Mercurial > repos > iuc > stacks2_denovomap

comparison stacks_denovomap.xml @ 6:89eb29319bf4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
author iuc
date Wed, 11 May 2022 06:50:13 +0000
parents 04db7fd6b238
children
comparison
equal deleted inserted replaced
5:04db7fd6b238 6:89eb29319bf4
94 </element> 94 </element>
95 </collection> 95 </collection>
96 </param> 96 </param>
97 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> 97 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
98 <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output> 98 <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output>
99 <output_collection name="tabs" count="6"> 99 <output_collection name="tabs" type="list" count="6">
100 <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="4"/> 100 <element name="PopA_01.tags">
101 <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="4"/> 101 <assert_contents>
102 <element name="PopA_01.alleles" file="ustacks/PopA_01.alleles.tsv" ftype="tabular" lines_diff="4"/> 102 <has_text text="# ustacks version" />
103 <element name="PopA_02.tags" file="ustacks/PopA_02.tags.tsv" ftype="tabular" lines_diff="4"/> 103 </assert_contents>
104 <element name="PopA_02.snps" file="ustacks/PopA_02.snps.tsv" ftype="tabular" lines_diff="4"/> 104 </element>
105 <element name="PopA_02.alleles" file="ustacks/PopA_02.alleles.tsv" ftype="tabular" lines_diff="4"/> 105 <element name="PopA_01.snps">
106 <assert_contents>
107 <has_text text="# ustacks version" />
108 </assert_contents>
109 </element>
110 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
111 <element name="PopA_02.tags">
112 <assert_contents>
113 <has_text text="# ustacks version" />
114 </assert_contents>
115 </element>
116 <element name="PopA_02.snps">
117 <assert_contents>
118 <has_text text="# ustacks version" />
119 </assert_contents>
120 </element>
121 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
106 </output_collection> 122 </output_collection>
107 <output_collection name="catalog" type="list" count="3"> 123 <output_collection name="catalog" type="list" count="3">
108 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="4"/> 124 <element name="catalog.alleles">
109 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="4"/> 125 <assert_contents>
110 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="4"/> 126 <has_text text="# cstacks version " />
127 </assert_contents>
128 </element>
129 <element name="catalog.snps" >
130 <assert_contents>
131 <has_text text="# cstacks version" />
132 </assert_contents>
133 </element>
134 <element name="catalog.tags">
135 <assert_contents>
136 <has_text text="# cstacks version" />
137 </assert_contents>
138 </element>
111 </output_collection> 139 </output_collection>
112 <output_collection name="matches" type="list" count="2"> 140 <output_collection name="matches" type="list" count="2">
113 <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="4"/> 141 <element name="PopA_01.matches">
114 <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="4"/> 142 <assert_contents>
143 <has_text text="# sstacks version" />
144 </assert_contents>
145 </element>
146 <element name="PopA_02.matches" >
147 <assert_contents>
148 <has_text text="# sstacks version" />
149 </assert_contents>
150 </element>
115 </output_collection> 151 </output_collection>
116 <output_collection name="bams" type="list" count="2"> 152 <output_collection name="bams" type="list" count="2">
117 <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/> 153 <element name="PopA_01.matches">
118 <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/> 154 <assert_contents>
155 <has_size value="1153" delta="200" />
156 </assert_contents>
157 </element>
158 <element name="PopA_02.matches" >
159 <assert_contents>
160 <has_size value="1169" delta="200" />
161 </assert_contents>
162 </element>
119 </output_collection> 163 </output_collection>
120 <output_collection name="gstacks_out" type="list" count="2"> 164 <output_collection name="gstacks_out" type="list" count="2">
121 <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/> 165 <element name="catalog.calls.vcf">
122 <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="diff"/> 166 <assert_contents>
123 </output_collection> 167 <has_text text="##fileformat=VCFv4.2" />
124 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> 168 </assert_contents>
125 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv" compare="diff"/> 169 </element>
170 <element name="catalog.fa.gz" >
171 <assert_contents>
172 <has_size value="334" delta="100" />
173 </assert_contents>
174 </element>
175 </output_collection>
176 <output name="out_haplotypes">
177 <assert_contents>
178 <has_text_matching expression="\#\s+Catalog\s+Locus\s+ID\s+Cnt" />
179 </assert_contents>
180 </output>
181 <output name="out_hapstats">
182 <assert_contents>
183 <has_text_matching expression="\#\s+Locus\s+ID\s+Chr\s+BP" />
184 </assert_contents>
185 </output>
126 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/> 186 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/>
127 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/> 187 <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
128 <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/> 188 <output name="out_sumstats">
189 <assert_contents>
190 <has_text_matching expression="\#\s+Locus\s+ID\s+Chr\s+BP" />
191 </assert_contents>
192 </output>
129 </test> 193 </test>
130 <!-- SE input as multi selection, defaults testing against the output of the pipeline components --> 194 <!-- SE input as multi selection, defaults testing against the output of the pipeline components -->
131 <test expect_num_outputs="11"> 195 <test expect_num_outputs="11">
132 <param name="input_type|input_type_select" value="single"/> 196 <param name="input_type|input_type_select" value="single"/>
133 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> 197 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>