# HG changeset patch
# User artbio
# Date 1666482554 0
# Node ID dc862983eb989def54dc13c718cf316e635aceaa
# Parent  ca2b04cdbf4d19cab4e5e73dce230c66c30f6d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a

diff -r ca2b04cdbf4d -r dc862983eb98 overlapping_reads.xml
--- a/overlapping_reads.xml	Sat Oct 23 22:54:47 2021 +0000
+++ b/overlapping_reads.xml	Sat Oct 22 23:49:14 2022 +0000
@@ -1,16 +1,16 @@
-<tool id="overlapping_reads" name="Get overlapping reads" version="3.3">
+<tool id="overlapping_reads" name="Get overlapping reads" version="3.4.1">
     <description />
     <requirements>
-        <requirement type="package" version="0.16.0.1=py37h45aed0b_3">pysam</requirement>
-        <requirement type="package" version="1.13=h8c37831_0">samtools</requirement>
+        <requirement type="package" version="0.18.0">pysam</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Tool exception" />
     </stdio>
       <command detect_errors="exit_code"><![CDATA[
-        samtools index '$input' &&
+        ln -f -s $input.metadata.bam_index input.bam.bai &&
+        ln -s $input input.bam &&
         python '$__tool_directory__'/overlapping_reads.py
-           --input '$input'
+           --input input.bam
            --minquery '$minquery'
            --maxquery '$maxquery'
            --mintarget '$mintarget'
diff -r ca2b04cdbf4d -r dc862983eb98 signature.r
--- a/signature.r	Sat Oct 23 22:54:47 2021 +0000
+++ b/signature.r	Sat Oct 22 23:49:14 2022 +0000
@@ -1,8 +1,8 @@
 ## Setup R error handling to go to stderr
-options(show.error.messages = F,
+options(show.error.messages = FALSE,
         error = function() {
             cat(geterrmessage(), file = stderr())
-            q("no", 1, F)
+            q("no", 1, FALSE)
         }
 )
 warnings()
@@ -26,12 +26,12 @@
     )
 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
 args <- parse_args(parser)
- 
+
 # data frames implementation
-h_dataframe <- read.delim(args$h_dataframe, header = F)
+h_dataframe <- read.delim(args$h_dataframe, header = FALSE)
 colnames(h_dataframe) <- c("chrom", "overlap", "sig", "z-score")
 h_dataframe$sig <- h_dataframe$sig * 100  # to get probs in %
-z_dataframe <- read.delim(args$z_dataframe, header = F)
+z_dataframe <- read.delim(args$z_dataframe, header = FALSE)
 colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score")
 
 # functions
@@ -77,7 +77,7 @@
                    pch = 19, lwd = 2,
                    as.table = TRUE,
                    layout = c(2, 12),
-                   newpage = T,
+                   newpage = TRUE,
                    ...)
            plot(p)
            dev.off()
diff -r ca2b04cdbf4d -r dc862983eb98 signature.xml
--- a/signature.xml	Sat Oct 23 22:54:47 2021 +0000
+++ b/signature.xml	Sat Oct 22 23:49:14 2022 +0000
@@ -1,20 +1,20 @@
-<tool id="signature" name="Small RNA Signatures" version="3.3>">
+<tool id="signature" name="Small RNA Signatures" version="3.4.1>">
     <description />
     <requirements>
-        <requirement type="package" version="1.13=h8c37831_0">samtools</requirement>
-        <requirement type="package" version="1.21.3=py37h31617e3_0">numpy</requirement>
-        <requirement type="package" version="0.16.0.1=py37h45aed0b_3">pysam</requirement>
-        <requirement type="package" version="1.7.1=r40hc72bb7e_0">r-optparse</requirement>
-        <requirement type="package" version="0.6_29=r40hc72bb7e_1">r-latticeextra</requirement>
-        <requirement type="package" version="2.3=r40hc72bb7e_1003">r-gridextra</requirement>
+        <requirement type="package" version="1.23.4">numpy</requirement>
+        <requirement type="package" version="0.18.0">pysam</requirement>
+        <requirement type="package" version="1.7.3">r-optparse</requirement>
+        <requirement type="package" version="0.6_30">r-latticeextra</requirement>
+        <requirement type="package" version="2.3">r-gridextra</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Tool exception" />
     </stdio>
       <command detect_errors="exit_code"><![CDATA[
-        samtools index '$input' &&
+        ln -f -s $input.metadata.bam_index input.bam.bai &&
+        ln -s $input input.bam &&
         python '$__tool_directory__'/signature.py
-           --input '$input'
+           --input input.bam
            --minquery '$minquery'
            --maxquery '$maxquery'
            --mintarget '$mintarget'
@@ -91,7 +91,7 @@
 Compute small RNA (piRNA, siRNA, ...) signatures.
 
 This tool computes (i) the number of pairs **aligned** reads by overlap classes (in nt) and associated z-scores,
-and (ii) the ping-pong signal (`Brennecke et al, 2009`_) and associated z-scores.
+and (ii) the ping-pong signal (Brennecke et al. Science. 2008;322: 1387–1392) and associated z-scores.
 
 **Note** that the number of pairs of aligned reads is disctint from the number of pairs of reads
 when these reads can be aligned at multiple positions in the genome. The two values are equal only
@@ -102,7 +102,6 @@
 genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes 
 for piRNA and siRNA signatures, see `Antoniewski (2014)`_.
 
-.. _Brennecke et al, 2009: http://dx.doi.org/10.1126/science.1165171
 .. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12
 
 **Input**
diff -r ca2b04cdbf4d -r dc862983eb98 test-data/global.pdf
Binary file test-data/global.pdf has changed
diff -r ca2b04cdbf4d -r dc862983eb98 test-data/lattice.pdf
Binary file test-data/lattice.pdf has changed