Mercurial > repos > iuc > sickle
diff sickle.xml @ 3:89c9361b93da draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7fded35b9fb8ba9ebfb4b4ab44f39bb51e9bc125
| author | iuc |
|---|---|
| date | Sat, 21 Jan 2017 13:08:43 -0500 |
| parents | 013275060443 |
| children | edaa8572219d |
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--- a/sickle.xml Wed Nov 09 05:54:27 2016 -0500 +++ b/sickle.xml Sat Jan 21 13:08:43 2017 -0500 @@ -12,11 +12,11 @@ #if str($readtype.single_or_paired) == "se": se -f "${readtype.input_single}" -o "$output_single" - #if $readtype.input_single.ext in ("fastq", "fastqsanger"): + #if $readtype.is_of_type("fastq", "fastqsanger"): -t sanger - #else if $readtype.input_single.ext == "fastqillumina": + #else if $readtype.input_single.is_of_type('fastqillumina'): -t illumina - #else if $readtype.input_single.ext == "fastqsolexa": + #else if $readtype.input_single.is_of_type('fastqsolexa'): -t solexa #end if #end if @@ -28,11 +28,11 @@ pe -c "${readtype.input_combo}" -m "$output_combo" -s "$output_combo_single" #end if - #if $readtype.input_combo.ext in ("fastq", "fastqsanger"): + #if $readtype.input_combo.is_of_type("fastq", "fastqsanger"): -t sanger - #else if $readtype.input_combo.ext == "fastqillumina": + #else if $readtype.input_combo.is_of_type('fastqillumina'): -t illumina - #else if $readtype.input_combo.ext == "fastqsolexa": + #else if $readtype.input_combo.is_of_type('fastqsolexa'): -t solexa #end if #end if @@ -40,11 +40,11 @@ #if str($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.ext in ("fastq", "fastqsanger"): + #if $readtype.input_paired1.is_of_type("fastq", "fastqsanger"): -t sanger - #else if $readtype.input_paired1.ext == "fastqillumina": + #else if $readtype.input_paired1.is_of_type('fastqillumina'): -t illumina - #else if $readtype.input_paired1.ext == "fastqsolexa": + #else if $readtype.input_paired1.is_of_type('fastqsolexa'): -t solexa #end if #end if @@ -52,11 +52,11 @@ #if str($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.ext in ("fastq", "fastqsanger"): + #if $readtype.input_paired.forward.is_of_type("fastq", "fastqsanger"): -t sanger - #else if $readtype.input_paired.forward.ext == "fastqillumina": + #else if $readtype.input_paired.forward.is_of_type('fastqillumina'): -t illumina - #else if $readtype.input_paired.forward.ext == "fastqsolexa": + #else if $readtype.input_paired.forward.is_of_type('fastqsolexa'): -t solexa #end if #end if