Mercurial > repos > iuc > stacks2_sstacks
diff stacks_sstacks.xml @ 2:0b8c84a7fdb5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
| author | iuc |
|---|---|
| date | Wed, 15 Jul 2020 17:20:51 -0400 |
| parents | e58e2ecb6285 |
| children | 09b8edb56d80 |
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--- a/stacks_sstacks.xml Mon Sep 30 14:14:39 2019 -0400 +++ b/stacks_sstacks.xml Wed Jul 15 17:20:51 2020 -0400 @@ -8,9 +8,8 @@ <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@ @LINK_CAT_INPUT@ @@ -34,7 +33,6 @@ @GAP_OPTIONS_ONOFF@ @TEE_APPEND_LOG@ -@CAT_LOG_TO_STDERR@ #if $popmap ## When using a popmap, stacks write to the input dir @@ -45,8 +43,8 @@ <inputs> <expand macro="input_stacks_macro"/> <expand macro="input_cat_macro"/> - <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" /> - <param argument="-x" type="boolean" checked="true" truevalue="" falsevalue="-x" label="Verify haplotype of matching locus" /> + <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M"/> + <param argument="-x" type="boolean" checked="true" truevalue="" falsevalue="-x" label="Verify haplotype of matching locus"/> <expand macro="gap_options_onoff"/> <expand macro="in_log"/> </inputs> @@ -58,101 +56,101 @@ <tests> <!-- test w default parameters and popmap --> - <test> + <test expect_num_outputs="2"> <param name="input_cat"> <collection type="list"> - <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> - <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> - <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> + <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> + <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> + <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> </collection> </param> <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"/> + <param name="add_log" value="yes"/> <assert_command> - <not_has_text text="-x" /> - <not_has_text text="--disable-gapped" /> - <has_text text="-M" /> + <not_has_text text="-x"/> + <not_has_text text="--disable-gapped"/> + <has_text text="-M"/> </assert_command> <output name="output_log" ftype="txt" file="sstacks/sstacks.log"/> <output_collection name="matches" type="list"> - <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="2"/> - <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="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"/> </output_collection> </test> <!-- test w default parameters --> - <test> + <test expect_num_outputs="2"> <param name="input_cat"> <collection type="list"> - <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> - <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> - <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> + <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> + <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> + <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> </collection> </param> <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" /> + <param name="add_log" value="yes"/> <assert_command> - <not_has_text text="-x" /> - <not_has_text text="--disable-gapped" /> - <not_has_text text="-M" /> + <not_has_text text="-x"/> + <not_has_text text="--disable-gapped"/> + <not_has_text text="-M"/> </assert_command> - <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> + <output name="output_log" ftype="txt"><assert_contents><has_text text="done."/></assert_contents></output> <output_collection name="matches" type="list" count="2"> - <element name="PopA_01.matches"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.matches"><assert_contents><has_text text="generated on " /></assert_contents></element> + <element name="PopA_01.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element> + <element name="PopA_02.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element> </output_collection> </test> <!-- test w non default parameters and popmap--> - <test> + <test expect_num_outputs="1"> <param name="input_cat"> <collection type="list"> - <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> - <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> - <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> + <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> + <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> + <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> </collection> </param> <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="gapped|use_gapped" value="yes" /> - <param name="x" value="-x" /> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> - <param name="add_log" value="yes" /> + <param name="gapped|use_gapped" value="yes"/> + <param name="x" value="-x"/> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> + <param name="add_log" value="no"/> <assert_command> - <has_text text="-x" /> - <not_has_text text="--disable-gapped" /> - <has_text text="-M" /> + <has_text text="-x"/> + <not_has_text text="--disable-gapped"/> + <has_text text="-M"/> </assert_command> - <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> + <assert_stderr><has_text text="done."/></assert_stderr> <output_collection name="matches" type="list" count="2"> - <element name="PopA_01.matches"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.matches"><assert_contents><has_text text="generated on " /></assert_contents></element> + <element name="PopA_01.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element> + <element name="PopA_02.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element> </output_collection> </test> </tests> @@ -200,5 +198,5 @@ @STACKS_INFOS@ ]]> </help> - <expand macro="citation" /> + <expand macro="citation"/> </tool>