# HG changeset patch
# User iuc
# Date 1538072632 14400
# Node ID f437057e46f1e3810538deac530a0a10def0a05e
# Parent  daae0a118c364d154335b3ebdd2d1a5e0d8b100c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7d7cd4324af66710b89801a1a1c79fb8abf0d146

diff -r daae0a118c36 -r f437057e46f1 geneBody_coverage.xml
--- a/geneBody_coverage.xml	Tue Sep 18 09:11:06 2018 -0400
+++ b/geneBody_coverage.xml	Thu Sep 27 14:23:52 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.2">
+<tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.3">
   <description>
     Read coverage over gene body.
   </description>
@@ -29,9 +29,9 @@
         #end for
         geneBody_coverage.py -i 'input_list.txt' -r '${refgene}' --minimum_length ${minimum_length} -o output
     #else
-        #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier)
-        ln -sf '${input}' '${safename}.bam' &&
-        ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' &&
+        #set $safename = re.sub('[^\w\-_]', '_', $batch_mode.input.element_identifier)
+        ln -sf '${batch_mode.input}' '${safename}.bam' &&
+        ln -sf '${batch_mode.input.metadata.bam_index}' '${safename}.bam.bai' &&
         geneBody_coverage.py -i '${safename}.bam' -r '${refgene}' --minimum_length ${minimum_length} -o output
     #end if
     ]]>
diff -r daae0a118c36 -r f437057e46f1 inner_distance.xml
--- a/inner_distance.xml	Tue Sep 18 09:11:06 2018 -0400
+++ b/inner_distance.xml	Thu Sep 27 14:23:52 2018 -0400
@@ -88,7 +88,7 @@
 
 1. output.inner_distance.txt:
     - first column is read ID
-    -second column is inner distance. Could be negative value if PE reads were overlapped or mapping error (e.g. Read1_start &lt; Read2_start, while Read1_end >> Read2_end due to spliced mapping of read1)
+    - second column is inner distance. Could be negative value if PE reads were overlapped or mapping error (e.g. Read1_start &lt; Read2_start, while Read1_end >> Read2_end due to spliced mapping of read1)
     - third column indicates how paired reads were mapped: PE_within_same_exon, PE_within_diff_exon,PE_reads_overlap
 2. output..inner_distance_freq.txt:
     - inner distance starts
diff -r daae0a118c36 -r f437057e46f1 tin.xml
--- a/tin.xml	Tue Sep 18 09:11:06 2018 -0400
+++ b/tin.xml	Thu Sep 27 14:23:52 2018 -0400
@@ -89,7 +89,7 @@
 
 * RIN has very limited sensitivity to measure substantially degraded RNA
   samples such as preserved clinical tissues. (ref:
-  http://www.illumina.com/documents/products/technotes/technote-truseq-rna-access.pdf).
+  https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote-truseq-rna-access.pdf).
 
 To overcome these limitations, we developed TIN, an algorithm that is able
 to measure RNA integrity at transcript level. TIN calculates a score (0 <=