Mercurial > repos > bgruening > hicup_digester
diff hicup_macros.xml @ 5:2edfb71706b3 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
| author | bgruening |
|---|---|
| date | Sat, 22 Oct 2022 08:41:11 +0000 |
| parents | a2f3a4129052 |
| children | e79c38f1752c |
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--- a/hicup_macros.xml Fri May 25 17:54:32 2018 -0400 +++ b/hicup_macros.xml Sat Oct 22 08:41:11 2022 +0000 @@ -1,11 +1,10 @@ <macros> - <token name="@VERSION@">0.6.1</token> + <token name="@VERSION@">0.8.3</token> <xml name="requirements_hicup"> <requirements> <requirement type="package" version="@VERSION@">hicup</requirement> - <requirement type="package" version="2.2.6">bowtie2</requirement> - <requirement type="package" version="1.2">samtools</requirement> - <requirement type="package" version="0.13.1">docutils</requirement> + <requirement type="package" version="2.4.5">bowtie2</requirement> + <requirement type="package" version="1.16.1">samtools</requirement> <yield/> </requirements> <version_command>hicup --version</version_command> @@ -35,12 +34,8 @@ </when> </conditional> </xml> - <xml name="input_files"> - <param name="input_first_sequence" type="data" format="fastq,fastq.gz" label="First input sequence" help="The first sequence:"/> - <param name="input_second_sequence" type="data" format="fastq,fastq.gz" label="Second input sequence" help="The second sequence:"/> - </xml> <xml name="re1"> - <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/> + <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme used e.g. A^GATCT,BglII. Some Hi-C protocols may use several enzymes. To specify several enzymes, use the ':' to separate them e.g. A^GATCT,BglII:A^AGCTT,HindIII:^GATC,DpnII. HiCUP accomodates N in restriction enzyme: e.g. :A^ANCTT"/> </xml> <xml name="re2"> <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags." @@ -54,4 +49,51 @@ <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill" help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/> </xml> + <token name="@PAIRED-END_INPUT@"><![CDATA[ + ## Taken from cutadapt except that I don't accept space in name + #import re + #set library_type = str($library.type) + #if $library_type == 'paired': + #set input_1 = $library.input_1 + #set input_2 = $library.input_2 + #else if $library_type == 'paired_collection' + #set input_1 = $library.input_1.forward + #set input_2 = $library.input_1.reverse + #end if + + #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"): + #set ext = ".fq.gz" + #else: + #set ext = ".fq" + #end if + #set read1 = "dataset1" + $ext + ln -f -s '${input_1}' '$read1' && + + #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"): + #set ext2 = ".fq.gz" + #else: + #set ext2 = ".fq" + #end if + #set read2 = "dataset2" + $ext2 + ln -f -s '${input_2}' '$read2' && + ]]> + </token> + <xml name="input_paired"> + <conditional name="library"> + <param name="type" type="select" label="How Paired-end reads are organized"> + <option value="paired">Separately</option> + <option value="paired_collection">Paired-end Collection</option> + </param> + + <when value="paired"> + <param name="input_1" format="fastq,fastq.gz" type="data" label="FASTQ/A file #1" help="Should be of datatype "fastq.gz"or "fasta"" /> + <param name="input_2" format="fastq,fastq.gz" type="data" label="FASTQ/A file #2" help="Should be of datatype "fastq.gz"or "fasta"" /> + </when> + + <when value="paired_collection"> + <param name="input_1" format="fastq,fastq.gz" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype "fastq.gz" or "fastq"" /> + </when> + + </conditional> + </xml> </macros>