Reduce whitespace in <command> tag (there are OS limits on command line length)

tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml

@@ -1,20 +1,21 @@
 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.1">
     <description>Search nucleotide database with nucleotide query sequence(s)</description>
     <command>
-      blastn
-       -query "$query"
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+blastn -query "$query"
 #if $db_opts.db_opts_selector == "db":
-       -db "$db_opts.database"
+  -db "$db_opts.database"
 #else:
-       -subject "$db_opts.subject"
+  -subject "$db_opts.subject"
 #end if
-       -task $blast_type
-       -evalue $evalue_cutoff
-       $adv_opts.filter_query
-       $adv_opts.strand
-       -out $output1
-       -outfmt $out_format
-       -num_threads 8
+-task $blast_type
+-evalue $evalue_cutoff
+$adv_opts.filter_query
+$adv_opts.strand
+-out $output1
+-outfmt $out_format
+-num_threads 8
     </command>
     <inputs>
         <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 

tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml

@@ -1,20 +1,22 @@
 <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.1">
     <description>Search protein database with protein query sequence(s)</description>
     <command>
-      blastp
-       -query "$query"
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+blastp
+-query "$query"
 #if $db_opts.db_opts_selector == "db":
-       -db "$db_opts.database"
+  -db "$db_opts.database"
 #else:
-       -subject "$db_opts.subject"
+  -subject "$db_opts.subject"
 #end if
-       -task $blast_type
-       -evalue $evalue_cutoff
-       $adv_opts.filter_query
-       $adv_opts.matrix
-       -out $output1
-       -outfmt $out_format
-       -num_threads 8
+-task $blast_type
+-evalue $evalue_cutoff
+$adv_opts.filter_query
+$adv_opts.matrix
+-out $output1
+-outfmt $out_format
+-num_threads 8
     </command>
     <inputs>
         <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 

tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml

@@ -1,20 +1,22 @@
 <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.1">
     <description>Search protein database with translated nucleotide query sequence(s)</description>
     <command>
-      blastx
-       -query "$query"
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+blastx
+-query "$query"
 #if $db_opts.db_opts_selector == "db":
-       -db "$db_opts.database"
+  -db "$db_opts.database"
 #else:
-       -subject "$db_opts.subject"
+  -subject "$db_opts.subject"
 #end if
-       -evalue $evalue_cutoff
-       $adv_opts.filter_query
-       $adv_opts.strand
-       $adv_opts.matrix
-       -out $output1
-       -outfmt $out_format
-       -num_threads 8
+-evalue $evalue_cutoff
+$adv_opts.filter_query
+$adv_opts.strand
+$adv_opts.matrix
+-out $output1
+-outfmt $out_format
+-num_threads 8
     </command>
     <inputs>
         <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 

tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml

@@ -1,19 +1,21 @@
 <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.1">
     <description>Search translated nucleotide database with protein query sequence(s)</description>
     <command>
-      tblastn
-       -query "$query"
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+tblastn
+-query "$query"
 #if $db_opts.db_opts_selector == "db":
-       -db "$db_opts.database"
+  -db "$db_opts.database"
 #else:
-       -subject "$db_opts.subject"
+  -subject "$db_opts.subject"
 #end if
-       -evalue $evalue_cutoff
-       $adv_opts.filter_query
-       $adv_opts.matrix
-       -out $output1
-       -outfmt $out_format
-       -num_threads 8
+-evalue $evalue_cutoff
+$adv_opts.filter_query
+$adv_opts.matrix
+-out $output1
+-outfmt $out_format
+-num_threads 8
     </command>
     <inputs>
         <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 

tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml

@@ -1,20 +1,22 @@
 <tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.1">
     <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
     <command>
-      tblastx
-       -query "$query"
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+tblastx
+-query "$query"
 #if $db_opts.db_opts_selector == "db":
-       -db "$db_opts.database"
+  -db "$db_opts.database"
 #else:
-       -subject "$db_opts.subject"
+  -subject "$db_opts.subject"
 #end if
-       -evalue $evalue_cutoff
-       $adv_opts.filter_query
-       $adv_opts.strand
-       $adv_opts.matrix
-       -out $output1
-       -outfmt $out_format
-       -num_threads 8
+-evalue $evalue_cutoff
+$adv_opts.filter_query
+$adv_opts.strand
+$adv_opts.matrix
+-out $output1
+-outfmt $out_format
+-num_threads 8
     </command>
     <inputs>
         <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>