--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmsearch.xml.orig	Tue Aug 31 08:40:07 2021 +0000
@@ -0,0 +1,102 @@
+<?xml version="1.0"?>
+<<<<<<< HEAD
+<tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy1">
+  <description>search profile(s) against a sequence database</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+@ADDTHREADS@
+=======
+<tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@">
+    <description>search profile(s) against a sequence database</description>
+    <expand macro="bio_tools"/>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+>>>>>>> c37d72558 (add more bio.tool IDs)
+hmmsearch
+
+@OFORMAT_WITH_OPTS@
+@THRESHOLDS@
+@CUT@
+@ACCEL_HEUR@
+@ADV_OPTS@
+@CPU@
+@SEED@
+
+'$hmmfile'
+'$seqdb'
+> '$output'
+  ]]></command>
+  <inputs>
+    <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_dom_pfam"/>
+    <expand macro="thresholds_xml"/>
+    <expand macro="cut"/>
+    <expand macro="accel_heur_xml"/>
+    <expand macro="adv_opts"/>
+    <expand macro="seed"/>
+  </inputs>
+  <outputs>
+    <expand macro="output_dom_pfam" tool="PHMMER"/>
+  </outputs>
+  <tests>
+    <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">
+          <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[
+@HELP_PRE@
+
+hmmsearch is used to search one or more profiles against a sequence database.
+For each profile in <hmmfile>, use that query profile to search the target
+database of sequences in <seqdb>, and output ranked lists of the sequences with
+the most significant matches to the profile. To build profiles from multiple
+alignments, see hmmbuild.
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_HELP@
+@THRESHOLDS_HELP@
+@CUT_HELP@
+@ACCEL_HEUR_HELP@
+@ADV_OPTS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+  ]]></help>
+  <expand macro="citation"/>
+</tool>