Mercurial > repos > artbio > repenrich
diff repenrich.xml @ 5:02a8941da83b draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
| author | artbio |
|---|---|
| date | Sun, 18 Nov 2018 17:07:02 -0500 |
| parents | d1f7ab78f7b5 |
| children | 6f4143893463 |
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--- a/repenrich.xml Sun Nov 18 12:53:01 2018 -0500 +++ b/repenrich.xml Sun Nov 18 17:07:02 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="repenrich" name="RepEnrich" version="1.5.0"> +<tool id="repenrich" name="RepEnrich" version="1.6.0"> <description>Repeat Element Profiling</description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> @@ -16,18 +16,26 @@ ## uncompress fastq.gz or fastqsanger.gz if needed #if $seq_method.seq_method_list == "single-read": - #if $input_fastq.is_of_type("fastq.gz", "fastqsanger.gz"): - gunzip < '$input_fastq' > '${input_base}.fastq' && + #if $seq_method.input_fastq.is_of_type("fastq.gz", "fastqsanger.gz"): + gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' && #else: - ln -f -s '$input_fastq' '${input_base}.fastq' && + ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' && + #end if + #elif $seq_method.seq_method_list == 'paired_collection': + #if $seq_method.input_fastq.forward.is_of_type("fastq.gz", "fastqsanger.gz"): + gunzip < '$seq_method.input_fastq.forward' > '${input_base}.fastq' && + gunzip < '$seq_method.input_fastq.reverse' > '${input_base}_2.fastq' && + #else: + ln -f -s '$seq_method.input_fastq.forward' '${input_base}.fastq' && + ln -f -s '$seq_method.input_fastq.reverse' '${input_base}_2.fastq' && #end if #else: - #if $input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"): - gunzip < '$input_fastq' > '${input_base}.fastq' && - gunzip < '$input2_fastq' > '${input_base}_2.fastq' && + #if $seq_method.input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"): + gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' && + gunzip < '$seq_method.input2_fastq' > '${input_base}_2.fastq' && #else: - ln -f -s '$input_fastq' '${input_base}.fastq' && - ln -f -s '$input2_fastq' '${input_base}_2.fastq' && + ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' && + ln -f -s '$seq_method.input2_fastq' '${input_base}_2.fastq' && #end if #end if @@ -67,13 +75,17 @@ <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select"> <option selected="True" value="single-read">Single-read sequencing</option> <option value="paired-end">Paired-end sequencing</option> + <option value="paired_collection">Paired-end Dataset Collection</option> </param> <when value="single-read"> - <param format="fastq,fastqsanger" label="Single-reads" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> + <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Single-reads" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> </when> <when value="paired-end"> - <param format="fastq,fastqsanger" label="1st paired-end sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> - <param format="fastq,fastqsanger" label="2nd paired-end sequencing dataset" name="input2_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> + <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="1st paired-end sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> + <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="2nd paired-end sequencing dataset" name="input2_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> + </when> + <when value="paired_collection"> + <param name="input_fastq" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" type="data_collection" collection_type="paired" label="Paired Collection" help="Must be of datatype "fastqsanger" or "fasta"" /> </when> </conditional> <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" />