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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_cells commit bdd7e8d396fd19cc96db67afa2dcb3c46451f27c |
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modified:
filter_cells.xml |
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| diff -r 6ffcbb980f07 -r 47cf889595ec filter_cells.xml --- a/filter_cells.xml Mon Jun 24 19:16:21 2019 -0400 +++ b/filter_cells.xml Sun Jul 07 08:29:39 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="filter_cells" name="Filter cells data" version="0.9.1"> +<tool id="filter_cells" name="Filter cells data" version="0.9.2"> <description>on total aligned reads and/or number of detected genes</description> <requirements> <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> @@ -46,7 +46,7 @@ help="Cells with number of aligned reads below this absolute threshold will be filtered out. Leave at 0 for no filtering" /> <param name="manage_cutoffs" type="select" label=" filter out intersection or union of cutoffs" help="If you use two cutoffs on number of detected genes and number of aligned reads, respectively, there are two options - for using these cutoffs in filtering: either excluding items that are below one or the other threshold (union) or + for using these cutoffs in filtering: either excluding items that are below one or the other threshold (union), or excluding items that are below both thresholds (intersection)" > <option value="union" selected="true">Union of cutoffs</option> <option value="intersect">Intersection of cutoffs</option> @@ -139,7 +139,7 @@ **What it does** -The tools takes a table of gene (rows) expression values (as number of reads aligned to genes) +The tool takes a table of gene (rows) expression values (as number of reads aligned to genes) in single cell RNAseq sequencing libraries (columns) and filters out cells with low number of detected genes and/or cells with low number of aligned reads. @@ -150,8 +150,8 @@ these threshold are excluded (cell cutoffs do not include the threshold values). If you choose to combine cutoffs for both the number of detected genes -and the total number of aligned reads, then you have 2 options: either exclude libraries that -do not satisfy one OR the other threshold (Union) or exclude libraries that do not satisfy +and the total number of aligned reads, then you have 2 options: either excluding libraries that +do not satisfy one OR the other threshold (Union) or excluding libraries that do not satisfy both thresholds (Intersection). Specifying a value both for an absolute and an percentile threshold of a variable @@ -161,7 +161,7 @@ this variable is not used to filter the cells. The tools returns a gene expression table for cells that were retained, a metadata table -that contains numbers of detected genes and aligned reads for retained cell library and +that contains numbers of detected genes and aligned reads for retained cell libraries and a pdf file with three plots illustrating the performed filtering operation. **Input** |