| Previous changeset 5:d1fda11e602f (2022-04-14) Next changeset 7:912f904a6e1e (2022-05-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084 |
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modified:
macros.xml stacks_ustacks.xml |
| b |
| diff -r d1fda11e602f -r bb0475c884ff macros.xml --- a/macros.xml Thu Apr 14 09:30:15 2022 +0000 +++ b/macros.xml Wed May 11 06:39:40 2022 +0000 |
| b |
| @@ -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> |
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| diff -r d1fda11e602f -r bb0475c884ff stacks_ustacks.xml --- a/stacks_ustacks.xml Thu Apr 14 09:30:15 2022 +0000 +++ b/stacks_ustacks.xml Wed May 11 06:39:40 2022 +0000 |
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| b'@@ -11,7 +11,7 @@\n trap ">&2 cat \'$output_log\'" err exit &&\n mkdir stacks_inputs stacks_outputs &&\n \n-#set $ID=1\n+#set $ID=int($processing_options.i)\n #for $sample in $input_type.fqinputs\n #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1")\n $create_links\n@@ -90,6 +90,9 @@\n <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">\n <expand macro="snp_options_full"/>\n </section>\n+ <section name="processing_options" title="Processing options" expanded="False">\n+ <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."/>\n+ </section>\n <expand macro="in_log"/>\n </inputs>\n \n@@ -122,12 +125,28 @@\n <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>\n <!-- 1st test checks for file content allowing differences in the 2 comment lines that contain date and version -->\n <output_collection name="tabs" type="list" count="6">\n- <element name="PopA_01.tags" ftype="tabular" file="ustacks/PopA_01.tags.tsv" lines_diff="4"/>\n- <element name="PopA_01.snps" ftype="tabular" file="ustacks/PopA_01.snps.tsv" lines_diff="4"/>\n- <element name="PopA_01.alleles" ftype="tabular" file="ustacks/PopA_01.alleles.tsv" lines_diff="4"/>\n- <element name="PopA_02.tags" ftype="tabular" file="ustacks/PopA_02.tags.tsv" lines_diff="4"/>\n- <element name="PopA_02.snps" ftype="tabular" file="ustacks/PopA_02.snps.tsv" lines_diff="4"/>\n- <element name="PopA_02.alleles" ftype="tabular" file="ustacks/PopA_02.alleles.tsv" lines_diff="4"/>\n+ <element name="PopA_01.tags">\n+ <assert_contents>\n+ <has_text text="# ustacks version" />\n+ </assert_contents>\n+ </element>\n+ <element name="PopA_01.snps">\n+ <assert_contents>\n+ <has_text text="# ustacks version" />\n+ </assert_contents>\n+ </element>\n+ <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />\n+ <element name="PopA_02.tags">\n+ <assert_contents>\n+ <has_text text="# ustacks version" />\n+ </assert_contents>\n+ </element>\n+ <element name="PopA_02.snps">\n+ <assert_contents>\n+ <has_text text="# ustacks version" />\n+ </assert_contents>\n+ </element>\n+ <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />\n </output_collection>\n </test>\n <!-- manual selected list of elements + default args, test for file equality -->\n@@ -137,12 +156,12 @@\n <param name="add_log" value="yes"/>\n <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>\n <output_collection name="tabs" count="6">\n- <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n- <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n- <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n- <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n- <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></ass'..b' <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n- <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n- <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n+ <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />\n </output_collection>\n </test>\n <!-- list of fwd reads, nondefault assembly and gapped alignment options, test for file presence -->\n@@ -247,14 +266,31 @@\n </assert_command>\n <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>\n <output_collection name="tabs" count="6">\n- <element name="PopA_01.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n- <element name="PopA_01.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n- <element name="PopA_01.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n- <element name="PopA_02.tags"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n- <element name="PopA_02.snps"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n- <element name="PopA_02.alleles"><assert_contents><has_text text="# ustacks completed on "/></assert_contents></element>\n+ <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />\n </output_collection>\n </test>\n+ <!-- test setting i -->\n+ <test expect_num_outputs="2">\n+ <param name="input_type|input_type_select" value="single"/>\n+ <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>\n+ <param name="add_log" value="yes"/>\n+ <param name="i" value="42"/>\n+ <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>\n+ <output_collection name="tabs" count="6">\n+ <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />\n+ <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />\n+ </output_collection>\n+ </test>\n+\n </tests>\n \n <help>\n' |