# HG changeset patch
# User artbio
# Date 1560953689 14400
# Node ID 02fdb062c1751d62e7314936ca4e839b438e99de
# Parent  444f58c5ea0356aa38c0951fb1c359c4f7be0214
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc-filter_cells commit e4aa2be8f78682bbd8c3f94ff05aeeca47bb5b5f

diff -r 444f58c5ea03 -r 02fdb062c175 filter_cells.R
--- a/filter_cells.R	Sun Jun 16 11:23:16 2019 -0400
+++ b/filter_cells.R	Wed Jun 19 10:14:49 2019 -0400
@@ -141,7 +141,7 @@
 ## Plot the results
 
 # Determine title from the parameter logics
-if(opt$percentile_counts > 0){
+if (opt$percentile_counts > 0){
     part_one = paste0("Cells with aligned reads counts below the ",
                       opt$percentile_counts,
                       "th percentile of aligned read counts")} else {
@@ -150,12 +150,16 @@
 }
 
 if(opt$percentile_genes > 0){
-    part_two = paste0("cells with number of detected genes below the ",
+    part_two = paste0("with number of detected genes below the ",
                       opt$percentile_genes,
                       "th percentile of detected gene counts")} else {
-    part_two = paste0("cells with number of detected genes below ",
+    part_two = paste0("with number of detected genes below ",
                       opt$absolute_genes)
 }
+if (opt$manage_cutoffs == "intersect") {
+    conjunction = " and\n" } else {
+    conjunction = " or\n"
+}
 
 # plot with ggplot2
 ggplot(QC_metrics, aes(nGenes, total_counts, colour = filtered)) +
@@ -166,7 +170,7 @@
                                      paste0("Filtered (", table(QC_metrics$filtered)[2], " cells)"))) +
      xlab("Detected genes per cell") + ylab("Aligned reads per cell (log10 scale)") +
      geom_vline(xintercept = genes_threshold) + geom_hline(yintercept = counts_threshold) +
-     ggtitle( paste0(part_one, " and\n", part_two, "\nwere filtered out")) +
+     ggtitle( paste0(part_one, conjunction, part_two, "\nwere filtered out")) +
      theme(plot.title = element_text(size = 8, face = "bold"))
 
 dev.off()
diff -r 444f58c5ea03 -r 02fdb062c175 filter_cells.xml
--- a/filter_cells.xml	Sun Jun 16 11:23:16 2019 -0400
+++ b/filter_cells.xml	Wed Jun 19 10:14:49 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="filter_cells" name="Filter cells data" version="0.4.0">
+<tool id="filter_cells" name="Filter cells data" version="0.4.1">
     <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>
@@ -45,7 +45,7 @@
         <param name="absolute_counts" value="0" type="integer" label="Absolute number of aligned read Threshold [integer]"
                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, their is two option
+               help="If you use two cutoffs on number of detected genes and number of aligned reads, respectively, their is two options
                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>
@@ -77,7 +77,7 @@
             <output name="output" file="intersect_percentile_gene-and-counts.tab" ftype="tabular"/>
             <output name="output_metada" file="intersect_percentile_gene-and-counts.meta" ftype="tabular"/>
         </test>
-        <test>
+       <test>
             <param name="input" value="input.tsv" ftype="txt"/>
             <param name="sep" value='tab' />
             <param name="percentile_genes" value="20"/>
diff -r 444f58c5ea03 -r 02fdb062c175 test-data/absolute_counts-only.pdf
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diff -r 444f58c5ea03 -r 02fdb062c175 test-data/absolute_gene-and-counts.pdf
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diff -r 444f58c5ea03 -r 02fdb062c175 test-data/absolute_gene-only.pdf
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diff -r 444f58c5ea03 -r 02fdb062c175 test-data/intersect_percentile_gene-and-counts.pdf
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diff -r 444f58c5ea03 -r 02fdb062c175 test-data/no-filtering.pdf
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diff -r 444f58c5ea03 -r 02fdb062c175 test-data/percentile_counts-only.pdf
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diff -r 444f58c5ea03 -r 02fdb062c175 test-data/percentile_gene-and-counts.pdf
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diff -r 444f58c5ea03 -r 02fdb062c175 test-data/percentile_gene-only.pdf
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