| Previous changeset 6:c50b7a3ff5ad (2016-02-04) Next changeset 8:a8b87bc0c3ad (2016-02-04) |
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Commit message:
planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty |
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modified:
STACKS_clone_filter.xml |
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| diff -r c50b7a3ff5ad -r 2059c028c07a STACKS_clone_filter.xml --- a/STACKS_clone_filter.xml Thu Feb 04 07:51:30 2016 -0500 +++ b/STACKS_clone_filter.xml Thu Feb 04 08:00:32 2016 -0500 |
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| @@ -18,6 +18,13 @@ -fwd $data_type.fwd -rev $data_type.rev #end if + $oligo_options +#if $oligo_len_1 > -1: + --oligo_len_1 $oligo_len_1 +#end if +#if $oligo_len_2 > -1: + --oligo_len_2 $oligo_len_2 +#end if </command> <inputs> @@ -34,14 +41,14 @@ <param name="rev" type="data" format="fastq" label="Reverse FASTQ" /> </when> </conditional> - <param name="oligo_len_1" type="integer" label="length of the single-end oligo sequence in data set"/> - <param name="oligo_len_2" type="integer" label="length of the paired-end oligo sequence in data set"/> + <param name="oligo_len_1" type="integer" label="length of the single-end oligo sequence in data set (-1 == ignore)"/> + <param name="oligo_len_2" type="integer" label="length of the paired-end oligo sequence in data set (-1 == ignore)"/> <param name="oligo_options" type="select" label="Oligo sequence options"> - <option value="inline_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</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_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</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> </param> |