diff vsnp_build_tables.xml @ 1:b60858c3eb91 draft

Uploaded

--- 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">