Mercurial > repos > iuc > stacks2_denovomap
diff stacks_denovomap.xml @ 6:89eb29319bf4 draft
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 |
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--- a/stacks_denovomap.xml Thu Apr 14 09:20:20 2022 +0000 +++ b/stacks_denovomap.xml Wed May 11 06:50:13 2022 +0000 @@ -96,36 +96,100 @@ </param> <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> <output ftype="txt" name="output_log"><assert_contents><has_text text="denovo_map.pl is done."/></assert_contents></output> - <output_collection name="tabs" count="6"> - <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="4"/> - <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="4"/> - <element name="PopA_01.alleles" file="ustacks/PopA_01.alleles.tsv" ftype="tabular" lines_diff="4"/> - <element name="PopA_02.tags" file="ustacks/PopA_02.tags.tsv" ftype="tabular" lines_diff="4"/> - <element name="PopA_02.snps" file="ustacks/PopA_02.snps.tsv" ftype="tabular" lines_diff="4"/> - <element name="PopA_02.alleles" file="ustacks/PopA_02.alleles.tsv" ftype="tabular" lines_diff="4"/> + <output_collection name="tabs" type="list" count="6"> + <element name="PopA_01.tags"> + <assert_contents> + <has_text text="# ustacks version" /> + </assert_contents> + </element> + <element name="PopA_01.snps"> + <assert_contents> + <has_text text="# ustacks version" /> + </assert_contents> + </element> + <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> + <element name="PopA_02.tags"> + <assert_contents> + <has_text text="# ustacks version" /> + </assert_contents> + </element> + <element name="PopA_02.snps"> + <assert_contents> + <has_text text="# ustacks version" /> + </assert_contents> + </element> + <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> </output_collection> <output_collection name="catalog" type="list" count="3"> - <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="4"/> - <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="4"/> - <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="4"/> + <element name="catalog.alleles"> + <assert_contents> + <has_text text="# cstacks version " /> + </assert_contents> + </element> + <element name="catalog.snps" > + <assert_contents> + <has_text text="# cstacks version" /> + </assert_contents> + </element> + <element name="catalog.tags"> + <assert_contents> + <has_text text="# cstacks version" /> + </assert_contents> + </element> </output_collection> <output_collection name="matches" type="list" count="2"> - <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="4"/> - <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="4"/> + <element name="PopA_01.matches"> + <assert_contents> + <has_text text="# sstacks version" /> + </assert_contents> + </element> + <element name="PopA_02.matches" > + <assert_contents> + <has_text text="# sstacks version" /> + </assert_contents> + </element> </output_collection> <output_collection name="bams" type="list" count="2"> - <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/> - <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/> + <element name="PopA_01.matches"> + <assert_contents> + <has_size value="1153" delta="200" /> + </assert_contents> + </element> + <element name="PopA_02.matches" > + <assert_contents> + <has_size value="1169" delta="200" /> + </assert_contents> + </element> </output_collection> <output_collection name="gstacks_out" type="list" count="2"> - <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/> - <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="diff"/> + <element name="catalog.calls.vcf"> + <assert_contents> + <has_text text="##fileformat=VCFv4.2" /> + </assert_contents> + </element> + <element name="catalog.fa.gz" > + <assert_contents> + <has_size value="334" delta="100" /> + </assert_contents> + </element> </output_collection> - <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> - <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv" compare="diff"/> + <output name="out_haplotypes"> + <assert_contents> + <has_text_matching expression="\#\s+Catalog\s+Locus\s+ID\s+Cnt" /> + </assert_contents> + </output> + <output name="out_hapstats"> + <assert_contents> + <has_text_matching expression="\#\s+Locus\s+ID\s+Chr\s+BP" /> + </assert_contents> + </output> <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/> <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/> - <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/> + <output name="out_sumstats"> + <assert_contents> + <has_text_matching expression="\#\s+Locus\s+ID\s+Chr\s+BP" /> + </assert_contents> + </output> </test> <!-- SE input as multi selection, defaults testing against the output of the pipeline components --> <test expect_num_outputs="11">