--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nhmmscan.xml.orig	Tue Aug 31 08:45:19 2021 +0000
@@ -0,0 +1,113 @@
+<?xml version="1.0"?>
+<<<<<<< HEAD
+<tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@+galaxy1">
+  <description>search DNA sequence(s) against a DNA profile database</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+@ADDTHREADS@
+=======
+<tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@">
+    <description>search DNA sequence(s) against a DNA 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@
+nhmmscan
+
+@OFORMAT_WITH_OPTS@
+@THRESHOLDS_NODOM@
+@CUT@
+@ACCEL_HEUR@
+--B1 $B1
+--B2 $B2
+--B3 $B3
+
+@ADV_OPTS@
+@LENGTHS@
+@CPU@
+@SEED@
+
+'$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_dfam_alisc"/>
+    <expand macro="thresholds_nodom"/>
+    <expand macro="cut"/>
+    <expand macro="accel_heur_xml"/>
+
+    <param argument="--B1" type="integer" value="110" label="window length for biased-composition modifier (MSV)" />
+    <param argument="--B2" type="integer" value="240" label="window length for biased-composition modifier (Vit)" />
+    <param argument="--B3" type="integer" value="1000" label="window length for biased-composition modifier (Fwd)" />
+
+    <expand macro="adv_opts"/>
+    <expand macro="lengths"/>
+    <expand macro="seed"/>
+  </inputs>
+  <outputs>
+    <expand macro="output_dfam_alisc" tool="NHMMSCAN"/>
+  </outputs>
+  <tests>
+    <test expect_num_outputs="3">
+      <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.nhmmscan_out" lines_diff="12">
+          <expand macro="assert_out" tool="nhmmscan"/>
+      </output>
+      <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10">
+          <!-- nhmmscan reports as hmmscan https://github.com/EddyRivasLab/hmmer/issues/190 -->
+          <expand macro="assert_tblout" tool="hmmscan"/>
+      </output>
+      <output name="dfamtblout" file="MADE1.nhmmscan_out.dfamtblout">
+          <assert_contents>
+              <has_line_matching expression="# hit scores"/>
+          </assert_contents>
+      </output>
+      <!--not test because https://github.com/EddyRivasLab/hmmer/issues/190 <output name="aliscoresout" file="MADE1.nhmmscan_out.aliscoresout" lines_diff="10" />-->
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+nhmmscan is used to search nucleotide sequences against collections of
+nucleotide 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.
+
+The <seqfile> may contain more than one query sequence. It can be in FASTA
+format, or several other common sequence file formats (genbank, embl, and
+uniprot, among others), or in alignment file formats (stockholm, aligned fasta,
+and others). See the --qformat option for a complete list.
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_N_HELP@
+@THRESHOLDS_NODOM_HELP@
+@CUT_HELP@
+@ACCEL_HEUR_HELP@
+@BIAS_COMP_HELP@
+@ADV_OPTS_HELP@
+@LENGTHS_HELP@
+@SEED_HELP@
+
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation"/>
+</tool>