| Previous changeset 25:3fb01a8c902d (2019-01-26) Next changeset 27:a86e80d3c09c (2020-11-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6 |
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modified:
hisat2.xml hisat2_macros.xml |
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| diff -r 3fb01a8c902d -r 0c16cad5e03b hisat2.xml --- a/hisat2.xml Sat Jan 26 04:45:24 2019 -0500 +++ b/hisat2.xml Sat Aug 03 06:09:26 2019 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy4" profile="17.01">\n+<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy5" profile="17.01">\n <description>A fast and sensitive alignment program</description>\n <macros>\n <import>hisat2_macros.xml</import>\n@@ -575,44 +575,146 @@\n \n <!-- BAM -->\n <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM)">\n- <expand macro="dbKeyActions" />\n+ <actions>\n+ <expand macro="dbKeyActions" />\n+ </actions>\n </data>\n \n <!-- Unaligned fastq (L) -->\n <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)">\n <filter>adv[\'output_options\'][\'output_options_selector\'] == "advanced" and adv[\'output_options\'][\'unaligned_file\'] is True</filter>\n- <expand macro="dbKeyActions" />\n+ <actions>\n+ <conditional name="library.type">\n+ <when value="single">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ <when value="paired_interleaved">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ </conditional>\n+ <expand macro="dbKeyActions" />\n+ </actions>\n </data>\n \n <!-- Aligned fastq (L) -->\n <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)">\n <filter>adv[\'output_options\'][\'output_options_selector\'] == "advanced" and adv[\'output_options\'][\'aligned_file\'] is True</filter>\n- <expand macro="dbKeyActions" />\n+ <actions>\n+ <conditional name="library.type">\n+ <when value="single">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ <when value="paired_interleaved">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ </conditional>\n+ <expand macro="dbKeyActions" />\n+ </actions>\n </data>\n \n <!-- Unaligned fastq (R) -->\n <data name="output_unaligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: unal'..b'ired">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ <when value="paired_interleaved">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ </conditional>\n+ <expand macro="dbKeyActions" />\n+ </actions>\n </data>\n \n <!-- Aligned fastq (R) -->\n <data name="output_aligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (R)">\n <filter>(library[\'type\'] == \'paired\' or library[\'type\'] == \'paired_collection\') and (adv[\'output_options\'][\'output_options_selector\'] == "advanced" and adv[\'output_options\'][\'aligned_file\'] is True) </filter>\n- <expand macro="dbKeyActions" />\n+ <actions>\n+ <conditional name="library.type">\n+ <when value="single">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ <when value="paired_interleaved">\n+ <action type="format">\n+ <option type="from_param" name="library.input_1" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ </conditional>\n+ <expand macro="dbKeyActions" />\n+ </actions>\n </data>\n \n- <!-- Alignment summary file -->\n- <data name="summary_file" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary" >\n- <filter>sum[\'summary_file\'] is True</filter>\n- <expand macro="dbKeyActions" />\n- </data>\n+ <!-- Alignment summary file -->\n+ <data name="summary_file" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary">\n+ <filter>sum[\'summary_file\'] is True</filter>\n+ <actions>\n+ <expand macro="dbKeyActions" />\n+ </actions>\n+ </data>\n \n- <!-- Novel Splice file -->\n- <data name="novel_splicesite_output" format="tabular" label="${tool.name} on ${on_string}: Novel Splice Sites" >\n- <filter>adv[\'spliced_options\'][\'spliced_options_selector\'] == \'advanced\' and adv[\'spliced_options\'][\'novel_splicesite_outfile\'] is True</filter>\n- <expand macro="dbKeyActions" />\n- </data>\n+ <!-- Novel Splice file -->\n+ <data name="novel_splicesite_output" format="tabular" label="${tool.name} on ${on_string}: Novel Splice Sites">\n+ <filter>adv[\'spliced_options\'][\'spliced_options_selector\'] == \'advanced\' and adv[\'spliced_options\'][\'novel_splicesite_outfile\'] is True</filter>\n+ <actions>\n+ <expand macro="dbKeyActions" />\n+ </actions>\n+ </data>\n \n \n </outputs>\n' |
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| diff -r 3fb01a8c902d -r 0c16cad5e03b hisat2_macros.xml --- a/hisat2_macros.xml Sat Jan 26 04:45:24 2019 -0500 +++ b/hisat2_macros.xml Sat Aug 03 06:09:26 2019 -0400 |
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| @@ -29,22 +29,20 @@ </xml> <xml name="dbKeyActions"> - <actions> - <conditional name="reference_genome.source"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="hisat2_indexes" column="1"> - <filter type="param_value" ref="reference_genome.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="reference_genome.history_item" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <conditional name="reference_genome.source"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="hisat2_indexes" column="1"> + <filter type="param_value" ref="reference_genome.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="reference_genome.history_item" param_attribute="dbkey" /> + </action> + </when> + </conditional> </xml> -</macros> \ No newline at end of file +</macros> |