Mercurial > repos > iuc > hisat2
diff hisat2.xml @ 2:c37b4554f794 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit a2aaa7c9fe7b343f95450ec428250317696a9fb7
author | iuc |
---|---|
date | Fri, 15 Jan 2016 03:33:11 -0500 |
parents | 6d4d39720545 |
children | b1e25f9b5eab |
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--- a/hisat2.xml Sat Oct 10 16:24:47 2015 -0400 +++ b/hisat2.xml Fri Jan 15 03:33:11 2016 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hisat2" name="HISAT2" version="1.0.0"> +<tool id="hisat2" name="HISAT2" version="1.0.1"> <description>A fast and sensitive alignment program</description> <macros> <import>hisat2_macros.xml</import> @@ -61,7 +61,7 @@ #end if #if str($alignment_options.alignment_options_selector) == "advanced": --n-ceil ${alignment_options.function_type},${alignment_options.constant_term},${alignment_options.coefficient} - ${alignment_options.skip_forward} ${alignment_options.skip_reverse} + ${alignment_options.skip_forward} ${alignment_options.skip_reverse} ${alignment_options.ignore_quals} #end if #if str($spliced_options.spliced_options_selector) == "advanced": --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty} @@ -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>