Mercurial > repos > iuc > stacks2_tsv2bam
diff stacks_tsv2bam.xml @ 2:bf0e43ab0416 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
| author | iuc |
|---|---|
| date | Wed, 15 Jul 2020 17:29:50 -0400 |
| parents | 8c2617661c49 |
| children | 69842dd5aa48 |
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--- a/stacks_tsv2bam.xml Mon Sep 30 14:20:19 2019 -0400 +++ b/stacks_tsv2bam.xml Wed Jul 15 17:29:50 2020 -0400 @@ -56,7 +56,7 @@ <expand macro="input_matches_macro"/> <!-- TODO add BAM? --> <expand macro="fastq_input" fastq_optional="true" se_option="reverse reads" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data."/> - <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 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"/> <expand macro="in_log"/> </inputs> @@ -67,31 +67,31 @@ <tests> <!-- test wo paired end data --> - <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="input_matches"> <collection type="list"> - <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" /> - <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" /> + <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> + <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> </collection> </param> - <param name="add_log" value="yes" /> + <param name="add_log" value="yes"/> <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="14"/> <output_collection name="bams" type="list" count="2"> <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/> @@ -99,96 +99,96 @@ </output_collection> </test> <!-- test w popmap, w reverse reads as multiple selection --> - <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="input_matches"> <collection type="list"> - <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" /> - <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" /> + <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> + <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> </collection> </param> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> <param name="input_type|input_type_select" value="single"/> - <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" /> - <param name="add_log" value="yes" /> - <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> + <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> + <param name="add_log" value="yes"/> + <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> <output_collection name="bams" type="list" count="2"/> </test> <!-- test w reverse reads as list --> - <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="input_matches"> <collection type="list"> - <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" /> - <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" /> + <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> + <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> </collection> </param> <param name="input_type|input_type_select" value="paired"/> <param name="input_type|fqinputs"> <collection type="list"> - <element name="PopA_01" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger" /> + <element name="PopA_01" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> <element name="PopA_02" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> </collection> </param> - <param name="add_log" value="yes" /> - <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> + <param name="add_log" value="yes"/> + <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> <output_collection name="bams" type="list" count="2"/> </test> <!-- test w paired reads as paired dataset list --> - <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="input_matches"> <collection type="list"> - <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" /> - <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" /> + <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> + <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> </collection> </param> <param name="input_type|input_type_select" value="paired"/> @@ -196,20 +196,20 @@ <collection type="list:paired"> <element name="PopA_01"> <collection type="paired"> - <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> + <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/> <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> </collection> </element> <element name="PopA_02"> <collection type="paired"> - <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> + <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> </collection> </element> </collection> </param> - <param name="add_log" value="yes" /> - <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> + <param name="add_log" value="yes"/> + <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> <output_collection name="bams" type="list" count="2"/> </test> </tests> @@ -251,5 +251,5 @@ @STACKS_INFOS@ ]]> </help> - <expand macro="citation" /> + <expand macro="citation"/> </tool>