Mercurial > repos > greg > vsnp_build_tables

changeset 1:b60858c3eb91 draft

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Uploaded
author greg
date Thu, 30 Apr 2020 15:31:55 -0400
parents 38a38babcb31
children 85384a9bfba2
files test-data/Mbovis-01D6_snps.fasta test-data/Mbovis-01D6_snps.newick test-data/Mbovis-01D_snps.fasta test-data/Mbovis-01D_snps.newick test-data/Mbovis-01_snps.fasta test-data/Mbovis-01_snps.newick vsnp_build_tables.py vsnp_build_tables.xml
diffstat 8 files changed, 15 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/Mbovis-01D6_snps.fasta	Tue Apr 21 10:00:22 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-(root,((((SRR1792271_zc,SRR1792272_zc),SRR1791772_zc),SRR8073662_zc),SRR1791698_zc_vcf),SRR1792265_zc);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01D6_snps.newick	Thu Apr 30 15:31:55 2020 -0400
@@ -0,0 +1,1 @@
+(root,((((SRR1792271_zc,SRR1792272_zc),SRR1791772_zc),SRR8073662_zc),SRR1791698_zc_vcf),SRR1792265_zc);
--- a/test-data/Mbovis-01D_snps.fasta	Tue Apr 21 10:00:22 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-(root,((((SRR1792271_zc,SRR1792272_zc),SRR1791772_zc),SRR8073662_zc),SRR1791698_zc_vcf),SRR1792265_zc);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01D_snps.newick	Thu Apr 30 15:31:55 2020 -0400
@@ -0,0 +1,1 @@
+(root,((((SRR1792271_zc,SRR1792272_zc),SRR1791772_zc),SRR8073662_zc),SRR1791698_zc_vcf),SRR1792265_zc);
--- a/test-data/Mbovis-01_snps.fasta	Tue Apr 21 10:00:22 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-(root,((((SRR1792271_zc,SRR1792272_zc),SRR1791772_zc),SRR8073662_zc),SRR1791698_zc_vcf),SRR1792265_zc);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mbovis-01_snps.newick	Thu Apr 30 15:31:55 2020 -0400
@@ -0,0 +1,1 @@
+(root,((((SRR1792271_zc,SRR1792272_zc),SRR1791772_zc),SRR8073662_zc),SRR1791698_zc_vcf),SRR1792265_zc);
--- a/vsnp_build_tables.py	Tue Apr 21 10:00:22 2020 -0400
+++ b/vsnp_build_tables.py	Thu Apr 30 15:31:55 2020 -0400
@@ -15,9 +15,10 @@
 # Maximum columns allowed in a LibreOffice
 # spreadsheet is 1024.  Excel allows for
 # 16,384 columns, but we'll set the lower
-# number as the maximum since Galaxy is
-# mostly run on Linux.
-MAXCOLS = 10000
+# number as the maximum.  Some browsers
+# (e.g., Firefox on Linux) are configured
+# to use LibreOffice for Excel spreadsheets.
+MAXCOLS = 1024
 OUTPUT_EXCEL_DIR = 'output_excel_dir'
 
 
@@ -245,7 +246,7 @@
             for line in fh:
                 line = re.sub('[:,]', '\n', line)
                 line = re.sub('[)(]', '', line)
-                line = re.sub('[0-9].*\.[0-9].*\n', '', line)
+                line = re.sub(r'[0-9].*\.[0-9].*\n', '', line)
                 line = re.sub('root\n', '', line)
         sample_order = line.split('\n')
         sample_order = list([_f for _f in sample_order if _f])
--- a/vsnp_build_tables.xml	Tue Apr 21 10:00:22 2020 -0400
+++ b/vsnp_build_tables.xml	Thu Apr 30 15:31:55 2020 -0400
@@ -20,21 +20,21 @@
     #for $i in $input_type_cond.input_avg_mq_json_collection:
         #set file_name = $i.file_name
         #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
-        ln -s $file_name $input_json_avg_mq_dir/$identifier &&
+        ln -s '$file_name' '$input_json_avg_mq_dir/$identifier' &&
     #end for
     #for $i in $input_type_cond.input_snps_json_collection:
         #set file_name = $i.file_name
         #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
-        ln -s $file_name $input_json_dir/$identifier &&
+        ln -s '$file_name' '$input_json_dir/$identifier' &&
     #end for
     #for $i in $input_type_cond.input_newick_collection:
         #set file_name = $i.file_name
         #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
-        ln -s $file_name $input_newick_dir/$identifier &&
+        ln -s '$file_name' '$input_newick_dir/$identifier' &&
     #end for
 #end if
 python '$__tool_directory__/vsnp_build_tables.py'
---processes $processes
+--processes \${GALAXY_SLOTS:-4}
 #if $input_type == "single":
     --input_avg_mq_json '$input_avg_mq_json'
     --input_snps_json '$input_snps_json'
@@ -107,7 +107,6 @@
             </when>
             <when value="no"/>
         </conditional>
-        <param name="processes" type="integer" min="1" max="20" value="8" label="Number of processes for job splitting"/>
     </inputs>
     <outputs>
         <collection name="excel" type="list">
@@ -136,9 +135,9 @@
             </param>
             <param name="input_newick_collection">
                 <collection type="list">
-                    <element name="Mbovis-01_snps.json" value="Mbovis-01_snps.json" dbkey="89"/>
-                    <element name="Mbovis-01D_snps.fasta" value="Mbovis-01D_snps.fasta" dbkey="89"/>
-                    <element name="Mbovis-01D6_snps.fasta" value="Mbovis-01D6_snps.fasta" dbkey="89"/>
+                    <element name="Mbovis-01_snps.newick" value="Mbovis-01_snps.newick" dbkey="89"/>
+                    <element name="Mbovis-01D_snps.newick" value="Mbovis-01D_snps.newick" dbkey="89"/>
+                    <element name="Mbovis-01D6_snps.newick" value="Mbovis-01D6_snps.newick" dbkey="89"/>
                 </collection>
             </param>
             <param name="input_avg_mq_json_collection">
@@ -190,7 +189,6 @@
 
  * **Choose the category for the files to be analyzed** -  select "Single files" or "Collections of files", then select the appropriate history items (single SNPs json, average MQ json and newick files, or collections of each) based on the selected option.
  * **Use Genbank file** - Select "yes" to annotate the tables using the information in the Genbank file.  Locally cached files, if available, provide the most widely used annotations, but more custom Genbank files can be chosen from the current history.
- * **Number of processes for job splitting** - Select the number of processes for splitting the job to shorten execution time.
     </help>
     <citations>
         <citation type="bibtex">