diff macros.xml @ 5:b2453ee52845 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"

--- a/macros.xml	Mon Jun 11 15:51:03 2018 -0400
+++ b/macros.xml	Tue Jun 16 05:29:04 2020 -0400
@@ -6,7 +6,7 @@
       <yield/>
     </requirements>
   </xml>
-  <token name="@TOOL_VERSION@">3.2</token>
+  <token name="@TOOL_VERSION@">3.3</token>
   <xml name="stdio">
     <stdio>
       <!-- Anything other than zero is an error -->
@@ -114,83 +114,96 @@
     <param argument="--EfN" type="integer" min="1" value="200" label="Number of sequences for Forward exp tail tau fit" />
     <param argument="--Eft" type="float" min="0" max="1" value="0.04" label="tail mass for Forward exponential tail tau fit" />
   </xml>
-  <token name="@OFORMAT_WITH_OPTS_NOPFAM@">
-#if 'tblout' in str($oformat):
-    --tblout '$tblout'
-#end if
-
-#if 'domtblout' in str($oformat):
-    --domtblout '$domtblout'
+  <token name="@OFORMAT_WITH_OPTS@">
+#if $oformat:      
+    #for o in str($oformat).split(','):
+        --$o '$getVar($o, 'MISSING_OUTPUT'+$o)'
+    #end for
 #end if
-
-$acc $noali $notextw
-  </token>
-  <xml name="oformat_with_opts_nopfam">
-    <!-- Options directing output -->
-    <param name="oformat" multiple="true" display="checkboxes" label="Output Formats" type="select">
-      <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
-      <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
-    </param>
-    <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
-    <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
-    <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
-  </xml>
-  <token name="@OFORMAT_WITH_OPTS@">
-#if 'tblout' in str($oformat):
-    --tblout '$tblout'
-#end if
-
-#if 'domtblout' in str($oformat):
-    --domtblout '$domtblout'
-#end if
-
-#if 'pfamtblout' in str($oformat):
-    --pfamtblout '$pfamtblout'
-#end if
-
 $acc $noali $notextw
   </token>
   <xml name="oformat_with_opts">
     <!-- Options directing output -->
     <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats">
       <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
-      <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
-      <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>
+      <yield/>
     </param>
     <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
     <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
     <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
   </xml>
+
+  <xml name="oformat_with_opts_dom">
+    <expand macro="oformat_with_opts">
+      <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
+      <yield/>
+    </expand>
+  </xml>
+
+  <xml name="oformat_with_opts_dom_pfam">
+    <expand macro="oformat_with_opts_dom">
+      <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>
+    </expand>
+  </xml>  
+
+  <xml name="oformat_with_opts_dfam_alisc">
+    <!-- Options directing output -->
+    <expand macro="oformat_with_opts">
+      <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
+      <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option>
+    </expand>
+  </xml>
+
+  <xml name="output" token_tool="">
+    <data name="output" format="txt" label="@TOOL@ on ${on_string}"/>
+    <data name="tblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence hits from HMM matches">
+      <filter>oformat and 'tblout' in oformat</filter>
+    </data>
+    <yield/>
+  </xml>
+  <xml name="output_dom" token_tool="">
+    <expand macro="output" tool="@TOOL@">
+      <data name="domtblout" format="txt" label="@TOOL@ on ${on_string}: per-domain hits from HMM matches">
+        <filter>oformat and 'domtblout' in oformat</filter>
+      </data>
+    </expand>
+    <yield/>
+  </xml>
+  <xml name="output_dom_pfam" token_tool="">
+    <expand macro="output_dom" tool="@TOOL@">
+      <data name="pfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches">
+        <filter>oformat and 'pfamtblout' in oformat</filter>
+      </data>
+    </expand>
+  </xml>
+  <xml name="output_dfam_alisc" token_tool="" token_ofvar="seqfile" token_invar="seqdb">
+    <expand macro="output" tool="@TOOL@">
+      <data name="dfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches">
+        <filter>oformat and 'dfamtblout' in oformat</filter>
+      </data>
+      <data name="aliscoresout" format="txt" label="@TOOL@ on ${on_string}: scores for positional matches">
+        <filter>oformat and 'aliscoresout' in oformat</filter>
+      </data>
+    </expand>
+  </xml>
+
+  <xml name="assert_out" token_tool="">
+    <assert_contents>
+      <has_line_matching expression="# @TOOL@.*"/>
+      <has_line_matching expression="\[ok\]"/>
+    </assert_contents>
+  </xml> 
+
+  <xml name="assert_tblout" token_tool="">
+    <assert_contents>
+      <has_line_matching expression="# Program:         @TOOL@"/>
+      <has_line_matching expression="# \[ok\]"/>
+    </assert_contents>
+  </xml> 
+
   <xml name="oformat_test">
       <param name="notextw" value="true" />
   </xml>
-  <!-- TODO: tblout will match 'pfamtblout,dfamtblout' -->
-  <token name="@OFORMAT_WITH_OPTS_N@">
-#if 'tblout' in str($oformat):
-    --tblout '$tblout'
-#end if
-
-#if 'dfamtblout' in str($oformat):
-    --dfamtblout '$dfamtblout'
-#end if
-
-#if 'aliscoresout' in str($oformat):
-    --aliscoresout '$aliscoresout'
-#end if
-
-$acc $noali $notextw
-  </token>
-  <xml name="oformat_with_opts_n">
-    <!-- Options directing output -->
-    <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats">
-      <option value="tblout" selected="true">Table of hits (--tblout)</option>
-      <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
-      <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option>
-    </param>
-    <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
-    <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
-    <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
-  </xml>
   <token name="@HSSI@">
 #if $hssi.hssi_select == "singlemx":
     --popen $hssi.popen
@@ -1077,7 +1090,7 @@
     # Freely distributed under the GNU General Public License (GPLv3).
     # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
-The wrappers were written by Eric Rasche and is licensed under Apache2_. The
+The wrappers were written by the IUC and are licensed under Apache2_. The
 documentation is copied from the HMMER3 documentation.
 
 .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0