diff phmmer.xml @ 3:ff6e24314c63 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6

--- a/phmmer.xml	Wed Apr 04 13:59:18 2018 -0400
+++ b/phmmer.xml	Sat Apr 07 03:48:11 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hmmer_phmmer" name="phmmer" version="@WRAPPER_VERSION@.0">
+<tool id="hmmer_phmmer" name="phmmer" version="@TOOL_VERSION@">
   <description>search a protein sequence against a protein database (BLASTP-like)</description>
   <macros>
     <import>macros.xml</import>
@@ -19,10 +19,10 @@
 @CPU@
 @SEED@
 
-$seqfile
-$seqdb
-> $output
-      ]]></command>
+'$seqfile'
+'$seqdb'
+> '$output'
+  ]]></command>
   <inputs>
     <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
     <!-- todo use Galaxy features like data libraries/data tables/??? -->
@@ -36,14 +36,14 @@
     <expand macro="seed"/>
   </inputs>
   <outputs>
-    <data format="txt" name="output" label="PHMMER search of $seqfile.name in $seqdb.name"/>
-    <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
+    <data name="output" format="txt" label="PHMMER search of $seqfile.name in $seqdb.name"/>
+    <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
       <filter>oformat and 'tblout' in oformat</filter>
     </data>
-    <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
+    <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
       <filter>oformat and 'domtblout' in oformat</filter>
     </data>
-    <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
+    <data name="pfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
       <filter>oformat and 'pfamtblout' in oformat</filter>
     </data>
   </outputs>
@@ -80,6 +80,6 @@
 @SEED_HELP@
 
 @ATTRIBUTION@
-]]></help>
+  ]]></help>
   <expand macro="citation"/>
 </tool>