diff nhmmscan.xml @ 4:2d406da5d34e draft

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

--- a/nhmmscan.xml	Mon Jun 11 15:51:28 2018 -0400
+++ b/nhmmscan.xml	Tue Jun 16 05:31:13 2020 -0400
@@ -10,7 +10,7 @@
 @INPUTHMMCHOICE@
 nhmmscan
 
-@OFORMAT_WITH_OPTS_N@
+@OFORMAT_WITH_OPTS@
 @THRESHOLDS_NODOM@
 @CUT@
 @ACCEL_HEUR@
@@ -31,7 +31,7 @@
     <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_n"/>
+    <expand macro="oformat_with_opts_dfam_alisc"/>
     <expand macro="thresholds_nodom"/>
     <expand macro="cut"/>
     <expand macro="accel_heur_xml"/>
@@ -45,29 +45,28 @@
     <expand macro="seed"/>
   </inputs>
   <outputs>
-    <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 name="dfamtblout" format="txt" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name against the profile database">
-      <filter>oformat and 'dfamtblout' in oformat</filter>
-    </data>
-    <data name="aliscoresout" format="txt" label="Scores for positional matches of $seqfile.name against the profile database">
-      <filter>oformat and 'aliscoresout' in oformat</filter>
-    </data>
+    <expand macro="output_dfam_alisc" tool="NHMMSCAN"/>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="3">
       <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" />
-      <output name="output" file="MADE1.nhmmscan_out" lines_diff="12" />
-      <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10" />
-      <output name="dfamtblout" file="MADE1.nhmmscan_out.dfamtblout" />
-      <output name="aliscoresout" file="MADE1.nhmmscan_out.aliscoresout" lines_diff="10" />
+      <output name="output" file="MADE1.nhmmscan_out" lines_diff="12">
+          <expand macro="assert_out" tool="nhmmscan"/>
+      </output>
+      <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10">
+          <!-- nhmmscan reports as hmmscan https://github.com/EddyRivasLab/hmmer/issues/190 -->
+          <expand macro="assert_tblout" tool="hmmscan"/>
+      </output>
+      <output name="dfamtblout" file="MADE1.nhmmscan_out.dfamtblout">
+          <assert_contents>
+              <has_line_matching expression="# hit scores"/>
+          </assert_contents>
+      </output>
+      <!--not test because https://github.com/EddyRivasLab/hmmer/issues/190 <output name="aliscoresout" file="MADE1.nhmmscan_out.aliscoresout" lines_diff="10" />-->
     </test>
   </tests>
   <help><![CDATA[