Mercurial > repos > iuc > featurecounts
diff featurecounts.xml @ 7:3ce1c701b0df draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17
| author | iuc |
|---|---|
| date | Mon, 30 Oct 2017 14:49:13 -0400 |
| parents | 9d60a36b5c6a |
| children | 2a8bb8223a45 |
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--- a/featurecounts.xml Thu Oct 26 15:11:19 2017 -0400 +++ b/featurecounts.xml Mon Oct 30 14:49:13 2017 -0400 @@ -30,7 +30,9 @@ $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J" - -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome' + #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome + -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome' + #end if #end if $extended_parameters.long_reads @@ -274,8 +276,8 @@ label="Exon-exon junctions" help="If specified, reads supporting each exon-exon junction will be counted" /> <when value="-J"> - <param name="genome" argument="-G" type="data" format="fasta" - label="Reference sequence (genome) file" + <param name="genome" argument="-G" type="data" format="fasta" optional="true" + label="Reference sequence file" help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" /> </when> <when value="" /> @@ -397,25 +399,31 @@ <data name="output_jcounts" format="tabular" label="${tool.name} on ${on_string}: junction counts"> - <filter>extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads == " -J"</filter> + <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter> <actions> <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.name}" /> </actions> </data> </outputs> <tests> - <test> + <test expect_num_outputs="4"> <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> <param name="format" value="tabdel_short" /> <param name="include_feature_length_file" value="true"/> <param name="ref_source" value="history" /> + <param name="count_exon_exon_junction_reads" value="-J"/> <output name="output_short" file="output_1_short.tab"> <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/> </output> - <output name="output_summary" file="output_1_summary.tab"/> + <output name="output_summary" file="output_1_summary.tab"> + <metadata name="column_names" value="Status,featureCounts_input1.bam"/> + </output> + <output name="output_jcounts" file="output_1_jcounts.tab"> + <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/> + </output> </test> - <test> + <test expect_num_outputs="3"> <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> <param name="format" value="tabdel_medium" /> @@ -428,7 +436,7 @@ <metadata name="column_names" value="Status,featureCounts_input1.bam"/> </output> </test> - <test> + <test expect_num_outputs="3"> <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> <param name="format" value="tabdel_full" /> @@ -445,48 +453,6 @@ </output> </test> - <test> - <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> - <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> - <param name="format" value="tabdel_short" /> - <param name="include_feature_length_file" value="true"/> - <param name="ref_source" value="history" /> - <output name="output_short" file="output_2_short.tab"> - <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/> - </output> - <output name="output_summary" file="output_2_summary.tab"> - <metadata name="column_names" value="Status,featureCounts_input1.bam"/> - </output> - </test> - <test> - <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> - <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> - <param name="format" value="tabdel_medium" /> - <param name="include_feature_length_file" value="true"/> - <param name="ref_source" value="history" /> - <output name="output_medium" file="output_2_medium.tab"> - <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/> - </output> - <output name="output_summary" file="output_2_summary.tab"> - <metadata name="column_names" value="Status,featureCounts_input1.bam"/> - </output> - </test> - <test> - <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> - <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> - <param name="format" value="tabdel_full" /> - <param name="include_feature_length_file" value="true"/> - <param name="ref_source" value="history" /> - <output name="output_full" file="output_2_full.tab"> - <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/> - </output> - <output name="output_summary" file="output_2_summary.tab"> - <metadata name="column_names" value="Status,featureCounts_input1.bam"/> - </output> - <output name="output_feature_lengths" file="output_feature_lengths.tab"> - <metadata name="column_names" value="Feature,Length"/> - </output> - </test> </tests> <help><![CDATA[