diff phmmer.xml @ 5:c1de05e20868 draft

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

--- a/phmmer.xml	Mon Jun 11 15:50:40 2018 -0400
+++ b/phmmer.xml	Tue Jun 16 05:34:01 2020 -0400
@@ -27,7 +27,7 @@
     <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
     <!-- todo use Galaxy features like data libraries/data tables/??? -->
     <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
-    <expand macro="oformat_with_opts"/>
+    <expand macro="oformat_with_opts_dom_pfam"/>
     <expand macro="hssi"/>
     <expand macro="thresholds_xml"/>
     <expand macro="accel_heur_xml"/>
@@ -36,28 +36,37 @@
     <expand macro="seed"/>
   </inputs>
   <outputs>
-    <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 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 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>
+    <expand macro="output_dom_pfam" tool="PHMMER"/>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="4">
       <param name="seqfile" value="globins45.fa"/>
       <param name="seqdb" value="uniprot_matches.fasta"/>
       <expand macro="oformat_test" />
       <expand macro="seed_test" />
-      <output name="output" file="phmmer.out" lines_diff="200"/>
+      <output name="output" file="phmmer.out" lines_diff="200">
+          <expand macro="assert_out" tool="phmmer"/>
+      </output>
       <!-- Lines diff is high due to a line of cpu/timing information for EACH sequence -->
-      <output name="domtblout" file="phmmer.domtblout" lines_diff="10"/>
-      <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="10"/>
-      <output name="tblout" file="phmmer.tblout" lines_diff="10"/>
+      <output name="domtblout" file="phmmer.domtblout" lines_diff="12">
+          <expand macro="assert_tblout" tool="phmmer"/>
+      </output>
+      <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="12">
+          <expand macro="assert_tblout" tool="phmmer"/>
+      </output>
+      <output name="tblout" file="phmmer.tblout" lines_diff="12">
+          <expand macro="assert_tblout" tool="phmmer"/>
+      </output>
+    </test>
+    <test expect_num_outputs="1">
+      <param name="seqfile" value="globins45.fa"/>
+      <param name="seqdb" value="uniprot_matches.fasta"/>
+      <expand macro="oformat_test" />
+      <param name="oformat" value=""/>
+      <expand macro="seed_test" />
+      <output name="output" file="phmmer.out" lines_diff="200">
+          <expand macro="assert_out" tool="phmmer"/>
+      </output>
     </test>
   </tests>
   <help><![CDATA[