Mercurial > repos > iuc > stacks_procrad
changeset 9:57910d476be9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
| author | iuc |
|---|---|
| date | Sun, 21 May 2017 18:52:17 -0400 |
| parents | bec1f08cdfcc |
| children | 8fe258d72ff3 |
| files | macros.xml stacks_procrad.xml test-data/clonefilter/R1_0001.1.fq.gz test-data/clonefilter/R2_0001.2.fq.gz test-data/clonefilter/Removed1_0001.1.1.fq.gz test-data/clonefilter/Removed1_0001.1.1.fq.single.gz test-data/clonefilter/Removed2_0001.2.2.fq.gz |
| diffstat | 7 files changed, 17 insertions(+), 8 deletions(-) [+] |
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--- a/macros.xml Thu Apr 27 04:19:34 2017 -0400 +++ b/macros.xml Sun May 21 18:52:17 2017 -0400 @@ -391,4 +391,19 @@ </when> </conditional> </xml> + + <xml name="barcode_encoding_single"> + <option value="--inline_null" selected="True">Barcode is inline with sequence</option> + <option value="--index_null">Barcode is provided in FASTQ header</option> + </xml> + + <xml name="barcode_encoding_pair"> + <option value="--inline_null" selected="True">Barcode is inline with sequence</option> + <option value="--null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option> + <option value="--index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option> + <option value="--inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option> + <option value="--index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option> + <option value="--inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option> + <option value="--index_inline">random oligo 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)</option> + </xml> </macros>
--- a/stacks_procrad.xml Thu Apr 27 04:19:34 2017 -0400 +++ b/stacks_procrad.xml Sun May 21 18:52:17 2017 -0400 @@ -90,8 +90,7 @@ <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" /> <param name="barcode_encoding" type="select" label="Barcode location"> - <option value="--inline_null" selected="True">Barcode is inline with sequence</option> - <option value="--index_null">Barcode is provided in FASTQ header</option> + <expand macro="barcode_encoding_single" /> </param> </when> <when value="paired"> @@ -99,12 +98,7 @@ <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" /> <param name="barcode_encoding" type="select" label="Barcode location"> - <option value="--inline_null" selected="True">Barcode is inline with sequence, only on the single-end read (read 1)</option> - <option value="--index_null">Barcode is provided in FASTQ header, only on the single-end read (read 1)</option> - <option value="--inline_inline">Barcode is inline with sequence, on both single and paired-end read (read 1 and 2)</option> - <option value="--index_index">Barcode is provided in FASTQ header, on both single and paired-end read (read 1 and 2)</option> - <option value="--inline_index">Barcode is inline with sequence on single-end read (read 1), and in FASTQ header for paired-end read (read 2)</option> - <option value="--index_inline">Barcode is provided in FASTQ header on single-end read (read 1), and is inline with sequence on paired-end read (read 2)</option> + <expand macro="barcode_encoding_pair" /> </param> </when> </conditional>