Mercurial > repos > iuc > stacks2_ustacks
changeset 6:bb0475c884ff draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
| author | iuc |
|---|---|
| date | Wed, 11 May 2022 06:39:40 +0000 |
| parents | d1fda11e602f |
| children | 912f904a6e1e |
| files | macros.xml stacks_ustacks.xml |
| diffstat | 2 files changed, 72 insertions(+), 32 deletions(-) [+] |
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--- a/macros.xml Thu Apr 14 09:30:15 2022 +0000 +++ b/macros.xml Wed May 11 06:39:40 2022 +0000 @@ -10,7 +10,7 @@ </xml> <token name="@TOOL_VERSION@">2.55</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">20.05</token> <xml name="citation"> @@ -632,4 +632,8 @@ <option value="--index_inline">@TYPE@ occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data) (--index_inline)</option> </expand> </xml> + <!-- for tests that check the output for "stacks completed" --> + <xml name="test_element_stacks_completed" token_element_name=""> + <element name="@ELEMENT_NAME@"><assert_contents><has_text text="stacks completed on" /></assert_contents></element> + </xml> </macros>
--- a/stacks_ustacks.xml Thu Apr 14 09:30:15 2022 +0000 +++ b/stacks_ustacks.xml Wed May 11 06:39:40 2022 +0000 @@ -11,7 +11,7 @@ trap ">&2 cat '$output_log'" err exit && mkdir stacks_inputs stacks_outputs && -#set $ID=1 +#set $ID=int($processing_options.i) #for $sample in $input_type.fqinputs #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1") $create_links @@ -90,6 +90,9 @@ <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False"> <expand macro="snp_options_full"/> </section> + <section name="processing_options" title="Processing options" expanded="False"> + <param argument="-i" type="integer" value="1" label="Start identifier at" help="If you are combining multiple ustacks runs at the cstacks stage, use this option to avoid having different samples with the same identifier."/> + </section> <expand macro="in_log"/> </inputs> @@ -122,12 +125,28 @@ <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> <!-- 1st test checks for file content allowing differences in the 2 comment lines that contain date and version --> <output_collection name="tabs" type="list" count="6"> - <element name="PopA_01.tags" ftype="tabular" file="ustacks/PopA_01.tags.tsv" lines_diff="4"/> - <element name="PopA_01.snps" ftype="tabular" file="ustacks/PopA_01.snps.tsv" lines_diff="4"/> - <element name="PopA_01.alleles" ftype="tabular" file="ustacks/PopA_01.alleles.tsv" lines_diff="4"/> - <element name="PopA_02.tags" ftype="tabular" file="ustacks/PopA_02.tags.tsv" lines_diff="4"/> - <element name="PopA_02.snps" ftype="tabular" file="ustacks/PopA_02.snps.tsv" lines_diff="4"/> - <element name="PopA_02.alleles" ftype="tabular" file="ustacks/PopA_02.alleles.tsv" lines_diff="4"/> + <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> </test> <!-- manual selected list of elements + default args, test for file equality --> @@ -137,12 +156,12 @@ <param name="add_log" value="yes"/> <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> <output_collection name="tabs" count="6"> - <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> + <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" /> + <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" /> + <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> </output_collection> </test> <!-- manual selected list of elements + non-default short args, test for file presence --> @@ -164,12 +183,12 @@ </assert_command> <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> <output_collection name="tabs" count="6"> - <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> + <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" /> + <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" /> + <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> </output_collection> </test> <!-- paired list, non-default model options, disabled gapped alignment, test for file presence --> @@ -210,12 +229,12 @@ </assert_command> <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> <output_collection name="tabs" count="6"> - <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> + <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" /> + <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" /> + <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> </output_collection> </test> <!-- list of fwd reads, nondefault assembly and gapped alignment options, test for file presence --> @@ -247,14 +266,31 @@ </assert_command> <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> <output_collection name="tabs" count="6"> - <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> - <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element> + <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" /> + <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" /> + <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> </output_collection> </test> + <!-- test setting i --> + <test expect_num_outputs="2"> + <param name="input_type|input_type_select" value="single"/> + <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> + <param name="add_log" value="yes"/> + <param name="i" value="42"/> + <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output> + <output_collection name="tabs" count="6"> + <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" /> + <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" /> + <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" /> + <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" /> + </output_collection> + </test> + </tests> <help>