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Commit message:
planemo upload commit 76cbd559320d2a639e35ed10cb2d9522a5a77ae0 |
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modified:
macros.xml |
| b |
| diff -r c0691d1977dd -r 2ee290d6c24d macros.xml --- a/macros.xml Sun Feb 25 13:07:44 2018 -0500 +++ b/macros.xml Mon Apr 16 16:38:04 2018 -0400 |
| [ |
| @@ -1,5 +1,41 @@ <?xml version="1.0"?> <macros> + <macro name="barcode2_conditional" > + <conditional name="barcode"> + <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?"> + <option value="first_read_only">Barcode on first read only</option> + <option value="both_reads">Barcode on both reads</option> + </param> + <when value="first_read_only"/> + <when value="both_reads"> + <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read" + help="Use this option to specify the format of the UMI/barcode for + the second read pair if required." > + </param> + </when> + </conditional> + </macro> + <xml name="input_types"> + <conditional name="input_type"> + <param name="type" type="select" label="Library type"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + <option value="paired_collection">Paired-end Dataset Collection</option> + </param> + <when value="single"> + <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> + </when> + <when value="paired"> + <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> + <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> + <expand macro="barcode2_conditional" /> + </when> + <when value="paired_collection"> + <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Reads in FASTQ format" /> + <expand macro="barcode2_conditional" /> + </when> + </conditional> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1101/gr.209601.116</citation> @@ -20,4 +56,33 @@ </requirements> </xml> <token name="@VERSION@">0.5.3</token> + <token name="@COMMAND_LINK@"><![CDATA[ + #set $gz = False + #if $input_type.type == 'single': + #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"): + ln -s '$input_type.input_single' input_single.gz && + #set $gz = True + #else + ln -s '$input_type.input_single' input_single.txt && + #end if + #elif $input_type.type == 'paired': + #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"): + ln -s '$input_type.input_read1' input_read1.gz && + ln -s '$input_type.input_read2' input_read2.gz && + #set $gz = True + #else + ln -s '$input_type.input_read1' input_read1.txt && + ln -s '$input_type.input_read2' input_read2.txt && + #end if + #else ## paired_collection + #if $input_type.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"): + ln -s '$input_type.input_readpair.forward' input_read1.gz && + ln -s '$input_type.input_readpair.reverse' input_read2.gz && + #set $gz = True + #else + ln -s '$input_type.input_readpair.forward' input_read1.txt && + ln -s '$input_type.input_readpair.reverse' input_read2.txt && + #end if + #end if + ]]></token> </macros> |