Mercurial > repos > matthias > stacks2_ustacks
diff stacks_ustacks.xml @ 5:ccbb048a4178 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
| author | matthias |
|---|---|
| date | Wed, 27 Feb 2019 09:47:34 -0500 |
| parents | 784278062e27 |
| children | 742c94cfb8cf |
line wrap: on
line diff
--- a/stacks_ustacks.xml Fri Jan 04 03:28:15 2019 -0500 +++ b/stacks_ustacks.xml Wed Feb 27 09:47:34 2019 -0500 @@ -1,37 +1,37 @@ -<tool id="stacks2_ustacks" name="Stacks2: ustacks" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> - <description>align short reads into stacks</description> +<tool id="stacks2_ustacks" name="Stacks2: ustacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> + <description>Indentify unique stacks</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ -@CLEAN_EXT@ + <expand macro="version_cmd"/> + <command detect_errors="aggressive"><![CDATA[ +@FASTQ_INPUT_FUNCTIONS@ mkdir stacks_inputs stacks_outputs && #set $ID=1 -#for $sample in $input_type.samples - #set $read_direction="forward" - @FASTQ_INPUT@ +#for $sample in $input_type.fqinputs + #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1") + $create_links ustacks - -f $data_path + -f '$data_path' -i $ID --name $name -m $m -M $M #if $N -N $N - #end if + #end if -p \${GALAXY_SLOTS:-1} -t $inputype $R $H - + ## Assembly $assembly_options.keep_high_cov --high_cov_thres $assembly_options.high_cov_thres @@ -40,9 +40,9 @@ #if str($assembly_options.k_len) --k_len $assembly_options.k_len #end if - + @GAP_OPTIONS@ - + ## snp_model #if str( $snp_options.select_model.model_type) == "bounded" --model_type bounded @@ -56,37 +56,23 @@ --model_type fixed --bc_err_freq $bc_err_freq #end if - + -o stacks_outputs - + @TEE_APPEND_LOG@ #set $ID=$ID+1 #end for -@CAT_LOG_TO_STDERR@ && +@CAT_LOG_TO_STDERR@ ## If input is in gz format, stacks will output gzipped files (no option to control this) #if $inputype.startswith('gz') - gunzip stacks_outputs/*.gz -#else - true + && gunzip stacks_outputs/*.gz #end if ]]></command> <inputs> - <expand macro="fastq_input_macro"/> + <expand macro="fastq_input" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"/> - <conditional name="input_type"> - <param name="input_type_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"> - <option value="manual" selected="true">single end or forward reads</option> - <option value="list">(paired) data set list</option> - </param> - <when value="manual"> - <param name="samples" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true"/> - </when> - <when value="list"> - <param name="samples" argument="-f" type="data_collection" collection_type="list,list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs"/> - </when> - </conditional> <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)"/> @@ -95,7 +81,7 @@ <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="--high_cov_thres" type="float" min="0.0" value="3.0" label="highly-repetitive stacks threshold" help="in standard deviation units"/> + <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)"/> </section> @@ -114,12 +100,27 @@ </outputs> <tests> - <!-- manual selected list of elements + default args, test for file equality --> + <!-- paired list, default options, test for file equality --> <test> - <param name="input_type|input_type_selector" value="manual"/> - <param name="input_type|samples" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> + <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="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="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> + </collection> + </element> + </collection> + </param> <param name="add_log" value="yes" /> - <output name="output_log" ftype="txt" file="ustacks/ustacks.log" lines_diff="2"/> + <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> <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"/> @@ -129,10 +130,25 @@ <element name="PopA_02.alleles" ftype="tabular" file="ustacks/PopA_02.alleles.tsv" lines_diff="2"/> </output_collection> </test> + <!-- manual selected list of elements + default args, test for file equality --> + <test> + <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" /> + <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> + </output_collection> + </test> <!-- manual selected list of elements + non-default short args, test for file presence --> <test> - <param name="input_type|input_type_selector" value="manual"/> - <param name="input_type|samples" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> + <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="-N" value="4"/> @@ -146,7 +162,7 @@ <has_text text="-R" /> <has_text text="-H" /> </assert_command> - <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> + <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> @@ -158,8 +174,8 @@ </test> <!-- paired list, non-default model options, disabled gapped alignment, test for file presence --> <test> - <param name="input_type|input_type_selector" value="list"/> - <param name="input_type|samples"> + <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"> @@ -192,7 +208,7 @@ <has_text text="--bc_err_freq 0.1" /> <has_text text="--disable-gapped" /> </assert_command> - <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> + <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> @@ -204,8 +220,8 @@ </test> <!-- list of fwd reads, nondefault assembly and gapped alignment options, test for file presence --> <test> - <param name="input_type|input_type_selector" value="list"/> - <param name="input_type|samples"> + <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_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> @@ -229,7 +245,7 @@ <has_text text="--max_gaps 3" /> <has_text text="--min_aln_len 3" /> </assert_command> - <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> + <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> @@ -253,7 +269,7 @@ **Input files** -One or more FASTQ, FASTA files. Can be given by selecting them manually, as data set list, or paired data set list. Note, for the latter ustacks only uses the forward reads -- reverse reads are incorporated in tsv2bam. +One or more FASTQ, FASTA files. Can be given by selecting them manually, as dataset list, or paired dataset list. Note, for the latter ustacks only uses the forward reads -- reverse reads are incorporated in tsv2bam. **Output files**