| Previous changeset 1:6d4d39720545 (2015-10-10) Next changeset 3:b1e25f9b5eab (2016-03-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit a2aaa7c9fe7b343f95450ec428250317696a9fb7 |
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modified:
hisat2.xml hisat2_macros.xml |
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| diff -r 6d4d39720545 -r c37b4554f794 hisat2.xml --- a/hisat2.xml Sat Oct 10 16:24:47 2015 -0400 +++ b/hisat2.xml Fri Jan 15 03:33:11 2016 -0500 |
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| @@ -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> |
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| diff -r 6d4d39720545 -r c37b4554f794 hisat2_macros.xml --- a/hisat2_macros.xml Sat Oct 10 16:24:47 2015 -0400 +++ b/hisat2_macros.xml Fri Jan 15 03:33:11 2016 -0500 |
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| @@ -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="@FTYPE@" label="Forward reads" name="reads_f" type="data" /> + <param format="@FTYPE@" label="Reverse reads" 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="@FTYPE@" label="Reads" 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 |