| Previous changeset 60:1421603cc95b (2022-11-26) Next changeset 62:473382134e56 (2023-02-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a |
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modified:
FPKM_count.xml RNA_fragment_size.xml RPKM_saturation.xml bam2wig.xml bam_stat.xml clipping_profile.xml deletion_profile.xml geneBody_coverage.xml geneBody_coverage2.xml infer_experiment.xml inner_distance.xml insertion_profile.xml junction_annotation.xml junction_saturation.xml mismatch_profile.xml read_GC.xml read_NVC.xml read_distribution.xml read_duplication.xml read_hexamer.xml read_quality.xml rseqc_macros.xml test-data/output.splice_events.pdf test-data/output.splice_junction.pdf tin.xml |
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added:
test-data/output.splice_junction.txt |
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| diff -r 1421603cc95b -r 5968573462fa FPKM_count.xml --- a/FPKM_count.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/FPKM_count.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,10 +1,11 @@ <tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>calculates raw read count, FPM, and FPKM for each gene</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> + <expand macro="requirements" /> <expand macro="stdio" /> |
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| diff -r 1421603cc95b -r 5968573462fa RNA_fragment_size.xml --- a/RNA_fragment_size.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/RNA_fragment_size.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -2,10 +2,10 @@ <description> calculates the fragment size for each gene/transcript </description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> |
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| diff -r 1421603cc95b -r 5968573462fa RPKM_saturation.xml --- a/RPKM_saturation.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/RPKM_saturation.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> |
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| diff -r 1421603cc95b -r 5968573462fa bam2wig.xml --- a/bam2wig.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/bam2wig.xml Sat Dec 10 11:23:05 2022 +0000 |
| [ |
| @@ -2,10 +2,11 @@ <description> converts all types of RNA-seq data from .bam to .wig </description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + + <expand macro="bio_tools"/> <expand macro="requirements" /> @@ -63,10 +64,10 @@ <data format="wig" name="output" from_work_dir="outfile.wig"> <filter>strand_type['strand_specific'] == 'none'</filter> </data> - <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)"> + <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string}: forward reads"> <filter>strand_type['strand_specific'] != 'none'</filter> </data> - <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)"> + <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string}: reverse reads"> <filter>strand_type['strand_specific'] != 'none'</filter> </data> </outputs> |
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| diff -r 1421603cc95b -r 5968573462fa bam_stat.xml --- a/bam_stat.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/bam_stat.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -2,11 +2,12 @@ <description> reads mapping statistics for a provided BAM or SAM file. </description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> + <expand macro="requirements" /> <expand macro="stdio" /> @@ -25,7 +26,7 @@ </inputs> <outputs> - <data format="txt" name="output" /> + <data format="txt" name="output" label="${tool.name} on ${on_string}: stats"/> </outputs> <tests> |
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| diff -r 1421603cc95b -r 5968573462fa clipping_profile.xml --- a/clipping_profile.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/clipping_profile.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -2,11 +2,12 @@ <description> estimates clipping profile of RNA-seq reads from BAM or SAM file </description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> + <expand macro="requirements" /> <expand macro="stdio" /> @@ -27,9 +28,9 @@ </inputs> <outputs> - <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" /> - <expand macro="xls_output_data" filename="output.clipping_profile.xls" /> - <expand macro="rscript_output_data" filename="output.clipping_profile.r" /> + <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" label="${tool.name} on ${on_string}: PDF"/> + <expand macro="xls_output_data" filename="output.clipping_profile.xls" label="${tool.name} on ${on_string}: XML"/> + <expand macro="rscript_output_data" filename="output.clipping_profile.r" label="${tool.name} on ${on_string}: Rscript"/> </outputs> <tests> |
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| diff -r 1421603cc95b -r 5968573462fa deletion_profile.xml --- a/deletion_profile.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/deletion_profile.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -2,11 +2,12 @@ <description> calculates the distributions of deleted nucleotides across reads </description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> + <expand macro="requirements" /> <expand macro="stdio" /> |
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| diff -r 1421603cc95b -r 5968573462fa geneBody_coverage.xml --- a/geneBody_coverage.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/geneBody_coverage.xml Sat Dec 10 11:23:05 2022 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>read coverage over gene body</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> <expand macro="stdio" /> <version_command><![CDATA[geneBody_coverage.py --version]]></version_command> @@ -50,12 +50,12 @@ </inputs> <outputs> - <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves pdf)" /> - <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap pdf)"> + <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string}: curves (PDF)" /> + <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string}: heatmap (PDF)"> <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) >= 3</filter> </data> - <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" /> - <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" /> + <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" label="${tool.name} on ${on_string}: Rscript"/> + <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string}: stats (TXT)" /> </outputs> <!-- PDF Files contain R version, must avoid checking for diff --> |
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| diff -r 1421603cc95b -r 5968573462fa geneBody_coverage2.xml --- a/geneBody_coverage2.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/geneBody_coverage2.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,10 +1,11 @@ <tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>read coverage over gene body</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> + <expand macro="requirements" /> <expand macro="stdio" /> |
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| diff -r 1421603cc95b -r 5968573462fa infer_experiment.xml --- a/infer_experiment.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/infer_experiment.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,10 +1,11 @@ <tool id="rseqc_infer_experiment" name="Infer Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>speculates how RNA-seq were configured</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> + <expand macro="requirements" /> <expand macro="stdio" /> |
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| diff -r 1421603cc95b -r 5968573462fa inner_distance.xml --- a/inner_distance.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/inner_distance.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,10 +1,11 @@ <tool id="rseqc_inner_distance" name="Inner Distance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>calculate the inner distance (or insert size) between two paired RNA reads</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> + <expand macro="requirements" /> <expand macro="stdio" /> @@ -34,10 +35,10 @@ </inputs> <outputs> - <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" /> - <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (text)"/> - <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (frequency text)" /> - <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" /> + <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/> + <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string}: TXT"/> + <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string}: frequency (TXT)" /> + <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" label="${tool.name} on ${on_string}: Rscript"/> </outputs> <tests> |
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| diff -r 1421603cc95b -r 5968573462fa insertion_profile.xml --- a/insertion_profile.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/insertion_profile.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -2,11 +2,12 @@ <description> calculates the distribution of inserted nucleotides across reads </description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> + <expand macro="requirements" /> <expand macro="stdio" /> |
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| diff -r 1421603cc95b -r 5968573462fa junction_annotation.xml --- a/junction_annotation.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/junction_annotation.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,10 +1,11 @@ <tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>compares detected splice junctions to reference gene model</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> + <expand macro="requirements"> <!-- Required due to conda solver bug: https://github.com/conda/conda/issues/6269 @@ -25,6 +26,7 @@ --out-prefix output --min-intron ${min_intron} --mapq ${mapq} + 2> >(tee -a stats.txt >&2) ]]> </command> @@ -37,10 +39,11 @@ </inputs> <outputs> - <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events pdf)"/> - <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction pdf)" /> - <expand macro="xls_output_data" filename="output.junction.xls" /> - <expand macro="rscript_output_data" filename="output.junction_plot.r" /> + <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string}: splice events (PDF)"/> + <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)" /> + <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)" /> + <expand macro="rscript_output_data" filename="output.junction_plot.r" label="${tool.name} on ${on_string}: Rscript"/> + <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats" /> </outputs> <tests> @@ -52,6 +55,7 @@ <output name="outputr" file="output.junction_plot_r" /> <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" /> <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" /> + <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2" /> </test> </tests> |
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| diff -r 1421603cc95b -r 5968573462fa junction_saturation.xml --- a/junction_saturation.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/junction_saturation.xml Sat Dec 10 11:23:05 2022 +0000 |
| [ |
| @@ -1,9 +1,9 @@ <tool id="rseqc_junction_saturation" name="Junction Saturation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>detects splice junctions from each subset and compares them to reference gene model</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> <expand macro="stdio" /> <version_command><![CDATA[junction_saturation.py --version]]></version_command> @@ -52,8 +52,8 @@ </inputs> <outputs> - <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" /> - <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" /> + <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string}: junction saturation (PDF)"/> + <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string}: junction saturation (Rscript)"/> </outputs> <tests> |
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| diff -r 1421603cc95b -r 5968573462fa mismatch_profile.xml --- a/mismatch_profile.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/mismatch_profile.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -2,10 +2,10 @@ <description> calculates the distribution of mismatches across reads </description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> |
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| diff -r 1421603cc95b -r 5968573462fa read_GC.xml --- a/read_GC.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/read_GC.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="rseqc_read_GC" name="Read GC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>determines GC% and read count</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> @@ -27,9 +27,9 @@ </inputs> <outputs> - <expand macro="pdf_output_data" filename="output.GC_plot.pdf" /> - <expand macro="xls_output_data" filename="output.GC.xls" /> - <expand macro="rscript_output_data" filename="output.GC_plot.r" /> + <expand macro="pdf_output_data" filename="output.GC_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/> + <expand macro="xls_output_data" filename="output.GC.xls" label="${tool.name} on ${on_string}: XLS"/> + <expand macro="rscript_output_data" filename="output.GC_plot.r" label="${tool.name} on ${on_string}: Rscript"/> </outputs> <tests> |
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| diff -r 1421603cc95b -r 5968573462fa read_NVC.xml --- a/read_NVC.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/read_NVC.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="rseqc_read_NVC" name="Read NVC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>to check the nucleotide composition bias</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> |
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| diff -r 1421603cc95b -r 5968573462fa read_distribution.xml --- a/read_distribution.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/read_distribution.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="rseqc_read_distribution" name="Read Distribution" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>calculates how mapped reads were distributed over genome feature</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> @@ -23,7 +23,7 @@ </inputs> <outputs> - <data format="txt" name="output" /> + <data format="txt" name="output" label="${tool.name} on ${on_string}: stats (TXT)"/> </outputs> <tests> |
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| diff -r 1421603cc95b -r 5968573462fa read_duplication.xml --- a/read_duplication.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/read_duplication.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,9 +1,9 @@ <tool id="rseqc_read_duplication" name="Read Duplication" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>determines reads duplication rate with sequence-based and mapping-based strategies</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> @@ -25,10 +25,10 @@ </inputs> <outputs> - <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" /> - <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position xls)"/> - <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence xls)"/> - <expand macro="rscript_output_data" filename="output.DupRate_plot.r" /> + <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/> + <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon (XLS)"/> + <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences (XLS)"/> + <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${tool.name} on ${on_string}: Rscript"/> </outputs> <tests> |
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| diff -r 1421603cc95b -r 5968573462fa read_hexamer.xml --- a/read_hexamer.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/read_hexamer.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -2,11 +2,10 @@ <description> calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences </description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> - + <expand macro="bio_tools"/> <expand macro="requirements" /> <expand macro="stdio" /> |
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| diff -r 1421603cc95b -r 5968573462fa read_quality.xml --- a/read_quality.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/read_quality.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,10 +1,9 @@ <tool id="rseqc_read_quality" name="Read Quality" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>determines Phred quality score</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> - + <expand macro="bio_tools"/> <expand macro="requirements"> <!-- Required due to conda solver bug: https://github.com/conda/conda/issues/6269 |
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| diff -r 1421603cc95b -r 5968573462fa rseqc_macros.xml --- a/rseqc_macros.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/rseqc_macros.xml Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">5.0.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@GALAXY_VERSION@">20.01</token> <xml name="requirements"> <requirements> @@ -105,16 +105,16 @@ <!-- Output --> - <xml name="pdf_output_data" token_filename="output.pdf"> - <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (pdf)" /> + <xml name="pdf_output_data" token_filename="output.pdf" token_label="${tool.name} on ${on_string}: PDF"> + <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="@LABEL@" /> </xml> - <xml name="xls_output_data" token_filename="output.xls"> - <data format="xls" name="outputxls" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (xls)" /> + <xml name="xls_output_data" token_filename="output.xls" token_label="${tool.name} on ${on_string}: XLS"> + <data format="xls" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@" /> </xml> - <xml name="rscript_output_data" token_filename="output.r"> - <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (rscript)"> + <xml name="rscript_output_data" token_filename="output.r" token_label="${tool.name} on ${on_string}: Rscript"> + <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="@LABEL@"> <filter>rscript_output</filter> </data> </xml> |
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| diff -r 1421603cc95b -r 5968573462fa test-data/output.splice_events.pdf |
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| Binary file test-data/output.splice_events.pdf has changed |
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| diff -r 1421603cc95b -r 5968573462fa test-data/output.splice_junction.pdf |
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| Binary file test-data/output.splice_junction.pdf has changed |
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| diff -r 1421603cc95b -r 5968573462fa test-data/output.splice_junction.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.splice_junction.txt Sat Dec 10 11:23:05 2022 +0000 |
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| @@ -0,0 +1,18 @@ +Reading reference bed file: /tmp/tmp5v623oz4/files/e/7/2/dataset_e7232361-03db-486f-9792-924d1ac24b1c.dat ... Done +Load BAM file ... Done + +=================================================================== +Total splicing Events: 4 +Known Splicing Events: 1 +Partial Novel Splicing Events: 1 +Novel Splicing Events: 1 +Filtered Splicing Events: 1 + +Total splicing Junctions: 3 +Known Splicing Junctions: 1 +Partial Novel Splicing Junctions: 1 +Novel Splicing Junctions: 1 + +=================================================================== +Create BED file ... +Create Interact file ... |
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| diff -r 1421603cc95b -r 5968573462fa tin.xml --- a/tin.xml Sat Nov 26 15:19:14 2022 +0000 +++ b/tin.xml Sat Dec 10 11:23:05 2022 +0000 |
| b |
| @@ -2,10 +2,10 @@ <description> evaluates RNA integrity at a transcript level </description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> |