Mercurial > repos > iuc > hmmer_hmmscan

diff hmmscan.xml @ 5:be7097d6e3ff 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 05:34:25 -0400
parents 1a83249ddfff
children d92dd2f040cd
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line diff
--- a/hmmscan.xml	Mon Jun 11 15:52:41 2018 -0400
+++ b/hmmscan.xml	Tue Jun 16 05:34:25 2020 -0400
@@ -26,7 +26,7 @@
     <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"/>
+    <expand macro="oformat_with_opts_dom_pfam"/>
     <expand macro="thresholds_xml"/>
     <expand macro="cut"/>
     <expand macro="accel_heur_xml"/>
@@ -34,28 +34,27 @@
     <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="domtblout" format="txt" label="Table of per-domain hits from HMM matches of $seqfile.name against the profile database">
-      <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 against the profile database">
-      <filter>oformat and 'pfamtblout' in oformat</filter>
-    </data>
+    <expand macro="output_dom_pfam" tool="HMMSCAN"/>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="4">
       <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.out" lines_diff="24"/>
-      <output name="tblout" file="MADE1.out.tblout" lines_diff="14"/>
-      <output name="domtblout" file="MADE1.out.domtblout" lines_diff="10"/>
-      <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="10"/>
+      <output name="output" file="MADE1.out" lines_diff="24">
+          <expand macro="assert_out" tool="hmmscan"/>
+      </output>
+      <output name="tblout" file="MADE1.out.tblout" lines_diff="14">
+          <expand macro="assert_tblout" tool="hmmscan"/>
+      </output>
+      <output name="domtblout" file="MADE1.out.domtblout" lines_diff="10">
+          <expand macro="assert_tblout" tool="hmmscan"/>
+      </output>
+      <output name="pfamtblout" file="MADE1.out.pfamtblout" lines_diff="10">
+          <expand macro="assert_tblout" tool="hmmscan"/>
+      </output>
     </test>
   </tests>
   <help><![CDATA[