Mercurial > repos > iuc > stacks2_denovomap

annotate stacks_denovomap.xml @ 7:33486216eec0 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
author iuc
date Mon, 23 May 2022 17:50:41 +0000
parents 89eb29319bf4
children
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1 <tool id="stacks2_denovomap" name="Stacks2: de novo map" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_cmd"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 @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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16 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, ".%d" )
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17 $link_command
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19 denovo_map.pl
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20 --samples stacks_inputs
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21 #if str($popmap) != 'None':
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22 --popmap '$popmap'
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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
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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" multiple="true" listtype="list:paired"/>
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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=""/>
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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)"/>
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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"/>
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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
diff changeset
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
diff changeset
98 <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
6
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
99 <output_collection name="tabs" type="list" count="6">
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
100 <element name="PopA_01.tags">
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
101 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
102 <has_text text="# ustacks version" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
103 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
104 </element>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
105 <element name="PopA_01.snps">
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
106 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
107 <has_text text="# ustacks version" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
108 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
109 </element>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
110 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
111 <element name="PopA_02.tags">
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
112 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
113 <has_text text="# ustacks version" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
114 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
115 </element>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
116 <element name="PopA_02.snps">
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
117 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
118 <has_text text="# ustacks version" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
119 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
120 </element>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
121 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
122 </output_collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
123 <output_collection name="catalog" type="list" count="3">
6
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
124 <element name="catalog.alleles">
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
125 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
126 <has_text text="# cstacks version " />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
127 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
128 </element>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
129 <element name="catalog.snps" >
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
130 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
131 <has_text text="# cstacks version" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
132 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
133 </element>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
134 <element name="catalog.tags">
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
135 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
136 <has_text text="# cstacks version" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
137 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
138 </element>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
139 </output_collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
140 <output_collection name="matches" type="list" count="2">
6
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
141 <element name="PopA_01.matches">
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
142 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
143 <has_text text="# sstacks version" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
144 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
145 </element>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
146 <element name="PopA_02.matches" >
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
147 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
148 <has_text text="# sstacks version" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
149 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
150 </element>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
151 </output_collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
152 <output_collection name="bams" type="list" count="2">
6
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
153 <element name="PopA_01.matches">
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
154 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
155 <has_size value="1153" delta="200" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
156 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
157 </element>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
158 <element name="PopA_02.matches" >
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
159 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
160 <has_size value="1169" delta="200" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
161 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
162 </element>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
163 </output_collection>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
164 <output_collection name="gstacks_out" type="list" count="2">
6
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
165 <element name="catalog.calls.vcf">
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
166 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
167 <has_text text="##fileformat=VCFv4.2" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
168 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
169 </element>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
170 <element name="catalog.fa.gz" >
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
171 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
172 <has_size value="334" delta="100" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
173 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
174 </element>
0
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
175 </output_collection>
6
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
176 <output name="out_haplotypes">
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
177 <assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
178 <has_text_matching expression="\#\s+Catalog\s+Locus\s+ID\s+Cnt" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
179 </assert_contents>
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
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180 </output>
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181 <output name="out_hapstats">
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182 <assert_contents>
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183 <has_text_matching expression="\#\s+Locus\s+ID\s+Chr\s+BP" />
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184 </assert_contents>
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185 </output>
2
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186 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
0
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187 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
6
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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188 <output name="out_sumstats">
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189 <assert_contents>
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190 <has_text_matching expression="\#\s+Locus\s+ID\s+Chr\s+BP" />
89eb29319bf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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191 </assert_contents>
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192 </output>
0
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193 </test>
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194 <!-- SE input as multi selection, defaults testing against the output of the pipeline components -->
2
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195 <test expect_num_outputs="11">
0
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196 <param name="input_type|input_type_select" value="single"/>
2
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197 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
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198 <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"
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199 <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
0
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200 <output_collection name="tabs" count="6"/>
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201 <output_collection name="catalog" type="list" count="3"/>
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202 <output_collection name="matches" type="list" count="2"/>
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203 <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
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204 <output_collection name="gstacks_out" type="list" count="2"/>
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205 <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
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206 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
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207 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
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208 <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
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209 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
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210 </test>
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211 <!-- SE input as list, non-defaults, testing only correct size of the collections -->
2
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212 <test expect_num_outputs="11">
0
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213 <param name="input_type|input_type_select" value="paired"/>
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214 <param name="input_type|fqinputs">
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215 <collection type="list">
2
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216 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
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217 <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
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218 </collection>
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219 </param>
2
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220 <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"
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221 <param name="assembly_options|M" value="3"/>
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222 <param name="assembly_options|n" value="3"/>
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223 <param name="model_options|var_alpha" value="0.1"/>
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224 <param name="model_options|gt_alpha" value="0.1"/>
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225 <param name="pe_options|rm_pcr_duplicates" value="--rm-pcr-duplicates"/>
0
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226 <param name="popfilter_options|min_samples_per_pop" value="1"/>
2
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227 <param name="popfilter_options|min_populations" value="0"/>
0
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228 <assert_command>
2
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229 <has_text text="-M 3"/>
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230 <has_text text="-n 3"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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231 <has_text text="--var-alpha 0.1"/>
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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232 <has_text text="--gt-alpha 0.1"/>
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233 <has_text text="--rm-pcr-duplicates"/>
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234 <has_text text="--min-samples-per-pop 1"/>
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235 <has_text text="--min-populations 0"/>
0
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236 </assert_command>
2
421c33b8bf17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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237 <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
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238 <output_collection name="tabs" count="6"/>
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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239 <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
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240 <output_collection name="matches" type="list" count="2"/>
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241 <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
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242 <output_collection name="gstacks_out" type="list" count="2"/>
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243 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
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244 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
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245 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
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246 <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
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247 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
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248 </test>
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249 </tests>
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250
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251 <help>
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252 <![CDATA[
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253 .. class:: infomark
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254
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255 **What it does**
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256
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257 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.
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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258
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259 --------
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260
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261 **Input files**
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262
b9822370f843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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263 FASTQ, FASTA
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264
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265 - Population map::
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266
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267 indv_01 1
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268 indv_02 1
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269 indv_03 1
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270 indv_04 2
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271 indv_05 2
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272 indv_06 2
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275 **Output files**
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277
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278 - XXX.tags.tsv file:
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279
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280 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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281
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282 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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283
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284
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285 - XXX.snps.tsv file:
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286
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287 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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288
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289 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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290
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292 - XXX.alleles.tsv file:
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293
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294 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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295
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296
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297 - XXX.matches.tsv file:
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298
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299 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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300
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301 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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302
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303
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304 - other files:
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305
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306 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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307
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308 @STACKS_INFOS@
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309 ]]>
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310 </help>
2
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311 <expand macro="citation"/>
0
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312 </tool>