# HG changeset patch
# User jackcurragh
# Date 1652435609 0
# Node ID f6ef1c85b0454090e25be3532be85b03b5b85e84
# Parent  d572097612777b7809d593344b74e02700539462
Uploaded

diff -r d57209761277 -r f6ef1c85b045 bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py
--- a/bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py	Fri Apr 22 11:08:21 2022 +0000
+++ b/bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py	Fri May 13 09:53:29 2022 +0000
@@ -412,9 +412,13 @@
         try:
             # prepare actual mapping commands
             if options.paired == 'paired':
-                cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
+                # cmd2 = 'bowtie %s %s -1 %s -2 %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output, options.output )
+                cmd2 = 'bowtie %s %s -1 %s -2 %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
+
             else:
-                cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
+                # cmd2 = 'bowtie %s %s %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output, options.output )
+                cmd2 = 'bowtie %s %s %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.output )
+
             # align
             tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
             with open(tmp, 'w') as tmp_stderr:
diff -r d57209761277 -r f6ef1c85b045 bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml
--- a/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Fri Apr 22 11:08:21 2022 +0000
+++ b/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Fri May 13 09:53:29 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bowtie_transcriptomic_wrapper" name="Align to transcriptome using Bowtie" version="1.2.0">
+<tool id="bowtie_transcriptomic_wrapper" name="Align to transcriptome using Bowtie" version="1.3.0">
   <description></description>
   <requirements>
     <requirement type="package" version="1.2.0">bowtie</requirement>
diff -r d57209761277 -r f6ef1c85b045 bowtie_transcriptome_wrapper/tool-data/bowtie_indices.loc.sample
--- a/bowtie_transcriptome_wrapper/tool-data/bowtie_indices.loc.sample	Fri Apr 22 11:08:21 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-homo_sapiens_gencode39	hg_gen39	Homo sapiens (genocode 39)	/data2/indices/bowtie/transcriptome/homo_sapiens_gencode39/homo_sapiens_gencode39_transcriptome
-homo_sapiens_gencode28	hg_gen28	Homo sapiens (genocode 28)	/data2/indices/bowtie/transcriptome/homo_sapiens_gencode28/homo_sapiens_gencode28_transcriptome
-mus_musculus_m28	m28	Mus musculus (m28)	/data2/indices/bowtie/transcriptome/mus_musculus_m28/mus_musculus_m28_transcriptome
-mus_musculus_m10	m10	Mus musculus (m10)	/data2/indices/bowtie/transcriptome/mus_musculus_m10/mus_musculus_m10_transcriptome
-drosophila_melanogaster_dm3	dm3	Drosophila melanogaster (dm3)	/data2/indices/bowtie/transcriptome/drosophila_melanogater_dm3/drosophila_melanogater_dm3_transcriptome
-drosophila_melanogaster_dm6	dm6	Drosophila melanogaster (dm6)	/data2/indices/bowtie/transcriptome/drosophila_melanogater_dm6/drosophila_melanogater_dm6_transcriptome
-sacCer_9	sacCer9	Saccharomyces cerevisiae (v9)	/data2/indices/bowtie/transcriptome/sacCer_9/sacCer_9_transcriptome
-sarCer_3	sacCer3	Saccharomyces cerevisiae (v3)	/data2/indices/bowtie/transcriptome/sacCer_3/sacCer_3_transcriptome
-E_coli_K12_MG1655	e_coli	Escherichia coli (K12 MG1655)	/data2/indices/bowtie/transcriptome/E_coli_K12_MG1655/E_coli_K12_MG1655_transcriptome
-Arabidopsis	araThal	Arabidopsis thaliana (TAIR10)	/data2/indices/bowtie/transcriptome/Arabidopsis/Arabidopsis_transcriptome
diff -r d57209761277 -r f6ef1c85b045 bowtie_transcriptome_wrapper/tool-data/bowtie_transcriptome_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_transcriptome_wrapper/tool-data/bowtie_transcriptome_indexes.loc.sample	Fri May 13 09:53:29 2022 +0000
@@ -0,0 +1,10 @@
+homo_sapiens_gencode39	hg_gen39	Homo sapiens (gencode 39) Transcriptome	/data2/indices/bowtie/transcriptome/homo_sapiens_gencode39/homo_sapiens_gencode39_transcriptome
+homo_sapiens_gencode28	hg_gen28	Homo sapiens (gencode 28) Transcriptome	/data2/indices/bowtie/transcriptome/homo_sapiens_gencode28/homo_sapiens_gencode28_transcriptome
+mus_musculus_m28	m28	Mus musculus (m28) Transcriptome	/data2/indices/bowtie/transcriptome/mus_musculus_m28/mus_musculus_m28_transcriptome
+mus_musculus_m10	m10	Mus musculus (m10) Transcriptome	/data2/indices/bowtie/transcriptome/mus_musculus_m10/mus_musculus_m10_transcriptome
+drosophila_melanogaster_dm3	dm3	Drosophila melanogaster (dm3) Transcriptome	/data2/indices/bowtie/transcriptome/drosophila_melanogater_dm3/drosophila_melanogater_dm3_transcriptome
+drosophila_melanogaster_dm6	dm6	Drosophila melanogaster (dm6) Transcriptome	/data2/indices/bowtie/transcriptome/drosophila_melanogater_dm6/drosophila_melanogater_dm6_transcriptome
+sacCer_9	sacCer9	Saccharomyces cerevisiae (v9) Transcriptome	/data2/indices/bowtie/transcriptome/sacCer_9/sacCer_9_transcriptome
+sarCer_3	sacCer3	Saccharomyces cerevisiae (v3) Transcriptome	/data2/indices/bowtie/transcriptome/sacCer_3/sacCer_3_transcriptome
+E_coli_K12_MG1655	e_coli	Escherichia coli (K12 MG1655) Transcriptome	/data2/indices/bowtie/transcriptome/E_coli_K12_MG1655/E_coli_K12_MG1655_transcriptome
+Arabidopsis	araThal	Arabidopsis thaliana (TAIR10) Transcriptome	/data2/indices/bowtie/transcriptome/Arabidopsis/Arabidopsis_transcriptome
diff -r d57209761277 -r f6ef1c85b045 bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample
--- a/bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample	Fri Apr 22 11:08:21 2022 +0000
+++ b/bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample	Fri May 13 09:53:29 2022 +0000
@@ -3,6 +3,6 @@
     <!-- Locations of indexes in the Bowtie mapper format -->
     <table name="bowtie_transcriptome_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices.loc" />
+        <file path="tool-data/bowtie_transcriptome_indexes.loc" />
     </table>
 </tables>