| Previous changeset 16:21e8ea8e1adb (2017-09-30) Next changeset 18:764756ab0eb5 (2018-03-26) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 7b3489c9010a339e83beb1f40044bd145cab967a |
|
modified:
hisat2.xml |
| b |
| diff -r 21e8ea8e1adb -r 40e1083a4430 hisat2.xml --- a/hisat2.xml Sat Sep 30 04:43:26 2017 -0400 +++ b/hisat2.xml Tue Nov 14 05:28:49 2017 -0500 |
| b |
| @@ -469,8 +469,8 @@ <param name="max_intron" type="integer" value="500000" min="0" label="Maximum intron length" /> <conditional name="no_spliced_alignment_options"> <param name="no_spliced_alignment" argument="--no-spliced-alignment" type="select" label="Disable spliced alignment"> + <option value="">False</option> <option value="--no-spliced-alignment">True</option> - <option value="">False</option> </param> <when value="--no-spliced-alignment"> <param name="minins" argument="-I" type="integer" value="0" min="0" label="Minimum fragment length for valid paired-end alignments" help="E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates. The larger the difference between -I and -X, the slower HISAT2 will run. This is because larger differences between -I and -X require that HISAT2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), HISAT2 is very efficient" /> @@ -480,10 +480,10 @@ </conditional> <param name="known_splice_gtf" type="data" format="gtf" optional="true" label="GTF file with known splice sites" /> <param name="tma" type="select" display="radio" label="Transcriptome assembly reporting"> - <option value="">Use default reporting.</option> - <option value="--tmo">Report only those alignments within known transcripts.</option> - <option value="--dta">Report alignments tailored for transcript assemblers including StringTie.</option> - <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks.</option> + <option value="">Use default reporting</option> + <option value="--tmo">Report only those alignments within known transcripts</option> + <option value="--dta">Report alignments tailored for transcript assemblers including StringTie</option> + <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks</option> </param> <param name="notmplen" argument="--no-templatelen-adjustment" type="boolean" truevalue="--no-templatelen-adjustment" falsevalue="" label="Disable automatic template length adjustment for RNA-seq reads" help="Default: false" /> </when> |