Mercurial > repos > iuc > hmmer_hmmsearch

diff hmmsearch.xml @ 5:b774ae8e1609 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 05:27:07 -0400
parents 6867ed975e25
children 192a5046d9a2
line wrap: on
line diff
--- a/hmmsearch.xml	Mon Jun 11 15:51:39 2018 -0400
+++ b/hmmsearch.xml	Tue Jun 16 05:27:07 2020 -0400
@@ -25,7 +25,7 @@
     <expand macro="input_hmm" />
     <!-- todo use Galaxy features like data libraries/data tables/??? -->
     <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/>
-    <expand macro="oformat_with_opts"/>
+    <expand macro="oformat_with_opts_dom_pfam"/>
     <expand macro="thresholds_xml"/>
     <expand macro="cut"/>
     <expand macro="accel_heur_xml"/>
@@ -33,27 +33,36 @@
     <expand macro="seed"/>
   </inputs>
   <outputs>
-    <data name="output" format="txt" label="HMM matches of $hmmfile.name in $seqdb.name"/>
-    <data name="tblout" format="txt" label="Table of per-sequence hits from HMM matches of $hmmfile.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 $hmmfile.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 $hmmfile.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="hmmfile" value="globins4.hmm"/>
       <param name="seqdb" value="uniprot_matches.fasta"/>
       <expand macro="oformat_test" />
       <expand macro="seed_test" />
-      <output name="output" file="uniprot_globins_match.out" lines_diff="20"/>
-      <output name="domtblout" file="globins.domtblout" lines_diff="14"/>
-      <output name="pfamtblout" file="globins.pfamtblout" lines_diff="10"/>
-      <output name="tblout" file="globins.tblout" lines_diff="14"/>
+      <output name="output" file="uniprot_globins_match.out" lines_diff="20">
+          <expand macro="assert_out" tool="hmmsearch"/>
+      </output>
+      <output name="domtblout" file="globins.domtblout" lines_diff="16">
+          <expand macro="assert_tblout" tool="hmmsearch"/>
+      </output>
+      <output name="pfamtblout" file="globins.pfamtblout" lines_diff="12">
+          <expand macro="assert_tblout" tool="hmmsearch"/>
+      </output>
+      <output name="tblout" file="globins.tblout" lines_diff="16">
+          <expand macro="assert_tblout" tool="hmmsearch"/>
+      </output>
+    </test>
+    <test expect_num_outputs="1">
+      <param name="hmmfile" value="globins4.hmm"/>
+      <param name="seqdb" value="uniprot_matches.fasta"/>
+      <expand macro="oformat_test" />
+      <param name="oformat" value=""/>
+      <expand macro="seed_test" />
+      <output name="output" file="uniprot_globins_match.out" lines_diff="20">
+          <expand macro="assert_out" tool="hmmsearch"/>
+      </output>
     </test>
   </tests>
   <help><![CDATA[