Yeah - those wrappers are not going to work with 15.05. Parameterized
XML macros were added in 15.07 it looks like
(http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html).

-John

On Thu, Dec 10, 2015 at 10:28 PM, Langhorst, Brad <langho...@neb.com> wrote:
> Hi:
>
> I’m at release_15.05
>
> Some of this was just wrapper bugs (missing @xxx@) looks like dave already
> fixed this...
> 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
>
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