| Previous changeset 0:e3fe061597ac (2015-06-11) Next changeset 2:4d91675e16e8 (2015-07-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 8000b1dd0d6b336707cf84867d11f690f6a26f5c |
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modified:
hisat.xml tool_dependencies.xml |
| b |
| diff -r e3fe061597ac -r 8bb3efa0dae8 hisat.xml --- a/hisat.xml Thu Jun 11 16:35:16 2015 -0400 +++ b/hisat.xml Tue Jul 21 15:33:12 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="hisat" name="HISAT" version="1.0.1"> +<tool id="hisat" name="HISAT" version="1.0.2"> <description>spliced aligner</description> <macros> <import>hisat_macros.xml</import> @@ -12,9 +12,9 @@ </stdio> <version_command>hisat --version</version_command> <command><![CDATA[ - #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gff) != 'None': - ln -s "${spliced_options.known_splice_gff}" splice_sites.gff && - extract_splice_sites.py splice_sites.gff > splice_sites.txt && + #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None': + ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf && + extract_splice_sites.py splice_sites.gtf > splice_sites.txt && #end if #if $reference_genome.reference_genome_source == "history": ln -s "$reference_genome.history_item" genome.fa && @@ -58,7 +58,7 @@ #if str($spliced_options.spliced_options_selector) == "advanced": --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty} --pen-intronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient_term} - #if str($spliced_options.known_splice_gff) != 'None': + #if str($spliced_options.known_splice_gtf) != 'None': --known-splicesite-infile splice_sites.txt #end if #end if @@ -183,7 +183,7 @@ </expand> <param name="min_intron" label="Minimum intron length" type="integer" value="20" /> <param name="max_intron" label="Maximum intron length" type="integer" value="500000" /> - <param name="known_splice_gff" label="GTF/GFF file with known splice sites" type="data" format="gff" optional="True" /> + <param name="known_splice_gtf" label="GTF file with known splice sites" type="data" format="gtf" optional="True" /> </when> </conditional> </inputs> |
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| diff -r e3fe061597ac -r 8bb3efa0dae8 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jun 11 16:35:16 2015 -0400 +++ b/tool_dependencies.xml Tue Jul 21 15:33:12 2015 -0400 |
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| @@ -4,6 +4,6 @@ <repository changeset_revision="e1f428b67305" name="package_hisat_0_1_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="1.2"> - <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |