Mercurial > repos > matthias > stacks2_refmap
diff macros.xml @ 3:93fb82c0fc94 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
| author | matthias |
|---|---|
| date | Tue, 18 Dec 2018 12:48:09 -0500 |
| parents | 39ebc7633942 |
| children | e1dbdd7175c8 |
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--- a/macros.xml Fri Nov 30 07:30:43 2018 -0500 +++ b/macros.xml Tue Dec 18 12:48:09 2018 -0500 @@ -8,7 +8,7 @@ </xml> <token name="@STACKS_VERSION@">2.2</token> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">2</token> <xml name="stdio"> <stdio> @@ -128,6 +128,7 @@ </data> </xml> + <!-- fastq input --> <xml name="fastq_input_macro" token_fastq_optional="false"> <conditional name="input_type"> @@ -139,7 +140,7 @@ <param name="samples" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/> </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" optional="@FASTQ_OPTIONAL@"/> + <param name="samples" argument="-f" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/> </when> </conditional> </xml> @@ -147,30 +148,33 @@ appends noting/.1/.2 to the link name for accessing the fastq data sets variables $name and $data_path--> <token name="@FASTQ_INPUT@"><![CDATA[ + ## TODO should use sample.identidfier if possible (see corresp. preproc macro) #set $name = $clean_ext($sample.name) #set $data_path = "stacks_inputs/" + $name #if $sample.is_collection: - #set $sample=$sample[$read_direction] + #set $cur_sample=$sample[$read_direction] + #else: + #set $cur_sample=$sample #end if #if $read_direction == "forward": #set $data_path = $data_path + ".1" #elif $read_direction == "reverse": #set $data_path = $data_path + ".2" #end if - #if $sample.is_of_type('fastqsanger') + #if $cur_sample.is_of_type('fastqsanger') #set $data_path = $data_path + ".fq" #set inputype = "fastq" - #else if $sample.is_of_type('fastqsanger.gz') + #else if $cur_sample.is_of_type('fastqsanger.gz') #set $data_path = $data_path + ".fq.gz" #set inputype = "gzfastq" - #else if $sample.is_of_type('fasta') + #else if $cur_sample.is_of_type('fasta') #set $data_path = $data_path + ".fa" #set inputype = "fasta" #else #set $data_path = $data_path + ".fa.gz" #set inputype = "gzfasta" #end if - ln -s '$sample' '${data_path}' && + ln -s '$cur_sample' '${data_path}' && ]]></token> <!-- macro and token for BAM input--> @@ -188,15 +192,6 @@ #end for ]]></token> - <xml name="discover_faqgz_output_macro" token_pattern="" token_dir=""> - <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/> - <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/" /> - <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/" /> - </xml> - <xml name="discover_faq_output_macro" token_pattern="" token_dir=""> - <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/" /> - <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/" /> - </xml> <token name="@CLEAN_EXT@"> <![CDATA[ #from os.path import splitext @@ -412,19 +407,19 @@ <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="alpha threshold for calling genotypes" /> </xml> - <xml name="barcode_encoding_single"> - <option value="--inline_null" selected="True">Barcode is inline with sequence, occurs only on single-end read</option> - <option value="--index_null">Barcode is provded in FASTQ header (Illumina i5 or i7 read)</option> + <xml name="barcode_encoding_single" token_type=""> + <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option> + <option value="--index_null">@TYPE@ is provded in FASTQ header (Illumina i5 or i7 read) (--index_null)</option> <yield/> </xml> - <xml name="barcode_encoding_pair"> - <expand macro="barcode_encoding_single"> - <option value="--null_index">barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided)</option> - <option value="--inline_inline">barcode is inline with sequence, occurs on single and paired-end read</option> - <option value="--index_index">barcode is provded in FASTQ header (Illumina i5 and i7 reads).</option> - <option value="--inline_index">barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read)</option> - <option value="--index_inline"></option> + <xml name="barcode_encoding_pair" token_type=""> + <expand macro="barcode_encoding_single" type="@TYPE@"> + <option value="--null_index">@TYPE@ is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided) (--null_index)</option> + <option value="--inline_inline">@TYPE@ is inline with sequence, occurs on single and paired-end read (--inline_inline)</option> + <option value="--index_index">@TYPE@ is provded in FASTQ header (Illumina i5 and i7 reads) (--index_index)</option> + <option value="--inline_index">@TYPE@ is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read) (--inline_index)</option> + <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> </macros>