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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34
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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35 ## Advanced Options
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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36 #if $k_len:
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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37 --k_len $k_len
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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38 #end if
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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39 $report_mmatches
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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40 @TEE_APPEND_LOG@
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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41 @CAT_LOG_TO_STDERR@
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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42
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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43 #if $popmap
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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44 ## When using a popmap, cstacks writes to the input dir
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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45 && mv stacks_inputs/catalog.*.tsv stacks_outputs/
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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46 #end if
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47
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48 ]]></command>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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49
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50 <inputs>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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51 <expand macro="input_stacks_macro"/>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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52
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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53 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M" />
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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54
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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55 <param argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample loci when building the catalog" help="(default 1; suggested: set to ustacks -M)"/>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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56
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57 <expand macro="gap_options"/>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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58 <param argument="--k_len" type="integer" min="5" max="31" value="" optional="true" label="K-mer size for matching between between catalog loci" help="default: automatic"/>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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59 <param argument="--report_mmatches" type="boolean" checked="false" truevalue="--report_mmatches" falsevalue="" label="Report query loci that match more than one catalog locus" />
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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60 <expand macro="in_log"/>
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61 </inputs>
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62
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63 <outputs>
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64 <expand macro="out_log"/>
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65 <expand macro="cstacks_outputs_macro"/>
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66 </outputs>
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67
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68 <tests>
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69 <!-- test w default options + popmap -->
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70 <test>
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71 <param name="input_stacks">
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72 <collection type="list">
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73 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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74 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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75 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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76 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
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77 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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78 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
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79 </collection>
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80 </param>
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81 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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82 <param name="add_log" value="yes" />
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83 <output name="output_log" ftype="txt" file="cstacks/cstacks.log"/>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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84 <output_collection name="catalog" type="list">
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85 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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86 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" />
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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87 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" />
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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88 </output_collection>
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89 </test>
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90 <!-- test w default options -->
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91 <test>
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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92 <param name="input_stacks">
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93 <collection type="list">
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94 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
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95 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
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96 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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97 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
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98 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
a034f8937db6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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99 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
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100 </collection>
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101 </param>
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102 <param name="add_log" value="yes" />
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103 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
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104 <output_collection name="catalog" type="list">
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105 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/>
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106 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" />
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107 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" />
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108 </output_collection>
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109 </test>
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110 <!-- test w non default options (wo gapped, because tested already in ustacks) -->
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111 <test>
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112 <param name="input_stacks">
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113 <collection type="list">
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114 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
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115 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
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116 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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117 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
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118 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
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119 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
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120 </collection>
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121 </param>
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122 <param name="n" value="2"/>
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123 <param name="k_len" value="23"/>
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124 <param name="report_mmatches" value="--report_mmatches" />
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125 <assert_command>
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126 <has_text text="--k_len 23" />
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127 <has_text text="-n 2" />
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128 <has_text text="--report_mmatches" />
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129 </assert_command>
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130 <param name="add_log" value="yes" />
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131 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
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132 <output_collection name="catalog" type="list">
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133 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/>
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134 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" />
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135 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" />
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136 </output_collection>
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137 </test>
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138 </tests>
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139 <help>
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140 <![CDATA[
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141 .. class:: infomark
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142
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143 **What it does**
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144
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145 A catalog can be built from any set of samples processed by ustacks. 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.
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146
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147 --------
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148
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149 **Input files**
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150
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151 Output from denovo_map or ustacks
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152
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153 **Output files**
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154
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155 - catalog.tags file:
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156
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157 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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158
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159 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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160
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161
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162 - catalog.snps file:
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163
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164 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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165
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166 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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167
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168
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169 - catalog.alleles file:
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170
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171 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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172
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173 @STACKS_INFOS@
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174 ]]>
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175 </help>
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176 <expand macro="citation" />
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177 </tool>