--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmscan.xml.orig	Tue Aug 31 08:46:36 2021 +0000
@@ -0,0 +1,93 @@
+<?xml version="1.0"?>
+<<<<<<< HEAD
+<tool id="hmmer_hmmscan" name="hmmscan" version="@TOOL_VERSION@+galaxy1">
+  <description>search protein sequence(s) against a protein profile database</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+@ADDTHREADS@
+=======
+<tool id="hmmer_hmmscan" name="hmmscan" version="@TOOL_VERSION@">
+    <description>search protein sequence(s) against a protein profile 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)
+@INPUTHMMCHOICE@
+hmmscan
+
+@OFORMAT_WITH_OPTS@
+@THRESHOLDS@
+@CUT@
+@ACCEL_HEUR@
+@ADV_OPTS@
+@CPU@
+@SEED@
+
+'$input_hmm_filename'
+'$seqfile'
+> '$output'
+  ]]></command>
+  <inputs>
+    <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_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="HMMSCAN"/>
+  </outputs>
+  <tests>
+    <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">
+          <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[
+@HELP_PRE@
+
+hmmscan is used to search protein sequences against collections of protein
+profiles. For each sequence in <seqfile>, use that query sequence to search the
+target database of profiles in <hmmfile>, and output ranked lists of the profiles
+with the most significant matches to the sequence.
+
+@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>