diff hmmscan.xml @ 1:b49a4465041d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde

--- a/hmmscan.xml	Sat Jun 25 15:06:16 2016 -0400
+++ b/hmmscan.xml	Mon Nov 14 15:11:16 2016 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hmmer_hmmscan" name="hmmscan" version="@WRAPPER_VERSION@.0">
+<tool id="hmmer_hmmscan" name="hmmscan" version="@WRAPPER_VERSION@.1">
   <description>search sequence(s) against a profile database</description>
   <macros>
     <import>macros.xml</import>
@@ -7,8 +7,10 @@
   <expand macro="requirements"/>
   <expand macro="stdio"/>
   <command><![CDATA[
-## "Press" database
-hmmpress $hmmfile;
+#if $input_hmm_conditional.input_hmm_source == "history":
+    ## "Press" database
+    hmmpress '$input_hmm_conditional.hmmfile' &&
+#end if
 ## Scan
 hmmscan
 
@@ -20,14 +22,16 @@
 @CPU@
 @SEED@
 
-$hmmfile
-$seqfile
-> $output;
-## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype
-rm ${hmmfile}.h3m ${hmmfile}.h3i ${hmmfile}.h3f ${hmmfile}.h3p;
+@INPUTHMMCHOICE@
+'$seqfile'
+> '$output'
+#if $input_hmm_conditional.input_hmm_source == "history":
+    ## Remove pressed database. Eventually will be replaced with a dedicated tool/datatype
+    && rm '${input_hmm_conditional.hmmfile}.h3m' '${input_hmm_conditional.hmmfile}.h3i' '${input_hmm_conditional.hmmfile}.h3f' '${input_hmm_conditional.hmmfile}.h3p';
+#end if
       ]]></command>
   <inputs>
-    <expand macro="input_hmm" />
+    <expand macro="input_hmm_choice" />
     <!-- todo use Galaxy features like data libraries/data tables/??? -->
     <param name="seqfile" type="data" format="fasta" label="Sequence file"/>
     <expand macro="oformat_with_opts"/>
@@ -38,20 +42,21 @@
     <expand macro="seed"/>
   </inputs>
   <outputs>
-    <data format="txt" name="output" label="HMM matches of $seqfile.name in $hmmfile.name"/>
-    <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name">
+    <data format="txt" name="output" label="HMM matches of $seqfile.name against the profile database"/>
+    <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database">
       <filter>'tblout' in oformat</filter>
     </data>
-    <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
+    <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name against the profile database">
       <filter>'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 $hmmfile.name">
+    <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database">
       <filter>'pfamtblout' in oformat</filter>
     </data>
   </outputs>
   <tests>
     <test>
-      <param name="hmmfile" value="MADE1.hmm"/>
+      <param name="input_hmm_conditional|input_hmm_source" value="history"/>
+      <param name="input_hmm_conditional|hmmfile" value="MADE1.hmm"/>
       <param name="seqfile" value="dna_target.fa"/>
       <expand macro="oformat_test" />
       <expand macro="seed_test" />