Mercurial > repos > bgruening > hicup_hicup
diff hicup_hicup.xml @ 7:68fb19094f84 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17
author | bgruening |
---|---|
date | Thu, 23 Feb 2023 18:04:00 +0000 |
parents | 6137fb382a02 |
children |
line wrap: on
line diff
--- a/hicup_hicup.xml Mon Oct 24 16:16:20 2022 +0000 +++ b/hicup_hicup.xml Thu Feb 23 18:04:00 2023 +0000 @@ -85,6 +85,7 @@ <data name="wrong_size_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*wrong_size.filter.bam" label="wrong_size.filter.bam"/> <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" /> <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" /> + <data name="ditag_size_distribution_txt" format="tabular" from_work_dir="*.ditag_size_distribution_report.txt" label="Report of ditag size distribution" /> <!-- Output of the deduplicator step --> <data name="cis_trans_piechart" format="svg" from_work_dir="*deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/> <data name="uniques_barchart" format="svg" from_work_dir="*deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" /> @@ -107,10 +108,15 @@ </conditional> <!-- outputs --> - <output name="hicup_results" file="HiCUP_summary_report.html" ftype="html" compare="sim_size"/> + <output name="hicup_results"> + <assert_contents> + <has_size value="4681214" delta="400000"/> + <has_text text="HiCUP Summary Report"/> + </assert_contents> + </output> <output name="dataset_hicup" file="dataset1_2.hicup.bam" compare="sim_size" ftype="qname_sorted.bam" /> - <output name="hicup_report" file="HiCUP_summary_report.txt" lines_diff="0"/> - <output name="digester_file" file="digester_file.txt" lines_diff="0"/> + <output name="hicup_report" file="HiCUP_summary_report_aQdQORylpl_22-59-39_22-02-2023.txt" lines_diff="0"/> + <output name="digester_file" file="digest_file.txt" lines_diff="0"/> <output_collection name="intermediate_results"> <!-- truncater step--> @@ -122,8 +128,8 @@ </element> <element name="dataset1_trunc" file="dataset1.trunc.fastq.gz" decompress="true"/> <element name="dataset2_trunc" file="dataset2.trunc.fastq.gz" decompress="true"/> - <element name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" compare="sim_size" /> - <element name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" compare="sim_size" /> + <element name="dataset1_truncater_barchart" file="dataset1.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size" /> + <element name="dataset2_truncater_barchart" file="dataset2.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size" /> <!-- mapper step --> <element name="hicup_mapper_summary"> @@ -132,9 +138,9 @@ <has_text_matching expression="\s+99742\s+2476\s+2.5\s+3725\s+3.7\s+12679\s+12.7\s+80862\s+81.1\s+1143\s+1.1"/> </assert_contents> </element> - <element name="result_pair" file="dataset1_2.pair.bam" lines_diff="5" ftype="qname_sorted.bam"/> - <element name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" compare="sim_size" /> - <element name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" compare="sim_size" /> + <element name="result_pair" file="dataset1_2.pair.bam" lines_diff="2" ftype="qname_sorted.bam"/> + <element name="dataset1_mapper_barchart" file="dataset1.trunc.fastq.gz.mapper_barchart.svg" ftype="svg" compare="sim_size" /> + <element name="dataset2_mapper_barchart" file="dataset2.trunc.fastq.gz.mapper_barchart.svg" ftype="svg" compare="sim_size" /> <!-- filter step--> <element name="hicup_filter_summary"> @@ -142,15 +148,16 @@ <has_text_matching expression="\s+1143\s+544\s+44\s+440\s+60\s+599\s+21\s+73\s+466\s+39\s+0\s+0"/> </assert_contents> </element> - <element name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="14" ftype="qname_sorted.bam" /> - <element name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> - <element name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> - <element name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> - <element name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> - <element name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> - <element name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> + <element name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="4" ftype="qname_sorted.bam" /> + <element name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> + <element name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> + <element name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> + <element name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> + <element name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> + <element name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> <element name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" compare="sim_size" /> <element name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" compare="sim_size" /> + <element name="ditag_size_distribution_txt" file="dataset1_2.ditag_size_distribution_report.txt" ftype="tabular"/> <!-- deduplicator step--> <element name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" compare="sim_size" />