| Previous changeset 3:89c9361b93da (2017-01-21) Next changeset 5:3905ccd5c631 (2017-04-13) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit a8611c912a8265de6f64a3e17cea63c87fa48b8e |
|
modified:
sickle.xml |
| b |
| diff -r 89c9361b93da -r edaa8572219d sickle.xml --- a/sickle.xml Sat Jan 21 13:08:43 2017 -0500 +++ b/sickle.xml Mon Jan 23 06:07:05 2017 -0500 |
| b |
| @@ -12,12 +12,12 @@ #if str($readtype.single_or_paired) == "se": se -f "${readtype.input_single}" -o "$output_single" - #if $readtype.is_of_type("fastq", "fastqsanger"): - -t sanger - #else if $readtype.input_single.is_of_type('fastqillumina'): + #if $readtype.input_single.is_of_type('fastqillumina'): -t illumina #else if $readtype.input_single.is_of_type('fastqsolexa'): -t solexa + #else: + -t sanger #end if #end if @@ -28,36 +28,36 @@ pe -c "${readtype.input_combo}" -m "$output_combo" -s "$output_combo_single" #end if - #if $readtype.input_combo.is_of_type("fastq", "fastqsanger"): - -t sanger - #else if $readtype.input_combo.is_of_type('fastqillumina'): + #if $readtype.input_combo.is_of_type('fastqillumina'): -t illumina #else if $readtype.input_combo.is_of_type('fastqsolexa'): -t solexa + #else: + -t sanger #end if #end if #if str($readtype.single_or_paired) == "pe_sep": pe -f "${readtype.input_paired1}" -r "${readtype.input_paired2}" -o "$output_paired1" -p "$output_paired2" -s "$output_paired_single" - #if $readtype.input_paired1.is_of_type("fastq", "fastqsanger"): - -t sanger - #else if $readtype.input_paired1.is_of_type('fastqillumina'): + #if $readtype.input_paired1.is_of_type('fastqillumina'): -t illumina #else if $readtype.input_paired1.is_of_type('fastqsolexa'): -t solexa + #else: + -t sanger #end if #end if #if str($readtype.single_or_paired) == "pe_collection": pe -f "${readtype.input_paired.forward}" -r "${readtype.input_paired.reverse}" -o "${output_paired_coll.forward}" -p "${output_paired_coll.reverse}" -s "$output_paired_coll_single" - #if $readtype.input_paired.forward.is_of_type("fastq", "fastqsanger"): - -t sanger - #else if $readtype.input_paired.forward.is_of_type('fastqillumina'): + #if $readtype.input_paired.forward.is_of_type('fastqillumina'): -t illumina #else if $readtype.input_paired.forward.is_of_type('fastqsolexa'): -t solexa + #else: + -t sanger #end if #end if |