| Previous changeset 19:97d1923c8c4b (2018-01-20) Next changeset 21:3ba8d4563129 (2018-04-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 1912a560c3ad87117f18570fcf3ba4af4f924340 |
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modified:
bowtie2_wrapper.xml |
| b |
| diff -r 97d1923c8c4b -r dc1639b66f12 bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Sat Jan 20 08:22:29 2018 -0500 +++ b/bowtie2_wrapper.xml Tue Jan 23 12:20:20 2018 -0500 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="bowtie2" name="Bowtie2" version="2.3.4" profile="17.01"> +<tool id="bowtie2" name="Bowtie2" version="2.3.4.1" profile="17.01"> <description>- map reads against reference genome</description> <macros> <import>bowtie2_macros.xml</import> @@ -282,9 +282,9 @@ #if str( $analysis_type.sam_options.sam_options_selector ) == "yes": ${analysis_type.sam_options.no_unal} ${analysis_type.sam_options.omit_sec_seq} - ${analysis_type.sam_options.sam-no-qname-trunc} + ${analysis_type.sam_options.sam_no_qname_trunc} ${analysis_type.sam_options.xeq} - ${analysis_type.sam_options.soft-clipped-unmapped-tlen} + ${analysis_type.sam_options.soft_clipped_unmapped_tlen} #end if #if str( $analysis_type.other_options.other_options_selector ) == "yes": @@ -503,9 +503,9 @@ <when value="yes"> <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/> <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/> - <param argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/> + <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/> <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/> - <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/> + <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/> </when> <when value="no"> <!-- do nothing --> |