diff tools/ncbi_blast_plus/ncbi_makeblastdb.xml @ 15:c16c30e9ad5b draft

Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)

--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Mon Dec 01 05:59:16 2014 -0500
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Sun Jul 05 10:37:27 2015 -0400
@@ -1,16 +1,16 @@
-<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.01">
+<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.03">
     <description>Make BLAST database</description>
     <macros>
         <token name="@BINARY@">makeblastdb</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command interpreter="python">check_no_duplicates.py
 ##First check for duplicates (since BLAST+ 2.2.28 fails to do so)
 ##and abort (via the ampersand ampersand trick) if any are found.
 #for i in $input_file#"${i}" #end for#
 &amp;&amp;
-makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}"
+makeblastdb -out "${os.path.join($outfile.files_path,'blastdb')}"
 $parse_seqids
 $hash_index
 ## Single call to -in with multiple filenames space separated with outer quotes
@@ -47,7 +47,6 @@
 ## Capture the stdout log information to the primary file (plain text):
 &gt; "$outfile"
     </command>
-    <expand macro="stdio" />
     <inputs>
         <param name="dbtype" type="select" display="radio" label="Molecule type of input">
             <option value="prot">protein</option>
@@ -97,6 +96,7 @@
     </outputs>
     <tests>
         <!-- Note the (two line) PIN file is not reproducible run to run.
+             The same applies to the NIN file for nucleotide database.
              Likewise there is a datestamp in the log file as well, so use contains comparison
              With and without the masking makes no difference.
              With and without the taxid the only real difference is in the *.phr file.
@@ -155,6 +155,25 @@
                 <extra_files type="file" value="four_human_proteins.fasta.psi" name="blastdb.psi" />
             </output>
         </test>
+        <test>
+            <param name="dbtype" value="nucl" />
+            <param name="input_file" value="three_human_mRNA.fasta" ftype="fasta" />
+            <param name="title" value="Just 3 human mRNA sequences" />
+            <param name="parse_seqids" value="" />
+            <param name="hash_index" value="true" />
+            <param name="taxselect" value="id" />
+            <param name="taxid" value="9606" />
+            <output name="out_file" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn">
+                <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" />
+                <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" lines_diff="2" />
+                <extra_files type="file" value="three_human_mRNA.fasta.nsq" name="blastdb.nsq" />
+                <extra_files type="file" value="three_human_mRNA.fasta.nog" name="blastdb.nog" />
+                <extra_files type="file" value="three_human_mRNA.fasta.nhd" name="blastdb.nhd" />
+                <extra_files type="file" value="three_human_mRNA.fasta.nhi" name="blastdb.nhi" />
+                <extra_files type="file" value="three_human_mRNA.fasta.nsd" name="blastdb.nsd" />
+                <extra_files type="file" value="three_human_mRNA.fasta.nsi" name="blastdb.nsi" />
+            </output>
+        </test>
     </tests>
     <help>
 **What it does**