# HG changeset patch
# User artbio
# Date 1635153655 0
# Node ID 9b48fd77345733e3585f0ef0fc66ab5b7ec617e1
# Parent  ba3ce7ee5b187bd4ce1746687c031f1d22c958ce
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 8c676ff51e50ed8c15636d9481acfbebc2f59229"

diff -r ba3ce7ee5b18 -r 9b48fd773457 small_rna_maps.xml
--- a/small_rna_maps.xml	Sun May 09 17:08:12 2021 +0000
+++ b/small_rna_maps.xml	Mon Oct 25 09:20:55 2021 +0000
@@ -1,14 +1,13 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="3.0.0">
+<tool id="small_rna_maps" name="small_rna_maps" version="3.1.0">
   <description></description>
   <requirements>
-        <requirement type="package" version="1.20.2=py38h9894fe3_0">numpy</requirement>
-        <requirement type="package" version="0.16.0.1=py38hbdc2ae9_1">pysam</requirement>
-        <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement>
-        <requirement type="package" version="0.6_29=r40h6115d3f_1">r-latticeextra</requirement>
-        <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement>
-        <requirement type="package" version="1.4.4=r40h0357c0b_1">r-reshape2</requirement>
-        <requirement type="package" version="0.8.0=h984e79f_0">sambamba</requirement>
-        <requirement type="package" version="1.10=h2e538c0_3">samtools</requirement>
+        <requirement type="package" version="1.21.3=py37h31617e3_0">numpy</requirement>
+        <requirement type="package" version="0.17.0=py37h45aed0b_0">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="1.4.4=r40h03ef668_1">r-reshape2</requirement>
+        <requirement type="package" version="0.8.1=h41abebc_0">sambamba</requirement>
         <requirement type="package" version="68.1=h58526e2_0">icu</requirement>
   </requirements>
   <stdio>
@@ -19,7 +18,7 @@
           #import os
           #for $file in $inputs
               sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' &&
-              samtools index '$file.element_identifier' &&
+              sambamba index -t \${GALAXY_SLOTS} '$file.element_identifier' &&
           #end for
           python '$__tool_directory__'/small_rna_maps.py
               --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) }