I don’t know about this @FTYPE@ stuff though.
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