diff diamond_makedb.xml @ 1:df7738595640 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e

--- a/diamond_makedb.xml	Sun Feb 08 10:05:26 2015 -0500
+++ b/diamond_makedb.xml	Mon Feb 06 07:08:25 2017 -0500
@@ -1,32 +1,38 @@
-<tool id="bg_diamond_makedb" name="Diamond makedb" version="0.6.13">
+<tool id="bg_diamond_makedb" name="Diamond makedb" version="@VERSION@">
     <description>Build database from a FASTA file</description>
-    <requirements>
-        <requirement type="package" version="0.6.13">diamond</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+
     <command>
     <!-- DB has two files, *.dmnd and *.tx -->
 <![CDATA[
-    diamond makedb 
+    diamond makedb
         --threads "\${GALAXY_SLOTS:-12}"
-        --in $infile
+        --in '$infile'
         --db ./database
-    &&
-    mv ./database.dmnd $outfile
 ]]>
     </command>
+
     <inputs>
         <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
     </inputs>
 
     <outputs>
-        <data format="diamond_database" name="outfile" label="Diamond database ${on_string}"/>
+        <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/>
     </outputs>
+
     <tests>
         <test>
-            <param name="infile" value="protein.fasta" ftype="fasta"/>
-            <output name="outfile" file="diamond_makedb_result1.dmnd" ftpye="diamond_database"/>
+            <param name="infile" value="db.fasta" ftype="fasta"/>
+            <output name="outfile" value="db.dmnd"/>
         </test>
     </tests>
+
     <help>
 <![CDATA[
 
@@ -36,7 +42,7 @@
 
 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
-about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500
+about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND is about 2,500
 times faster than BLASTX, finding more than 94% of all matches.
 
 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
@@ -44,7 +50,6 @@
 
 ]]>
     </help>
-    <citations>
-        <citation type="doi">10.1038/nmeth.3176</citation>
-    </citations>
+
+    <expand macro="citations" />
 </tool>