On Dec 10, 2015, at 5:32 PM, John Chilton <jmchilton@gmail.com> wrote:

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 <Langhorst@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