| Previous changeset 19:fbf98f24097b (2018-04-10) Next changeset 21:0b1c04a90182 (2018-07-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d9ebd463afa1a41799aa53e9a68d0ea51093007e |
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modified:
hisat2.xml hisat2_macros.xml |
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| diff -r fbf98f24097b -r 6ab42baa56e9 hisat2.xml --- a/hisat2.xml Tue Apr 10 18:41:43 2018 -0400 +++ b/hisat2.xml Wed May 30 12:02:20 2018 -0400 |
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| @@ -536,31 +536,38 @@ <outputs> <!-- BAM --> - <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM) " /> + <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM)"> + <expand macro="dbKeyActions" /> + </data> <!-- Unaligned fastq (L) --> <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)"> <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True</filter> + <expand macro="dbKeyActions" /> </data> <!-- Aligned fastq (L) --> <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)"> <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True</filter> + <expand macro="dbKeyActions" /> </data> <!-- Unaligned fastq (R) --> <data name="output_unaligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (R)"> <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True) </filter> + <expand macro="dbKeyActions" /> </data> <!-- Aligned fastq (R) --> <data name="output_aligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (R)"> <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True) </filter> + <expand macro="dbKeyActions" /> </data> <!-- Alignment summary file --> <data name="summary_file" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary" > <filter>sum['summary_file'] is True</filter> + <expand macro="dbKeyActions" /> </data> </outputs> |
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| diff -r fbf98f24097b -r 6ab42baa56e9 hisat2_macros.xml --- a/hisat2_macros.xml Tue Apr 10 18:41:43 2018 -0400 +++ b/hisat2_macros.xml Wed May 30 12:02:20 2018 -0400 |
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| @@ -27,4 +27,24 @@ </conditional> </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> + </xml> + </macros> \ No newline at end of file |