Mercurial > repos > iuc > stacks2_tsv2bam
diff stacks_tsv2bam.xml @ 4:69842dd5aa48 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
author | iuc |
---|---|
date | Wed, 01 Sep 2021 11:32:48 +0000 |
parents | bf0e43ab0416 |
children | a4b4bd84f69e |
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--- a/stacks_tsv2bam.xml Tue Apr 27 09:28:24 2021 +0000 +++ b/stacks_tsv2bam.xml Wed Sep 01 11:32:48 2021 +0000 @@ -3,7 +3,9 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"/> + <expand macro="requirements"> + <requirement type="package" version="1.13">samtools</requirement> + </expand> <expand macro="version_cmd"/> <command detect_errors="aggressive"><![CDATA[ @FASTQ_INPUT_FUNCTIONS@ @@ -48,6 +50,9 @@ 2>&1 && mv stacks_inputs/*matches.bam stacks_outputs + +## see comment in gstacks +&& for b in stacks_outputs/*matches.bam; do (samtools view -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done ]]></command> <inputs> @@ -66,7 +71,7 @@ </outputs> <tests> - <!-- test wo paired end data --> + <!-- test wo paired end data (this is not the default used in denovomap .. which is used for generating the test data therefore we only test if a list of two bams is generated) --> <test expect_num_outputs="2"> <param name="input_cat"> <collection type="list"> @@ -93,10 +98,39 @@ </param> <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"/> - <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/> - </output_collection> + <output_collection name="bams" type="list" count="2"/> + </test> + <!-- test w popmap, w reverse reads as multiple selection --> + <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"/> + </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"/> + </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"/> + </collection> + </param> + <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> + <output_collection name="bams" type="list" count="2"/> </test> <!-- test w popmap, w reverse reads as multiple selection --> <test expect_num_outputs="2">