Mercurial > repos > iuc > stacks2_cstacks
diff stacks_cstacks.xml @ 2:fcce77c09289 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
| author | iuc |
|---|---|
| date | Thu, 16 Jul 2020 07:23:04 -0400 |
| parents | da351b9031de |
| children | 0cd2df8af811 |
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--- a/stacks_cstacks.xml Mon Sep 30 14:18:15 2019 -0400 +++ b/stacks_cstacks.xml Thu Jul 16 07:23:04 2020 -0400 @@ -8,11 +8,10 @@ <command detect_errors="aggressive"><![CDATA[ #import re -mkdir stacks_inputs stacks_outputs -&& +trap ">&2 cat '$output_log'" err exit && +mkdir stacks_inputs stacks_outputs && @LINK_STACKS_INPUT@ - cstacks -p \${GALAXY_SLOTS:-1} @@ -38,25 +37,23 @@ #end if $report_mmatches @TEE_APPEND_LOG@ -@CAT_LOG_TO_STDERR@ #if $popmap ## When using a popmap, cstacks writes to the input dir && mv stacks_inputs/catalog.*.tsv stacks_outputs/ #end if - ]]></command> <inputs> <expand macro="input_stacks_macro"/> - <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M" /> + <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M"/> <param argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample loci when building the catalog" help="(default 1; suggested: set to ustacks -M)"/> <expand macro="gap_options"/> <param argument="--k_len" type="integer" min="5" max="31" value="" optional="true" label="K-mer size for matching between between catalog loci" help="default: automatic"/> - <param argument="--report_mmatches" type="boolean" checked="false" truevalue="--report_mmatches" falsevalue="" label="Report query loci that match more than one catalog locus" /> + <param argument="--report_mmatches" type="boolean" checked="false" truevalue="--report_mmatches" falsevalue="" label="Report query loci that match more than one catalog locus"/> <expand macro="in_log"/> </inputs> @@ -67,72 +64,84 @@ <tests> <!-- test w default options + popmap --> - <test> + <test expect_num_outputs="2"> <param name="input_stacks"> <collection type="list"> - <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> - <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> - <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> - <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> - <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> - <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> + <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> + <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> + <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> + <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> + <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> + <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> </collection> </param> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> - <param name="add_log" value="yes" /> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> + <assert_command> + <has_text text="-M "/> + <has_text text="--max_gaps 2.0"/> + <has_text text="--min_aln_len 0.8"/> + </assert_command> + <param name="add_log" value="yes"/> <output name="output_log" ftype="txt" file="cstacks/cstacks.log"/> + <!-- 1st test checks for file content allowing differences in the 2 comment lines that contain date and version --> <output_collection name="catalog" type="list"> - <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/> - <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" /> - <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" /> + <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"/> </output_collection> </test> <!-- test w default options --> - <test> + <test expect_num_outputs="2"> <param name="input_stacks"> <collection type="list"> - <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> - <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> - <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> - <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> - <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> - <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> + <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> + <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> + <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> + <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> + <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> + <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> </collection> </param> - <param name="add_log" value="yes" /> - <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> + <assert_command> + <not_has_text text="-M "/> + <has_text text="--max_gaps 2.0"/> + <has_text text="--min_aln_len 0.8"/> + </assert_command> + <param name="add_log" value="yes"/> + <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> <output_collection name="catalog" type="list"> - <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/> - <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" /> - <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" /> + <element name="catalog.alleles"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element> + <element name="catalog.snps"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element> + <element name="catalog.tags"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element> </output_collection> </test> <!-- test w non default options (wo gapped, because tested already in ustacks) --> - <test> + <test expect_num_outputs="1"> <param name="input_stacks"> <collection type="list"> - <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> - <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> - <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> - <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> - <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> - <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> + <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> + <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> + <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> + <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> + <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> + <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> </collection> </param> <param name="n" value="2"/> <param name="k_len" value="23"/> - <param name="report_mmatches" value="--report_mmatches" /> + <param name="report_mmatches" value="--report_mmatches"/> <assert_command> - <has_text text="--k_len 23" /> - <has_text text="-n 2" /> - <has_text text="--report_mmatches" /> + <not_has_text text="-M "/> + <has_text text="--k_len 23"/> + <has_text text="-n 2"/> + <has_text text="--report_mmatches"/> </assert_command> - <param name="add_log" value="yes" /> - <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> + <param name="add_log" value="no"/> + <assert_stderr><has_text text="done."/></assert_stderr> <output_collection name="catalog" type="list"> - <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/> - <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" /> - <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" /> + <element name="catalog.alleles"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element> + <element name="catalog.snps"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element> + <element name="catalog.tags"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element> </output_collection> </test> </tests> @@ -173,5 +182,5 @@ @STACKS_INFOS@ ]]> </help> - <expand macro="citation" /> + <expand macro="citation"/> </tool>