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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05 |
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modified:
hisat2.xml test-data/hisat_output_1.bam test-data/hisat_output_2.bam test-data/hisat_output_3.bam |
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| diff -r 4d0a3173cde0 -r 2dbb7f0ea66f hisat2.xml --- a/hisat2.xml Thu Feb 16 08:50:24 2017 -0500 +++ b/hisat2.xml Tue Apr 04 08:15:43 2017 -0400 |
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| b'@@ -1,13 +1,13 @@\n <?xml version="1.0"?>\n-<tool id="hisat2" name="HISAT2" version="2.0.3.3">\n+<tool id="hisat2" name="HISAT2" version="2.0.5">\n <description>A fast and sensitive alignment program</description>\n <macros>\n <import>hisat2_macros.xml</import>\n </macros>\n <requirements>\n <!-- Conda dependency -->\n- <requirement type="package" version="2.0.3">hisat2</requirement>\n- <requirement type="package" version="1.2">samtools</requirement>\n+ <requirement type="package" version="2.0.5">hisat2</requirement>\n+ <requirement type="package" version="1.4">samtools</requirement>\n </requirements>\n <stdio>\n <regex match="hisat2-align exited with value 1" source="both" level="fatal"/>\n@@ -17,25 +17,25 @@\n <version_command>hisat2 --version</version_command>\n <command><![CDATA[\n #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != \'None\':\n- ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf &&\n+ ln -s \'${spliced_options.known_splice_gtf}\' splice_sites.gtf &&\n hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&\n #end if\n #if $reference_genome.reference_genome_source == "history":\n- ln -s "$reference_genome.history_item" genome.fa &&\n- hisat2-build genome.fa genome && \n+ ln -s \'$reference_genome.history_item\' genome.fa &&\n+ hisat2-build -p \\${GALAXY_SLOTS:-1} genome.fa genome &&\n #set index_path = \'genome\'\n #else:\n #set index_path = $reference_genome.index.fields.path\n #end if\n- hisat2 -p \\${GALAXY_SLOTS:-1} -x "${index_path}"\n+ hisat2 -p \\${GALAXY_SLOTS:-1} -x \'${index_path}\'\n #if str($input_format.paired.paired_selector) == \'paired\':\n- -1 "${input_format.paired.reads_f}" -2 "${input_format.paired.reads_r}"\n+ -1 \'${input_format.paired.reads_f}\' -2 \'${input_format.paired.reads_r}\'\n @paired_end_options@\n #else if str($input_format.paired.paired_selector) == \'paired_collection\':\n- -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}"\n+ -1 \'${input_format.paired.reads.forward}\' -2 \'${input_format.paired.reads.reverse}\'\n @paired_end_options@\n #else:\n- -U "${input_format.paired.reads}"\n+ -U \'${input_format.paired.reads}\'\n #if str( $input_format.paired.unaligned_file ) == "true":\n --un \'$output_unaligned_reads_l\'\n #end if\n@@ -46,9 +46,13 @@\n #if $input_format.input_format_selector == \'fasta\':\n -f\n #end if\n- #if $max_primary:\n+ #if str($max_primary)\n -k ${max_primary}\n #end if\n+ #if str($max_seeds)\n+ --max-seeds $max_seeds\n+ #end if\n+ $secondary\n #if str($input_options.input_options_selector) == "advanced":\n #if int( $input_options.skip ) > 0:\n -s ${input_options.skip}\n@@ -59,8 +63,10 @@\n -5 ${input_options.trim_five} -3 ${input_options.trim_three}\n #end if\n #if str($scoring_options.scoring_options_selector) == "advanced":\n- --ma ${scoring_options.match_bonus} --np ${scoring_options.ambiguous_penalty}\n+ --ma ${scoring_options.match_bonus}\n --mp ${scoring_options.max_mismatch},${scoring_options.min_mismatch}\n+ ${scoring_options.no_softclip}\n+ --np ${scoring_options.ambiguous_penalty}\n --rdg ${scoring_options.read_open_penalty},${scoring_options.read_extend_penalty}\n --rfg ${scoring_options.ref_open_penalty},${scoring_options.ref_extend_penalty}\n --sp ${scoring_options.soft_clip_penalty_max},${scoring_options.soft_clip_penalty_min}\n@@ -77,7 +83,11 @@\n #if str($spliced_options.known_splice_gtf'..b'n type="from_data_table" name="hisat2_indexes" column="1" offset="0">\n+ <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>\n+ <filter type="param_value" ref="reference_genome.index" column="0"/>\n+ </option>\n+ </action>\n+ </when>\n+ <when value="history">\n+ <action type="metadata" name="dbkey">\n+ <option type="from_param" name="reference_genome.history_item" param_attribute="dbkey" />\n+ </action>\n+ </when>\n+ </conditional>\n </actions>\n </data>\n- <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >\n+ <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)" >\n <filter>input_format[\'paired\'][\'unaligned_file\'] is True</filter>\n <actions>\n <conditional name="input_format.paired.paired_selector">\n@@ -284,7 +307,7 @@\n </conditional>\n </actions>\n </data>\n- <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)" >\n+ <data name="output_unaligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (R)" >\n <filter>input_format[\'paired\'][\'unaligned_file\'] is True and input_format[\'paired\'][\'paired_selector\'] != \'single\'</filter>\n <actions>\n <conditional name="input_format.paired.paired_selector">\n@@ -301,7 +324,7 @@\n </conditional>\n </actions>\n </data>\n- <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads${\' (L)\' if str($input_format.paired.paired_selector) != \'single\' else \'\'}" >\n+ <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads${\' (L)\' if str($input_format.paired.paired_selector) != \'single\' else \'\'}" >\n <filter>input_format[\'paired\'][\'aligned_file\'] is True</filter>\n <actions>\n <conditional name="input_format.paired.paired_selector">\n@@ -323,7 +346,7 @@\n </conditional>\n </actions>\n </data>\n- <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)" >\n+ <data name="output_aligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (R)" >\n <filter>input_format[\'paired\'][\'aligned_file\'] is True and input_format[\'paired\'][\'paired_selector\'] != \'single\'</filter>\n <actions>\n <conditional name="input_format.paired.paired_selector">\n@@ -388,10 +411,8 @@\n <param name="reference_genome_source" value="history" />\n <param name="history_item" value="phiX.fa" ftype="fasta" />\n <param name="reads" value="test_unaligned_reads.fasta" ftype="fasta" />\n- \n <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />\n </test>\n- \n <test>\n <param name="input_format_selector" value="fasta" />\n <param name="paired_selector" value="paired" />\n@@ -403,7 +424,6 @@\n <param name="history_item" value="phiX.fa" ftype="fasta" />\n <param name="reads_f" value="test_unaligned_reads.fasta" ftype="fasta" />\n <param name="reads_r" value="test_unaligned_reads.fasta" ftype="fasta" />\n- \n <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />\n <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" />\n </test>\n' |
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| diff -r 4d0a3173cde0 -r 2dbb7f0ea66f test-data/hisat_output_1.bam |
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| Binary file test-data/hisat_output_1.bam has changed |
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| diff -r 4d0a3173cde0 -r 2dbb7f0ea66f test-data/hisat_output_2.bam |
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| Binary file test-data/hisat_output_2.bam has changed |
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| diff -r 4d0a3173cde0 -r 2dbb7f0ea66f test-data/hisat_output_3.bam |
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| Binary file test-data/hisat_output_3.bam has changed |