Hi:
I’m at release_15.05
Some of this was just wrapper bugs (missing @xxx@) looks like dave already fixed thishttps://github.com/nebiolabs/tools-iuc/commit/c07682dc096113a4eb1da10a061cfbee6e769474... I don’t know about this @FTYPE@ stuff though.
it’s working for me like this:
diff -r 6d4d39720545 hisat2.xml --- a/hisat2.xml Sat Oct 10 16:24:47 2015 -0400 +++ b/hisat2.xml Thu Dec 10 17:07:38 2015 -0500 @@ -193,7 +193,7 @@ <option value="R">First Strand (R/RF)</option> <option value="F">Second Strand (F/FR)</option> </param> - <param argument="--no-spliced-alignment" name="ignore_quals" type="boolean" truevalue="--no-spliced-alignment" falsevalue="" label="Disable spliced alignment" /> + <param argument="--no-spliced-alignment" name="no_spliced_alignment" type="boolean" truevalue="--no-spliced-alignment" falsevalue="" label="Disable spliced alignment" /> <param format="gtf" label="GTF file with known splice sites" name="known_splice_gtf" optional="True" type="data" /> <param display="radio" label="Transcriptome assembly reporting" name="tma" type="select"> <option value="">Use default reporting.</option> diff -r 6d4d39720545 hisat2_macros.xml --- a/hisat2_macros.xml Sat Oct 10 16:24:47 2015 -0400 +++ b/hisat2_macros.xml Thu Dec 10 17:07:38 2015 -0500 @@ -25,12 +25,12 @@ <expand macro="paired_end_conditional" /> </when> <when value="paired"> - <param format="@FTYPE@" label="Forward reads" multiple="true" name="reads_f" type="data" /> - <param format="@FTYPE@" label="Reverse reads" multiple="true" name="reads_r" type="data" /> + <param format="fastqsanger" label="Forward reads" multiple="true" name="reads_f" type="data" /> + <param format="fastqsanger" label="Reverse reads" multiple="true" name="reads_r" type="data" /> <expand macro="paired_end_conditional" /> </when> <when value="single"> - <param format="@FTYPE@" label="Reads" multiple="true" name="reads" type="data" /> + <param format="fastqsanger" label="Reads" multiple="true" name="reads" type="data" /> </when> </conditional> </xml> @@ -56,7 +56,7 @@ ${input_format.paired.paired_end_options.no_discordant} #end if </token> - <token name="strandedness_parameters"> + <token name="@strandedness_parameters@"> #if str($spliced_options.spliced_options_selector) == "advanced": #if str($spliced_options.rna_strandness).strip() != '': --rna-strandness $spliced_options.rna_strandness — Brad Langhorst, Ph.D. Development Scientist New England Biolabs