Mercurial > repos > iuc > stacks2_ustacks
diff stacks_ustacks.xml @ 2:d033e1ccb386 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
| author | iuc |
|---|---|
| date | Thu, 16 Jul 2020 07:31:44 -0400 |
| parents | 21d2aa544835 |
| children | d1fda11e602f |
line wrap: on
line diff
--- a/stacks_ustacks.xml Mon Sep 30 14:16:43 2019 -0400 +++ b/stacks_ustacks.xml Thu Jul 16 07:31:44 2020 -0400 @@ -8,9 +8,8 @@ <command detect_errors="aggressive"><![CDATA[ @FASTQ_INPUT_FUNCTIONS@ -mkdir stacks_inputs stacks_outputs - -&& +trap ">&2 cat '$output_log'" err exit && +mkdir stacks_inputs stacks_outputs && #set $ID=1 #for $sample in $input_type.fqinputs @@ -58,12 +57,12 @@ #end if -o stacks_outputs - @TEE_APPEND_LOG@ + && #set $ID=$ID+1 #end for -@CAT_LOG_TO_STDERR@ +true ## If input is in gz format, stacks will output gzipped files (no option to control this) #if $inputype.startswith('gz') && gunzip stacks_outputs/*.gz @@ -76,11 +75,11 @@ <param argument="-m" type="integer" value="3" label="Minimum depth of coverage required to create a stack"/> <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/> <param argument="-N" type="integer" value="" optional="true" label="Maximum distance allowed to align secondary reads to primary stacks" help="(default: M + 2)"/> - <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" /> - <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" /> + <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads"/> + <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads"/> <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True"> - <param argument="--keep_high_cov" type="boolean" checked="false" truevalue="--keep_high_cov" falsevalue="" label="Disable the algorithm that removes highly-repetitive stacks and nearby errors. " /> - <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" /> + <param argument="--keep_high_cov" type="boolean" checked="false" truevalue="--keep_high_cov" falsevalue="" label="Disable the algorithm that removes highly-repetitive stacks and nearby errors. "/> + <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags"/> <param argument="--high_cov_thres" type="float" min="0.0" value="3.0" label="Highly-repetitive stacks threshold" help="in standard deviation units"/> <param argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/> <param argument="--k_len" type="integer" value="" min="7" max="31" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/> @@ -101,91 +100,92 @@ <tests> <!-- paired list, default options, test for file equality --> - <test> + <test expect_num_outputs="2"> <param name="input_type|input_type_select" value="paired"/> <param name="input_type|fqinputs"> <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> + <!-- 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="2"/> - <element name="PopA_01.snps" ftype="tabular" file="ustacks/PopA_01.snps.tsv" lines_diff="2"/> - <element name="PopA_01.alleles" ftype="tabular" file="ustacks/PopA_01.alleles.tsv" lines_diff="2"/> - <element name="PopA_02.tags" ftype="tabular" file="ustacks/PopA_02.tags.tsv" lines_diff="2"/> - <element name="PopA_02.snps" ftype="tabular" file="ustacks/PopA_02.snps.tsv" lines_diff="2"/> - <element name="PopA_02.alleles" ftype="tabular" file="ustacks/PopA_02.alleles.tsv" lines_diff="2"/> + <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"/> </output_collection> </test> <!-- manual selected list of elements + default args, test for file equality --> - <test> + <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="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> + <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="generated on " /></assert_contents></element> - <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> + <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> </output_collection> </test> <!-- manual selected list of elements + non-default short args, test for file presence --> - <test> + <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="m" value="2" /> - <param name="M" value="3" /> + <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> + <param name="m" value="2"/> + <param name="M" value="3"/> <param name="N" value="4"/> - <param name="R" value="-R" /> - <param name="H" value="-H" /> - <param name="add_log" value="yes" /> + <param name="R" value="-R"/> + <param name="H" value="-H"/> + <param name="add_log" value="yes"/> <assert_command> - <has_text text="-m 2" /> - <has_text text="-M 3" /> - <has_text text="-N 4" /> - <has_text text="-R" /> - <has_text text="-H" /> + <has_text text="-m 2"/> + <has_text text="-M 3"/> + <has_text text="-N 4"/> + <has_text text="-R"/> + <has_text text="-H"/> </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="generated on " /></assert_contents></element> - <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> + <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> </output_collection> </test> <!-- paired list, non-default model options, disabled gapped alignment, test for file presence --> - <test> + <test expect_num_outputs="2"> <param name="input_type|input_type_select" value="paired"/> <param name="input_type|fqinputs"> <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> @@ -198,61 +198,61 @@ <param name="bound_high" value="0.5"/> <param name="bc_err_freq" value="0.1"/> </conditional> - <param name="gapped|use_gapped" value="no" /> - <param name="add_log" value="yes" /> + <param name="gapped|use_gapped" value="no"/> + <param name="add_log" value="yes"/> <assert_command> - <has_text text="--model_type snp" /> - <has_text text="--alpha 0.1" /> - <not_has_text text="--bound_low 0.1" /> - <not_has_text text="--bound_high 0.5" /> - <not_has_text text="--bc_err_freq 0.1" /> - <has_text text="--disable-gapped" /> + <has_text text="--model_type snp"/> + <has_text text="--alpha 0.1"/> + <not_has_text text="--bound_low 0.1"/> + <not_has_text text="--bound_high 0.5"/> + <not_has_text text="--bc_err_freq 0.1"/> + <has_text text="--disable-gapped"/> </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="generated on " /></assert_contents></element> - <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> + <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> </output_collection> </test> <!-- list of fwd reads, nondefault assembly and gapped alignment options, test for file presence --> - <test> + <test expect_num_outputs="2"> <param name="input_type|input_type_select" value="paired"/> <param name="input_type|fqinputs"> <collection type="list"> - <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> + <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/> <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> </collection> </param> <param name="assembly_options|keep_high_cov" value="true"/> - <param name="assembly_options|d" value="-d" /> + <param name="assembly_options|d" value="-d"/> <param name="assembly_options|high_cov_thres" value="2.0"/> - <param name="assembly_options|max_locus_stacks" value="4" /> + <param name="assembly_options|max_locus_stacks" value="4"/> <param name="assembly_options|k_len" value="12"/> - <param name="gapped|use_gapped" value="yes" /> - <param name="gapped|max_gaps" value="3" /> + <param name="gapped|use_gapped" value="yes"/> + <param name="gapped|max_gaps" value="3"/> <param name="gapped|min_aln_len" value="0.7"/> - <param name="add_log" value="yes" /> + <param name="add_log" value="yes"/> <assert_command> - <has_text text="--keep_high_cov" /> - <has_text text="-d" /> - <has_text text="--high_cov_thres 2.0" /> - <has_text text="--max_locus_stacks 4" /> - <has_text text="--k_len 12" /> - <has_text text="--max_gaps 3" /> - <has_text text="--min_aln_len 0.7" /> + <has_text text="--keep_high_cov"/> + <has_text text="-d"/> + <has_text text="--high_cov_thres 2.0"/> + <has_text text="--max_locus_stacks 4"/> + <has_text text="--k_len 12"/> + <has_text text="--max_gaps 3"/> + <has_text text="--min_aln_len 0.7"/> </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="generated on " /></assert_contents></element> - <element name="PopA_01.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_01.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.tags"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.snps"><assert_contents><has_text text="generated on " /></assert_contents></element> - <element name="PopA_02.alleles"><assert_contents><has_text text="generated on " /></assert_contents></element> + <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> </output_collection> </test> </tests> @@ -294,5 +294,5 @@ @STACKS_INFOS@ ]]> </help> - <expand macro="citation" /> + <expand macro="citation"/> </tool>