Mercurial > repos > iuc > rgrnastar
changeset 8:d5659efd66aa draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
| author | iuc |
|---|---|
| date | Sat, 09 Jun 2018 14:33:39 -0400 |
| parents | a70a7eebb435 |
| children | 0a563fd2f22e |
| files | macros.xml rg_rnaStar.xml |
| diffstat | 2 files changed, 27 insertions(+), 69 deletions(-) [+] |
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--- a/macros.xml Wed May 16 17:31:03 2018 -0400 +++ b/macros.xml Sat Jun 09 14:33:39 2018 -0400 @@ -17,4 +17,23 @@ <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="true" help="Exon junction information for mapping splices"/> <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/> </xml> + <xml name="dbKeyActions"> + <actions> + <conditional name="refGenomeSource.geneSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="rnastar_index2" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </xml> </macros>
--- a/rg_rnaStar.xml Wed May 16 17:31:03 2018 -0400 +++ b/rg_rnaStar.xml Sat Jun 09 14:33:39 2018 -0400 @@ -384,91 +384,30 @@ </inputs> <outputs> - <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/> + <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"> + <expand macro="dbKeyActions" /> + </data> <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction"> <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter> - <actions> - <conditional name="refGenomeSource.geneSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="rnastar_index" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /> </data> <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam"> <filter>params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0</filter> - <actions> - <conditional name="refGenomeSource.geneSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="rnastar_index" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /> </data> <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab"> - <actions> - <conditional name="refGenomeSource.geneSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="rnastar_index" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /> </data> <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="Aligned.sortedByCoord.out.bam"> - <actions> - <conditional name="refGenomeSource.geneSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="rnastar_index" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /> </data> <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab"> <filter>quantMode is True</filter> + <expand macro="dbKeyActions" /> </data> </outputs>