# HG changeset patch
# User iuc
# Date 1661380235 0
# Node ID 2d8c943f3e8d6a0085edf2b409928a295a86ceb1
# Parent  66ff749232244b1dc5fbf949236a4121896164bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8

diff -r 66ff74923224 -r 2d8c943f3e8d telescope_assign.xml
--- a/telescope_assign.xml	Tue Sep 03 18:12:09 2019 -0400
+++ b/telescope_assign.xml	Wed Aug 24 22:30:35 2022 +0000
@@ -1,20 +1,25 @@
-<?xml version="1.0"?>
-<tool id="telescope_assign" name="Reassign reads" version="@VERSION@">
+<tool id="telescope_assign" name="Reassign reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>with TELESCOPE using a statistical model</description>
+    <xrefs>
+        <xref type="bio.tools">Telescope-expression</xref>
+    </xrefs>
     <macros>
-        <token name="@VERSION@">1.0.3</token>
+        <token name="@TOOL_VERSION@">1.0.3</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
-        <requirement type="package" version="@VERSION@">telescope</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">telescope</requirement>
         <requirement type="package" version="1.9">samtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         mkdir tempdir &&
         mkdir outdir &&
+        
         telescope assign '$input_alignment' '$input_gtf'
             --tempdir tempdir
             --outdir outdir
-            --ncpu \${GALAXY_SLOTS:-1}
+            ## Not supported https://github.com/mlbendall/telescope/blob/6cd55256c6016feffdbfe10346bfecfcb1e30965/README.md?plain=1#L129
+            ## --ncpu \${GALAXY_SLOTS:-1}
             $updated_sam
             #if str($advanced.advanced_options) == 'select':
                 --reassign_mode $advanced.reassign_mode
@@ -31,7 +36,7 @@
         #if $updated_sam
             &&
             if [ -f outdir/telescope-updated.bam ] ; then
-                samtools sort outdir/telescope-updated.bam > '$updated_alignment' ;
+                samtools sort -T "\${TMPDIR:-.}" outdir/telescope-updated.bam > '$updated_alignment' ;
             else
                 echo 'Updated alignment file not found.' ;
                 exit 1 ;
@@ -170,4 +175,4 @@
     <citations>
         <citation type="doi">10.1101/398172</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>