Mercurial > repos > iuc > hisat2
changeset 8:4d0a3173cde0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 379063161020578e1bd306769116c1b691216b35
| author | iuc |
|---|---|
| date | Thu, 16 Feb 2017 08:50:24 -0500 |
| parents | 5ba8e317529a |
| children | 2dbb7f0ea66f |
| files | hisat2.xml tool_dependencies.xml |
| diffstat | 2 files changed, 5 insertions(+), 17 deletions(-) [+] |
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--- a/hisat2.xml Sat Jan 21 15:42:34 2017 -0500 +++ b/hisat2.xml Thu Feb 16 08:50:24 2017 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hisat2" name="HISAT2" version="2.0.3.2"> +<tool id="hisat2" name="HISAT2" version="2.0.3.3"> <description>A fast and sensitive alignment program</description> <macros> <import>hisat2_macros.xml</import> @@ -7,7 +7,6 @@ <requirements> <!-- Conda dependency --> <requirement type="package" version="2.0.3">hisat2</requirement> - <requirement type="package" version="2.0.3">hisat</requirement> <requirement type="package" version="1.2">samtools</requirement> </requirements> <stdio> @@ -16,8 +15,7 @@ <exit_code range="1:" /> </stdio> <version_command>hisat2 --version</version_command> - <command> - <![CDATA[ + <command><![CDATA[ #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None': ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf && hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt && @@ -106,8 +104,7 @@ && mv '${right}' '${output_aligned_reads_r}' #end if #end if - ]]> - </command> + ]]></command> <inputs> <conditional name="input_format"> <param label="Input data format" name="input_format_selector" type="select"> @@ -161,8 +158,8 @@ <when value="advanced"> <param argument="-s" min="0" label="Skip the first N reads or pairs in the input" name="skip" type="integer" value="0" /> <param argument="-u" min="0" help="Align the first N reads or read pairs from the input (after the first N reads or pairs have been skipped), then stop." label="Stop after aligning N reads" name="stop_after" type="integer" value="0" /> - <param argument="-5" min="0" help="Trim N bases from 5' (left) end of each read before alignment" label="Trim 5' end" name="trim_five" type="integer" value="0" /> - <param argument="-3" min="0" help="Trim N bases from 3' (right) end of each read before alignment" label="Trim 3' end" name="trim_three" type="integer" value="0" /> + <param name="trim_five" argument="-5" min="0" help="Trim N bases from 5' (left) end of each read before alignment" label="Trim 5' end" type="integer" value="0" /> + <param name="trim_three" argument="-3" min="0" help="Trim N bases from 3' (right) end of each read before alignment" label="Trim 3' end" type="integer" value="0" /> </when> </conditional> <conditional name="scoring_options">
--- a/tool_dependencies.xml Sat Jan 21 15:42:34 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="hisat" version="2.0.3"> - <repository changeset_revision="dc03603edd43" name="package_hisat_2_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="1.2"> - <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>