Mercurial > repos > kkonganti > cfsan_centriflaken
changeset 75:eeddd4dfd7f5
"planemo upload"
| author | kkonganti |
|---|---|
| date | Wed, 13 Jul 2022 16:23:56 -0400 |
| parents | 270e8f69228b |
| children | 0e35724b49f0 |
| files | cfsan_centriflaken.xml |
| diffstat | 1 files changed, 14 insertions(+), 9 deletions(-) [+] |
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--- a/cfsan_centriflaken.xml Wed Jul 13 14:45:49 2022 -0400 +++ b/cfsan_centriflaken.xml Wed Jul 13 16:23:56 2022 -0400 @@ -9,15 +9,20 @@ mkdir -p cpipes-input || exit 1; pwd_path=\$(pwd); #if (str($input_read_type_cond.input_read_type) == "single_long"): - #for $key in $input_read_type_cond.input.keys() - ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key'; + #for _, $unpaired in enumerate($input_read_type_cond.input): + #if not $unpaired.ext.endswith(('.fastq', '.fastq.gz')): + #set read_R1 = str($unpaired.name) + str($unpaired.ext) + #else: + #set read_R1 = str($unpaired.name) + #end if + ln -sf '$unpaired' './cpipes-input/$read_R1'; #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_name = str($pair.forward.name) - #set read_R2_name = str($pair.reverse.name) - ln -sf '$pair.forward' './cpipes-input/$read_R1_name'; - ln -sf '$pair.reverse' './cpipes-input/$read_R2_name'; + #for _, $pair in enumerate($input_read_type_cond.input_pair) + #set read_R1 = str($pair.forward.name) + str($pair.forward.ext) + #set read_R2 = str($pair.reverse.name) + str($pair.reverse.ext) + ln -sf '$pair.forward' './cpipes-input/$read_R1'; + ln -sf '$pair.reverse' './cpipes-input/$read_R2'; #end for #end if $__tool_directory__/0.2.1/cpipes @@ -65,7 +70,7 @@ <option value="paired">Paired-End reads</option> </param> <when value="single_long"> - <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" + <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz" label="Dataset list of unpaired short reads or long reads" /> <conditional name="pipeline_cond"> <param name="pipeline" type="select" label="CPIPES Workflow name" @@ -91,7 +96,7 @@ <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,fastqsanger.gz,fastqsanger" + <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"