Mercurial > repos > bgruening > hicup_hicup
comparison 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 |
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| 6:852e1fac4802 | 7:68fb19094f84 |
|---|---|
| 83 <data name="same_circularised_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_circularised.filter.bam" label="same_circularised.filter.bam" /> | 83 <data name="same_circularised_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_circularised.filter.bam" label="same_circularised.filter.bam" /> |
| 84 <data name="same_internal_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_internal.filter.bam" label="same_internal.filter.bam" /> | 84 <data name="same_internal_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_internal.filter.bam" label="same_internal.filter.bam" /> |
| 85 <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"/> | 85 <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"/> |
| 86 <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" /> | 86 <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" /> |
| 87 <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" /> | 87 <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" /> |
| 88 <data name="ditag_size_distribution_txt" format="tabular" from_work_dir="*.ditag_size_distribution_report.txt" label="Report of ditag size distribution" /> | |
| 88 <!-- Output of the deduplicator step --> | 89 <!-- Output of the deduplicator step --> |
| 89 <data name="cis_trans_piechart" format="svg" from_work_dir="*deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/> | 90 <data name="cis_trans_piechart" format="svg" from_work_dir="*deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/> |
| 90 <data name="uniques_barchart" format="svg" from_work_dir="*deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" /> | 91 <data name="uniques_barchart" format="svg" from_work_dir="*deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" /> |
| 91 <data name="hicup_deduplicator_summary" format="tabular" from_work_dir="hicup_deduplicator_summary*.txt" label="Hicup Deduplicator Summary" /> | 92 <data name="hicup_deduplicator_summary" format="tabular" from_work_dir="hicup_deduplicator_summary*.txt" label="Hicup Deduplicator Summary" /> |
| 92 </collection> | 93 </collection> |
| 105 <param name="source" value="history" /> | 106 <param name="source" value="history" /> |
| 106 <param name="own_file" value="chr21And22FromHg38.fasta"/> | 107 <param name="own_file" value="chr21And22FromHg38.fasta"/> |
| 107 </conditional> | 108 </conditional> |
| 108 | 109 |
| 109 <!-- outputs --> | 110 <!-- outputs --> |
| 110 <output name="hicup_results" file="HiCUP_summary_report.html" ftype="html" compare="sim_size"/> | 111 <output name="hicup_results"> |
| 112 <assert_contents> | |
| 113 <has_size value="4681214" delta="400000"/> | |
| 114 <has_text text="HiCUP Summary Report"/> | |
| 115 </assert_contents> | |
| 116 </output> | |
| 111 <output name="dataset_hicup" file="dataset1_2.hicup.bam" compare="sim_size" ftype="qname_sorted.bam" /> | 117 <output name="dataset_hicup" file="dataset1_2.hicup.bam" compare="sim_size" ftype="qname_sorted.bam" /> |
| 112 <output name="hicup_report" file="HiCUP_summary_report.txt" lines_diff="0"/> | 118 <output name="hicup_report" file="HiCUP_summary_report_aQdQORylpl_22-59-39_22-02-2023.txt" lines_diff="0"/> |
| 113 <output name="digester_file" file="digester_file.txt" lines_diff="0"/> | 119 <output name="digester_file" file="digest_file.txt" lines_diff="0"/> |
| 114 | 120 |
| 115 <output_collection name="intermediate_results"> | 121 <output_collection name="intermediate_results"> |
| 116 <!-- truncater step--> | 122 <!-- truncater step--> |
| 117 <element name="hicup_truncater_summary"> | 123 <element name="hicup_truncater_summary"> |
| 118 <assert_contents> | 124 <assert_contents> |
| 120 <has_text_matching expression="\s+99742\s+7114\s+7.13\s+92628\s+92.87\s+22.63"/> | 126 <has_text_matching expression="\s+99742\s+7114\s+7.13\s+92628\s+92.87\s+22.63"/> |
| 121 </assert_contents> | 127 </assert_contents> |
| 122 </element> | 128 </element> |
| 123 <element name="dataset1_trunc" file="dataset1.trunc.fastq.gz" decompress="true"/> | 129 <element name="dataset1_trunc" file="dataset1.trunc.fastq.gz" decompress="true"/> |
| 124 <element name="dataset2_trunc" file="dataset2.trunc.fastq.gz" decompress="true"/> | 130 <element name="dataset2_trunc" file="dataset2.trunc.fastq.gz" decompress="true"/> |
| 125 <element name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" compare="sim_size" /> | 131 <element name="dataset1_truncater_barchart" file="dataset1.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size" /> |
| 126 <element name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" compare="sim_size" /> | 132 <element name="dataset2_truncater_barchart" file="dataset2.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size" /> |
| 127 | 133 |
| 128 <!-- mapper step --> | 134 <!-- mapper step --> |
| 129 <element name="hicup_mapper_summary"> | 135 <element name="hicup_mapper_summary"> |
| 130 <assert_contents> | 136 <assert_contents> |
| 131 <has_text_matching expression="\s+99742\s+2658\s+2.7\s+3885\s+3.9\s+12437\s+12.5\s+80762\s+81.0\s+1143\s+1.1"/> | 137 <has_text_matching expression="\s+99742\s+2658\s+2.7\s+3885\s+3.9\s+12437\s+12.5\s+80762\s+81.0\s+1143\s+1.1"/> |
| 132 <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"/> | 138 <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"/> |
| 133 </assert_contents> | 139 </assert_contents> |
| 134 </element> | 140 </element> |
| 135 <element name="result_pair" file="dataset1_2.pair.bam" lines_diff="5" ftype="qname_sorted.bam"/> | 141 <element name="result_pair" file="dataset1_2.pair.bam" lines_diff="2" ftype="qname_sorted.bam"/> |
| 136 <element name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" compare="sim_size" /> | 142 <element name="dataset1_mapper_barchart" file="dataset1.trunc.fastq.gz.mapper_barchart.svg" ftype="svg" compare="sim_size" /> |
| 137 <element name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" compare="sim_size" /> | 143 <element name="dataset2_mapper_barchart" file="dataset2.trunc.fastq.gz.mapper_barchart.svg" ftype="svg" compare="sim_size" /> |
| 138 | 144 |
| 139 <!-- filter step--> | 145 <!-- filter step--> |
| 140 <element name="hicup_filter_summary"> | 146 <element name="hicup_filter_summary"> |
| 141 <assert_contents> | 147 <assert_contents> |
| 142 <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"/> | 148 <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"/> |
| 143 </assert_contents> | 149 </assert_contents> |
| 144 </element> | 150 </element> |
| 145 <element name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="14" ftype="qname_sorted.bam" /> | 151 <element name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
| 146 <element name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> | 152 <element name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
| 147 <element name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> | 153 <element name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
| 148 <element name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> | 154 <element name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
| 149 <element name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> | 155 <element name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
| 150 <element name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> | 156 <element name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
| 151 <element name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="14" ftype="qname_sorted.bam" /> | 157 <element name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
| 152 <element name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" compare="sim_size" /> | 158 <element name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" compare="sim_size" /> |
| 153 <element name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" compare="sim_size" /> | 159 <element name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" compare="sim_size" /> |
| 160 <element name="ditag_size_distribution_txt" file="dataset1_2.ditag_size_distribution_report.txt" ftype="tabular"/> | |
| 154 | 161 |
| 155 <!-- deduplicator step--> | 162 <!-- deduplicator step--> |
| 156 <element name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" compare="sim_size" /> | 163 <element name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" compare="sim_size" /> |
| 157 <element name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" compare="sim_size" /> | 164 <element name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" compare="sim_size" /> |
| 158 <element name="hicup_deduplicator_summary" > | 165 <element name="hicup_deduplicator_summary" > |