# HG changeset patch
# User bgruening
# Date 1564670833 14400
# Node ID 0b656f8c5637f443a63db687d97b8c476ffe10e4
# Parent  b6aa3b6ba129761e95b72dcd261ba9b3da9f6f62
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ec1f38df34e6862abd0b8e7cc0521e25f9933567

diff -r b6aa3b6ba129 -r 0b656f8c5637 bismark_bowtie2_wrapper.xml
--- a/bismark_bowtie2_wrapper.xml	Tue Jul 30 10:33:02 2019 -0400
+++ b/bismark_bowtie2_wrapper.xml	Thu Aug 01 10:47:13 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy1" profile="18.01">
+<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy2" profile="18.01">
     <description>Bisulfite reads mapper</description>
     <requirements>
         <requirement type="package" version="0.22.1">bismark</requirement>
@@ -16,29 +16,29 @@
             #else
                 #set read1 = 'input_1.fq'
             #end if
-            ln -s '${singlePaired.input_singles}' ${read1} &&
+            ln -s '${singlePaired.input_singles}' '${read1}' &&
         #else:
             #set $mate1 = list()
             #set $mate2 = list()
             #for $mate_pair in $singlePaired.mate_list
 
                 #if $mate_pair.input_mate1.ext == "fasta":
-                    #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa'
+                    #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa'
                 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
-                    #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz'
+                    #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz'
                 #else
-                    #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq'
+                    #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq'
                 #end if
-                ln -s '${mate_pair.input_mate1}' ${read1} &&
+                ln -s '${mate_pair.input_mate1}' '${read1}' &&
 
                 #if $mate_pair.input_mate2.ext == "fasta":
-                    #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa'
+                    #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa'
                 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
-                    #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz'
+                    #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz'
                 #else
-                    #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq'
+                    #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq'
                 #end if
-                ln -s '${mate_pair.input_mate2}' ${read2} &&
+                ln -s '${mate_pair.input_mate2}' '${read2}' &&
 
                 $mate1.append( str($read1) )
                 $mate2.append( str($read2) )
@@ -448,7 +448,7 @@
             <param name="bismark_stdout" value="true"/>
             <param name="isReportOutput" value="true"/>
 
-            <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="80">
+            <output name="output_stdout" file="summary.txt" ftype="txt" lines_diff="94">
                  <assert_contents>
                      <has_text text="Sequences analysed in total:" />
                      <has_text text="44115" />
@@ -472,7 +472,7 @@
             <param name="bismark_stdout" value="true"/>
             <param name="isReportOutput" value="true"/>
 
-            <output name="output_stdout" file="summary_short.txt" ftype="txt" lines_diff="80">
+            <output name="output_stdout" file="summary_short.txt" ftype="txt" lines_diff="94">
                  <assert_contents>
                      <has_text text="Sequences analysed in total:" />
                      <has_text text="1000" />
@@ -499,7 +499,7 @@
             <param name="bismark_stdout" value="true"/>
             <param name="isReportOutput" value="true"/>
 
-            <output name="output_stdout" file="summary_mate.txt" ftype="txt" lines_diff="80">
+            <output name="output_stdout" file="summary_mate.txt" ftype="txt" lines_diff="94">
                  <assert_contents>
                      <has_text text="Sequence pairs analysed in total:" />
                      <has_text text="1000" />
diff -r b6aa3b6ba129 -r 0b656f8c5637 test-data/summary.txt
--- a/test-data/summary.txt	Tue Jul 30 10:33:02 2019 -0400
+++ b/test-data/summary.txt	Thu Aug 01 10:47:13 2019 -0400
@@ -79,7 +79,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:00
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -118,7 +118,7 @@
     ebwtTotSz: 252096
     color: 0
     reverse: 0
-Total time for call to driver() for forward index: 00:00:00
+Total time for call to driver() for forward index: xxxx
 Reading reference sizes
   Time reading reference sizes: 00:00:00
 Calculating joined length
@@ -162,7 +162,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:01
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -264,7 +264,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:00
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -303,7 +303,7 @@
     ebwtTotSz: 252096
     color: 0
     reverse: 0
-Total time for call to driver() for forward index: 00:00:00
+Total time for call to driver() for forward index: xxxx
 Reading reference sizes
   Time reading reference sizes: 00:00:00
 Calculating joined length
@@ -347,7 +347,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:01
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -487,9 +487,8 @@
 C methylated in Unknown context (CN or CHN):	16.7%
 
 
-Bismark completed in 0d 0h 0m 8s
+Bismark completed in xxxx
 
 ====================
 Bismark run complete
 ====================
-
diff -r b6aa3b6ba129 -r 0b656f8c5637 test-data/summary_mate.txt
--- a/test-data/summary_mate.txt	Tue Jul 30 10:33:02 2019 -0400
+++ b/test-data/summary_mate.txt	Thu Aug 01 10:47:13 2019 -0400
@@ -79,7 +79,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:00
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -118,7 +118,7 @@
     ebwtTotSz: 252096
     color: 0
     reverse: 0
-Total time for call to driver() for forward index: 00:00:00
+Total time for call to driver() for forward index: xxxx
 Reading reference sizes
   Time reading reference sizes: 00:00:00
 Calculating joined length
@@ -162,7 +162,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:00
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -264,7 +264,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:00
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -303,7 +303,7 @@
     ebwtTotSz: 252096
     color: 0
     reverse: 0
-Total time for call to driver() for forward index: 00:00:00
+Total time for call to driver() for forward index: xxxx
 Reading reference sizes
   Time reading reference sizes: 00:00:00
 Calculating joined length
@@ -347,7 +347,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:00
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -492,9 +492,8 @@
 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0
 
 
-Bismark completed in 0d 0h 0m 5s
+Bismark completed in xxxx
 
 ====================
 Bismark run complete
 ====================
-
diff -r b6aa3b6ba129 -r 0b656f8c5637 test-data/summary_short.txt
--- a/test-data/summary_short.txt	Tue Jul 30 10:33:02 2019 -0400
+++ b/test-data/summary_short.txt	Thu Aug 01 10:47:13 2019 -0400
@@ -79,7 +79,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:00
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -118,7 +118,7 @@
     ebwtTotSz: 252096
     color: 0
     reverse: 0
-Total time for call to driver() for forward index: 00:00:00
+Total time for call to driver() for forward index: xxxx
 Reading reference sizes
   Time reading reference sizes: 00:00:00
 Calculating joined length
@@ -162,7 +162,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:00
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -264,7 +264,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:00
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -303,7 +303,7 @@
     ebwtTotSz: 252096
     color: 0
     reverse: 0
-Total time for call to driver() for forward index: 00:00:00
+Total time for call to driver() for forward index: xxxx
 Reading reference sizes
   Time reading reference sizes: 00:00:00
 Calculating joined length
@@ -347,7 +347,7 @@
   No samples; assembling all-inclusive block
   Sorting block of length 756159 for bucket 1
   (Using difference cover)
-  Sorting block time: 00:00:00
+  Sorting block time: xxxx
 Returning block of 756160 for bucket 1
 Exited Ebwt loop
 fchr[A]: 0
@@ -487,9 +487,8 @@
 Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0
 
 
-Bismark completed in 0d 0h 0m 5s
+Bismark completed in xxxx
 
 ====================
 Bismark run complete
 ====================
-