diff jackhmmer.xml @ 5:5113c71c7031 draft

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

--- a/jackhmmer.xml	Mon Jun 11 15:51:14 2018 -0400
+++ b/jackhmmer.xml	Tue Jun 16 05:32:33 2020 -0400
@@ -9,7 +9,7 @@
   <command><![CDATA[
 jackhmmer
 -N $N
-@OFORMAT_WITH_OPTS_NOPFAM@
+@OFORMAT_WITH_OPTS@
 @HSSI@
 @THRESHOLDS@
 @ACCEL_HEUR@
@@ -31,7 +31,7 @@
     <!-- todo use Galaxy features like data libraries/data tables/??? -->
     <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
     <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
-    <expand macro="oformat_with_opts_nopfam"/>
+    <expand macro="oformat_with_opts_dom"/>
     <expand macro="hssi"/>
     <expand macro="thresholds_xml"/>
     <expand macro="accel_heur_xml"/>
@@ -43,23 +43,33 @@
     <expand macro="seed"/>
   </inputs>
   <outputs>
-    <data name="output" format="txt" label="JACKHMMER 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>
+    <expand macro="output_dom_pfam" tool="JACKHMMER"/>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="3">
       <param name="seqfile" value="uniprot_matches.fasta"/>
       <param name="seqdb" value="globins45.fa"/>
       <expand macro="oformat_test" />
       <expand macro="seed_test" />
-      <output name="output" file="jackhmmer.out" lines_diff="180"/>
-      <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10"/>
-      <output name="tblout" file="jackhmmer.tblout" lines_diff="10"/>
+      <output name="output" file="jackhmmer.out" lines_diff="180">
+          <expand macro="assert_out" tool="jackhmmer"/>
+      </output>
+      <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10">
+          <expand macro="assert_tblout" tool="jackhmmer"/>
+      </output>
+      <output name="tblout" file="jackhmmer.tblout" lines_diff="10">
+          <expand macro="assert_tblout" tool="jackhmmer"/>
+      </output>
+    </test>
+    <test expect_num_outputs="1">
+      <param name="seqfile" value="uniprot_matches.fasta"/>
+      <param name="seqdb" value="globins45.fa"/>
+      <expand macro="oformat_test" />
+      <param name="oformat" value=""/>
+      <expand macro="seed_test" />
+      <output name="output" file="jackhmmer.out" lines_diff="180">
+          <expand macro="assert_out" tool="jackhmmer"/>
+      </output>
     </test>
   </tests>
   <help><![CDATA[