Mercurial > repos > iuc > stacks2_denovomap

annotate stacks_denovomap.xml @ 2:421c33b8bf17 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Wed, 15 Jul 2020 17:25:36 -0400
parents afdbc7fcce70
children ad5ab22ffe24
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b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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1 <tool id="stacks2_denovomap" name="Stacks2: de novo map" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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2 <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description>
b9822370f843 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>
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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 @FASTQ_INPUT_FUNCTIONS@
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10 mkdir stacks_inputs stacks_outputs &&
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12 #if $output_log
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13 ln -s '$output_log' stacks_outputs/denovo_map.log &&
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14 #end if
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b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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16 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, ".%d" )
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17 $link_command
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19 denovo_map.pl
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20 --samples stacks_inputs
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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21 #if str($popmap) != 'None':
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22 --popmap '$popmap'
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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23 #end if
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24 -o stacks_outputs
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25 -T \${GALAXY_SLOTS:-1}
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27 -M $assembly_options.M
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28 -n $assembly_options.n
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29 --var-alpha $model_options.var_alpha
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30 --gt-alpha $model_options.gt_alpha
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31 #if $input_type.input_type_select == "paired"
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32 --paired
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33 #end if
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34 $pe_options.rm_pcr_duplicates
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35 --min-samples-per-pop $popfilter_options.min_samples_per_pop
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36 --min-populations $popfilter_options.min_populations
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37
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38 ## the catalog.calls output is a gzip-ed vcf extract it
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39 ## to make it usable in Galaxy (with the downside that we
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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40 ## need to gzip it again for downstream calls like populations)
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41 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
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42 ]]></command>
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43
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44 <inputs>
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45 <expand macro="fastq_input"/>
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46 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map"/>
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47 <section name="assembly_options" title="Assembly options" expanded="true">
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48 <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual" help="used in ustacks"/>
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49 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog" help="used in cstacks; suggested: set to -M"/>
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50 </section>
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51 <section name="model_options" title="SNP model options" expanded="true">
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52 <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
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53 </section>
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54 <section name="pe_options" title="Paired-end options" expanded="true">
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55 <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="remove all but one set of read pairs of the same sample that have the same insert length" help=""/>
0
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56 </section>
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57 <section name="popfilter_options" title="Population filtering options" expanded="true">
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58 <param argument="--min-samples-per-pop" name="min_samples_per_pop" type="integer" value="0" label="minimum percentage of individuals in a population required to process a locus for that population" help="(for populations; default: 0)"/>
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59 <param argument="--min-populations" name="min_populations" type="integer" value="1" label="minimum number of populations a locus must be present in to process a locus" help="(for populations; default: 1)"/>
0
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60 </section>
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61 <expand macro="in_log"/>
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62 </inputs>
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63 <outputs>
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64 <expand macro="out_log"/> <!-- pipeline also writes tsv2bam.log, gstacks.log, populations.log .. could be a collection -->
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65 <expand macro="ustacks_outputs_macro" tooladd="(ustacks)"/>
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66 <expand macro="cstacks_outputs_macro" tooladd="(cstacks)"/>
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67 <expand macro="sstacks_outputs_macro" tooladd="(sstacks)"/>
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68 <expand macro="tsv2bam_outputs_macro" tooladd="(tsv2bam)"/>
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69 <expand macro="gstacks_outputs_macro" tooladd="(gstacks)"/>
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70 <expand macro="populations_output_light" tooladd="(populations)"/>
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71 </outputs>
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72
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73 <tests>
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74 <!-- paired input using also reverse reads,
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75 the results are tested for equality, the tools corresponding the the programs
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76 used in the pipeline have also a test (should be the first) that test for
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77 equality thereby it is "ensured" that the pipeline w defaults is doing the same
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78 as the components w defaults. -->
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79 <test expect_num_outputs="11">
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80 <param name="input_type|input_type_select" value="paired"/>
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81 <param name="input_type|fqinputs">
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82 <collection type="list:paired">
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83 <element name="PopA_01">
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84 <collection type="paired">
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85 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
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86 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
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87 </collection>
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88 </element>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
89 <element name="PopA_02">
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
90 <collection type="paired">
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
91 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
92 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
93 </collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
94 </element>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
95 </collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
96 </param>
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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97 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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98 <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
99 <output_collection name="tabs" count="6">
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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100 <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="4"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
101 <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="4"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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102 <element name="PopA_01.alleles" file="ustacks/PopA_01.alleles.tsv" ftype="tabular" lines_diff="4"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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103 <element name="PopA_02.tags" file="ustacks/PopA_02.tags.tsv" ftype="tabular" lines_diff="4"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
104 <element name="PopA_02.snps" file="ustacks/PopA_02.snps.tsv" ftype="tabular" lines_diff="4"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
105 <element name="PopA_02.alleles" file="ustacks/PopA_02.alleles.tsv" ftype="tabular" lines_diff="4"/>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
106 </output_collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
107 <output_collection name="catalog" type="list" count="3">
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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108 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="4"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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109 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="4"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
110 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="4"/>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
111 </output_collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
112 <output_collection name="matches" type="list" count="2">
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
113 <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="4"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
114 <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="4"/>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
115 </output_collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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116 <output_collection name="bams" type="list" count="2">
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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117 <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
118 <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
119 </output_collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
120 <output_collection name="gstacks_out" type="list" count="2">
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
121 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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122 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="sim_size" delta_frac="0.01"/>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
123 </output_collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
124 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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125 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv" compare="sim_size" delta_frac="0.01"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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126 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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127 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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128 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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129 </test>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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130 <!-- SE input as multi selection, defaults testing against the output of the pipeline components -->
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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131 <test expect_num_outputs="11">
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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132 <param name="input_type|input_type_select" value="single"/>
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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133 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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134 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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135 <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
136 <output_collection name="tabs" count="6"/>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
137 <output_collection name="catalog" type="list" count="3"/>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
138 <output_collection name="matches" type="list" count="2"/>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
139 <output_collection name="bams" type="list" count="2"/>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
140 <output_collection name="gstacks_out" type="list" count="2"/>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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141 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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142 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
143 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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144 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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145 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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146 </test>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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147 <!-- SE input as list, non-defaults, testing only correct size of the collections -->
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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148 <test expect_num_outputs="11">
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
149 <param name="input_type|input_type_select" value="paired"/>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
150 <param name="input_type|fqinputs">
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
151 <collection type="list">
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
152 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
153 <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
154 </collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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diff changeset
155 </param>
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
156 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
157 <param name="assembly_options|M" value="3"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
158 <param name="assembly_options|n" value="3"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
159 <param name="model_options|var_alpha" value="0.1"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
160 <param name="model_options|gt_alpha" value="0.1"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
161 <param name="pe_options|rm_pcr_duplicates" value="--rm-pcr-duplicates"/>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
162 <param name="popfilter_options|min_samples_per_pop" value="1"/>
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
163 <param name="popfilter_options|min_populations" value="0"/>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
164 <assert_command>
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
165 <has_text text="-M 3"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
166 <has_text text="-n 3"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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167 <has_text text="--var-alpha 0.1"/>
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168 <has_text text="--gt-alpha 0.1"/>
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169 <has_text text="--rm-pcr-duplicates"/>
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170 <has_text text="--min-samples-per-pop 1"/>
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171 <has_text text="--min-populations 0"/>
0
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172 </assert_command>
2
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173 <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
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174 <output_collection name="tabs" count="6"/>
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175 <output_collection name="catalog" type="list" count="3"/>
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176 <output_collection name="matches" type="list" count="2"/>
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177 <output_collection name="bams" type="list" count="2"/>
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178 <output_collection name="gstacks_out" type="list" count="2"/>
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179 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
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180 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
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181 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
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182 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
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183 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
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184 </test>
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185 </tests>
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186
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187 <help>
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188 <![CDATA[
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189 .. class:: infomark
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190
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191 **What it does**
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192
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193 This program will run each of the Stacks components: first, running ustacks on each of the samples specified, building loci and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci that were marked as 'parents' or 'samples' on the command line, and finally, sstacks will be executed to match each sample against the catalog. A bit more detail on this process can be found in the FAQ. The denovo_map.pl program will also load the results of each stage of the analysis: individual loci, the catalog, and matches against the catalog into the database (although this can be disabled). After matching, the program will build a database index to speed up access (index_radtags.pl) and enable web-based filtering.
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194
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195 --------
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196
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197 **Input files**
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198
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199 FASTQ, FASTA
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200
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201 - Population map::
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202
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203 indv_01 1
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204 indv_02 1
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205 indv_03 1
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206 indv_04 2
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207 indv_05 2
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208 indv_06 2
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209
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210
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211 **Output files**
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212
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213
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214 - XXX.tags.tsv file:
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215
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216 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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217
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218 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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219
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220
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221 - XXX.snps.tsv file:
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222
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223 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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224
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225 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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226
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227
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228 - XXX.alleles.tsv file:
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229
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230 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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231
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232
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233 - XXX.matches.tsv file:
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234
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235 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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236
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237 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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238
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239
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240 - other files:
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241
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242 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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243
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244 @STACKS_INFOS@
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245 ]]>
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246 </help>
2
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247 <expand macro="citation"/>
0
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248 </tool>