diff hmmscan.xml @ 3:1a83249ddfff draft

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

--- a/hmmscan.xml	Wed Apr 04 14:02:12 2018 -0400
+++ b/hmmscan.xml	Sat Apr 07 03:51:55 2018 -0400
@@ -1,17 +1,13 @@
 <?xml version="1.0"?>
-<tool id="hmmer_hmmscan" name="hmmscan" version="@WRAPPER_VERSION@.1">
-  <description>search sequence(s) against a profile database</description>
+<tool id="hmmer_hmmscan" name="hmmscan" version="@TOOL_VERSION@">
+  <description>search protein sequence(s) against a protein profile database</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
   <command><![CDATA[
-#if $input_hmm_conditional.input_hmm_source == "history":
-    ## "Press" database
-    hmmpress '$input_hmm_conditional.hmmfile' &&
-#end if
-## Scan
+@INPUTHMMCHOICE@
 hmmscan
 
 @OFORMAT_WITH_OPTS@
@@ -22,14 +18,10 @@
 @CPU@
 @SEED@
 
-@INPUTHMMCHOICE@
+'$input_hmm_filename'
 '$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>
+  ]]></command>
   <inputs>
     <expand macro="input_hmm_choice" />
     <!-- todo use Galaxy features like data libraries/data tables/??? -->
@@ -42,15 +34,15 @@
     <expand macro="seed"/>
   </inputs>
   <outputs>
-    <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 name="output" format="txt" label="HMM matches of $seqfile.name against the profile database"/>
+    <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $seqfile.name against the profile database">
+      <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 against the profile database">
-      <filter>'domtblout' in oformat</filter>
+    <data name="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name against the profile database">
+      <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 against the profile database">
-      <filter>'pfamtblout' in oformat</filter>
+    <data name="pfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database">
+      <filter>oformat and 'pfamtblout' in oformat</filter>
     </data>
   </outputs>
   <tests>
@@ -61,9 +53,9 @@
       <expand macro="oformat_test" />
       <expand macro="seed_test" />
       <output name="output" file="MADE1.out" lines_diff="24"/>
-      <output name="tblout" file="MADE1.out.tblout" lines_diff="20"/>
-      <output name="domtblout" file="MADE1.out.domtblout" lines_diff="20"/>
-      <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="20"/>
+      <output name="tblout" file="MADE1.out.tblout" lines_diff="14"/>
+      <output name="domtblout" file="MADE1.out.domtblout" lines_diff="10"/>
+      <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="10"/>
     </test>
   </tests>
   <help><![CDATA[
@@ -84,6 +76,6 @@
 @SEED_HELP@
 
 @ATTRIBUTION@
-]]></help>
+  ]]></help>
   <expand macro="citation"/>
 </tool>