Mercurial > repos > kkonganti > cfsan_centriflaken
changeset 85:022230c283f2
"planemo upload"
| author | kkonganti |
|---|---|
| date | Wed, 13 Jul 2022 17:02:56 -0400 |
| parents | de5b87ce9fe4 |
| children | 7e421f421b5e |
| files | cfsan_centriflaken.xml |
| diffstat | 1 files changed, 11 insertions(+), 7 deletions(-) [+] |
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--- a/cfsan_centriflaken.xml Wed Jul 13 16:51:33 2022 -0400 +++ b/cfsan_centriflaken.xml Wed Jul 13 17:02:56 2022 -0400 @@ -10,17 +10,22 @@ pwd_path=\$(pwd); #if (str($input_read_type_cond.input_read_type) == "single_long"): #for _, $unpaired in enumerate($input_read_type_cond.input): + #set read1 = str($unpaired.name) #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')): - #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext) - #else: - #set read1 = str($unpaired.name) + #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext) #end if ln -sf '$unpaired' './cpipes-input/$read1'; #end for #elif (str($input_read_type_cond.input_read_type) == "paired"): #for _, $pair in enumerate($input_read_type_cond.input_pair) - #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext) - #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext) + #set read_R1 = str($pair.forward.name) + #set read_R2 = str($pair.reverse.name) + #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')): + #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext) + #end if + #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')): + #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext) + #end if ln -sf '$pair.forward' './cpipes-input/$read_R1'; ln -sf '$pair.reverse' './cpipes-input/$read_R2'; #end for @@ -96,8 +101,7 @@ <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired FASTQ"/> </when> <when value="paired"> - <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" - label="List of Dataset pairs" /> + <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="List of Dataset pairs" /> <conditional name="pipeline_cond"> <param name="pipeline" type="select" label="CPIPES Workflow name" help="Auto selected centriflaken_hy for paired-end short reads.">