Mercurial > repos > iuc > hisat2
changeset 26:0c16cad5e03b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
author | iuc |
---|---|
date | Sat, 03 Aug 2019 06:09:26 -0400 |
parents | 3fb01a8c902d |
children | a86e80d3c09c |
files | hisat2.xml hisat2_macros.xml |
diffstat | 2 files changed, 133 insertions(+), 33 deletions(-) [+] |
line wrap: on
line diff
--- a/hisat2.xml Sat Jan 26 04:45:24 2019 -0500 +++ b/hisat2.xml Sat Aug 03 06:09:26 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy4" profile="17.01"> +<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy5" profile="17.01"> <description>A fast and sensitive alignment program</description> <macros> <import>hisat2_macros.xml</import> @@ -575,44 +575,146 @@ <!-- BAM --> <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM)"> - <expand macro="dbKeyActions" /> + <actions> + <expand macro="dbKeyActions" /> + </actions> </data> <!-- Unaligned fastq (L) --> <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)"> <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True</filter> - <expand macro="dbKeyActions" /> + <actions> + <conditional name="library.type"> + <when value="single"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="ext" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> + </action> + </when> + <when value="paired_interleaved"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> + </action> + </when> + </conditional> + <expand macro="dbKeyActions" /> + </actions> </data> <!-- Aligned fastq (L) --> <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)"> <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True</filter> - <expand macro="dbKeyActions" /> + <actions> + <conditional name="library.type"> + <when value="single"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="ext" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> + </action> + </when> + <when value="paired_interleaved"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> + </action> + </when> + </conditional> + <expand macro="dbKeyActions" /> + </actions> </data> <!-- Unaligned fastq (R) --> <data name="output_unaligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (R)"> <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True) </filter> - <expand macro="dbKeyActions" /> + <actions> + <conditional name="library.type"> + <when value="single"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="ext" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> + </action> + </when> + <when value="paired_interleaved"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> + </action> + </when> + </conditional> + <expand macro="dbKeyActions" /> + </actions> </data> <!-- Aligned fastq (R) --> <data name="output_aligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (R)"> <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True) </filter> - <expand macro="dbKeyActions" /> + <actions> + <conditional name="library.type"> + <when value="single"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="ext" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> + </action> + </when> + <when value="paired_interleaved"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> + </action> + </when> + </conditional> + <expand macro="dbKeyActions" /> + </actions> </data> - <!-- Alignment summary file --> - <data name="summary_file" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary" > - <filter>sum['summary_file'] is True</filter> - <expand macro="dbKeyActions" /> - </data> + <!-- Alignment summary file --> + <data name="summary_file" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary"> + <filter>sum['summary_file'] is True</filter> + <actions> + <expand macro="dbKeyActions" /> + </actions> + </data> - <!-- Novel Splice file --> - <data name="novel_splicesite_output" format="tabular" label="${tool.name} on ${on_string}: Novel Splice Sites" > - <filter>adv['spliced_options']['spliced_options_selector'] == 'advanced' and adv['spliced_options']['novel_splicesite_outfile'] is True</filter> - <expand macro="dbKeyActions" /> - </data> + <!-- Novel Splice file --> + <data name="novel_splicesite_output" format="tabular" label="${tool.name} on ${on_string}: Novel Splice Sites"> + <filter>adv['spliced_options']['spliced_options_selector'] == 'advanced' and adv['spliced_options']['novel_splicesite_outfile'] is True</filter> + <actions> + <expand macro="dbKeyActions" /> + </actions> + </data> </outputs>
--- a/hisat2_macros.xml Sat Jan 26 04:45:24 2019 -0500 +++ b/hisat2_macros.xml Sat Aug 03 06:09:26 2019 -0400 @@ -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>