Mercurial > repos > iuc > hmmer_nhmmer

diff nhmmer.xml @ 5:b4fe2f703b4b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author iuc
date Tue, 16 Jun 2020 05:38:43 -0400
parents c8e81e43bff1
children 314b778b8ffa
line wrap: on
line diff
--- a/nhmmer.xml	Mon Jun 11 15:52:05 2018 -0400
+++ b/nhmmer.xml	Tue Jun 16 05:38:43 2020 -0400
@@ -9,7 +9,7 @@
   <command><![CDATA[
 nhmmer
 
-@OFORMAT_WITH_OPTS_N@
+@OFORMAT_WITH_OPTS@
 @HSSI@
 @THRESHOLDS_NODOM@
 @CUT@
@@ -27,7 +27,7 @@
   <inputs>
     <expand macro="input_hmm" />
     <param name="seqfile" type="data" format="fasta" label="Target sequence file"/>
-    <expand macro="oformat_with_opts_n"/>
+    <expand macro="oformat_with_opts_dfam_alisc"/>
     <expand macro="hssi"/>
     <expand macro="thresholds_nodom"/>
     <expand macro="cut" />
@@ -39,27 +39,37 @@
     <expand macro="seed"/>
   </inputs>
   <outputs>
-    <data format="txt" name="output" label="NHMMER search of $seqfile.name in $hmmfile.name"/>
-
-    <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name">
-      <filter>oformat and 'tblout' in oformat</filter>
-    </data>
-    <data format="txt" name="dfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name">
-      <filter>oformat and 'pfamtblout' in oformat</filter>
-    </data>
-    <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name">
-      <filter>oformat and 'aliscoresout' in oformat</filter>
-    </data>
+    <expand macro="output_dfam_alisc" tool="NHMMER"/>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="4">
       <param name="hmmfile" value="MADE1.hmm"/>
       <param name="seqfile" value="dna_target.fa"/>
       <expand macro="oformat_test" />
+      <param name="oformat" value="tblout,dfamtblout,aliscoresout"/>
       <expand macro="seed_test" />
-      <output name="output" file="nhmmer.out" lines_diff="10" />
-      <output name="tblout" file="nhmmer.out.tblout" lines_diff="10" />
-      <output name="dfamtblout" file="nhmmer.out.dfamtblout" lines_diff="10" />
+      <output name="output" file="nhmmer.out" lines_diff="16">
+        <expand macro="assert_out" tool="nhmmer"/>
+      </output>
+      <output name="tblout" file="nhmmer.out.tblout" lines_diff="12">
+        <expand macro="assert_tblout" tool="nhmmer"/>
+      </output>
+      <output name="aliscoresout" file="nhmmer.out.aliscoresout" lines_diff="10"/>
+      <output name="dfamtblout" file="nhmmer.out.dfamtblout" lines_diff="10">
+        <assert_contents>
+          <has_line_matching expression="# hit scores"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="1">
+      <param name="hmmfile" value="MADE1.hmm"/>
+      <param name="seqfile" value="dna_target.fa"/>
+      <expand macro="oformat_test" />
+      <param name="oformat" value=""/>
+      <expand macro="seed_test" />
+      <output name="output" file="nhmmer.out" lines_diff="16">
+        <expand macro="assert_out" tool="nhmmer"/>
+      </output>
     </test>
   </tests>
   <help><![CDATA[