Mercurial > repos > petr-novak > re_utils
diff summarize_cluster_table.xml @ 22:58807b35777a draft
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
| author | petr-novak |
|---|---|
| date | Wed, 02 Aug 2023 11:31:12 +0000 |
| parents | 2f1b5d5c5dd5 |
| children | 628b235d76c7 |
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--- a/summarize_cluster_table.xml Thu Jul 27 09:46:13 2023 +0000 +++ b/summarize_cluster_table.xml Wed Aug 02 11:31:12 2023 +0000 @@ -1,42 +1,58 @@ -<tool id="summarize_annotation" name="Repeat proportions from CLUSTER_TABLE" version="1.0.0"> - <description> Simple utility to summarize final annotations from RepeatExplorer CLUSTER_TABLE</description> - <requirements> - <requirement type="package">r-optparse</requirement> - </requirements> - - <command interpreter="Rscript" detect_errors="exit_code" > - $__tool_directory__/summarize_cluster_table.R - --cluster_table=$cluster_table - --output=$output +<tool id="summarize_annotation" name="Repeat proportions from CLUSTER_TABLE" + version="1.0.0.3"> + <description>Simple utility to summarize final annotations from RepeatExplorer + CLUSTER_TABLE + </description> + <requirements> + <requirement type="package">r-optparse</requirement> + </requirements> + <required_files> + <include type="literal" path="summarize_cluster_table.R"/> + </required_files> + <command interpreter="Rscript" detect_errors="exit_code"> + Rscript $__tool_directory__/summarize_cluster_table.R + --cluster_table=$cluster_table + --output=$output </command> <inputs> - <param format="txt" type="data" name="cluster_table" label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv" help="CLUSTER_TABLE.csv must contains completed Final_annotation column" /> + <param format="txt" type="data" name="cluster_table" + label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv" + help="CLUSTER_TABLE.csv must contains completed Final_annotation column"/> </inputs> <outputs> - <data format="tabular" name="output" label="Summary of repeat proportions from ${cluster_table.hid}"/> + <data format="tabular" name="output" + label="Summary of repeat proportions from ${cluster_table.hid}"/> </outputs> <help> - **The tool calculates genome proportions of identified repeats based on cluster annotations in CLUSTER_TABLE.csv** - - The column "Final_annotation" must be filled in the input file CLUSTER_TABLE.csv. Contamination and organelle clusters are discarded from quantification. Table header with information about numbers of analyzed reads should remain unchanged - see example below. + **The tool calculates genome proportions of identified repeats based on cluster + annotations in CLUSTER_TABLE.csv** - Example of CLUSTER_TABLE.csv: :: + The column "Final_annotation" must be filled in the input file CLUSTER_TABLE.csv. + Contamination and organelle clusters are discarded from quantification. Table + header with information about numbers of analyzed reads should remain unchanged - + see example below. + + Example of CLUSTER_TABLE.csv: :: - Number_of_reads_in_clusters 1185180 - Number_of_clusters 62148 - Number_of_superclusters 62031 - Number_of_singlets 314820 - Number_of_analyzed_reads 1500000 - Cluster Supercluster Size Size_adjusted Automatic_annotation TAREAN_annotation Final_annotation - 10 4 11967 11967 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE Other All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE - 137 5 2094 2094 All/repeat Other All/repeat - 112 9 3117 3117 All/repeat/rDNA/45S_rDNA Other All/repeat/rDNA/45S_rDNA - 16 11 10078 10078 All/repeat/satellite Putative satellites (high confidence) All/repeat/satellite - 125 22 2630 2630 All/organelle/plastid Other All/organelle/plastid - 124 40 2645 2645 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana Putative LTR elements All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana + Number_of_reads_in_clusters 1185180 + Number_of_clusters 62148 + Number_of_superclusters 62031 + Number_of_singlets 314820 + Number_of_analyzed_reads 1500000 + Cluster Supercluster Size Size_adjusted Automatic_annotation TAREAN_annotation + Final_annotation + 10 4 11967 11967 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE Other + All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE + 137 5 2094 2094 All/repeat Other All/repeat + 112 9 3117 3117 All/repeat/rDNA/45S_rDNA Other All/repeat/rDNA/45S_rDNA + 16 11 10078 10078 All/repeat/satellite Putative satellites (high confidence) + All/repeat/satellite + 125 22 2630 2630 All/organelle/plastid Other All/organelle/plastid + 124 40 2645 2645 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana Putative + LTR elements All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana </help> </tool>