diff nhmmer.xml.orig @ 11:405dd85a9408 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nhmmer.xml.orig	Tue Aug 31 08:43:59 2021 +0000
@@ -0,0 +1,115 @@
+<?xml version="1.0"?>
+<<<<<<< HEAD
+<tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@+galaxy1">
+  <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+@ADDTHREADS@
+=======
+<tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@">
+    <description>search a DNA model or alignment against a DNA database (BLASTN-like)</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)
+nhmmer
+
+@OFORMAT_WITH_OPTS@
+@HSSI@
+@THRESHOLDS_NODOM@
+@CUT@
+@ACCEL_HEUR@
+@FORMAT_SELECTOR@
+@ADV_OPTS@
+@LENGTHS@
+@CPU@
+@SEED@
+
+'$hmmfile'
+'$seqfile'
+> '$output'
+  ]]></command>
+  <inputs>
+    <expand macro="input_hmm" />
+    <param name="seqfile" type="data" format="fasta" label="Target sequence file"/>
+    <expand macro="oformat_with_opts_dfam_alisc"/>
+    <expand macro="hssi"/>
+    <expand macro="thresholds_nodom"/>
+    <expand macro="cut" />
+    <expand macro="accel_heur_xml"/>
+    <expand macro="format_selector_noprot"/>
+    <expand macro="adv_opts"/>
+    <expand macro="lengths"/>
+    <!-- TODO: block_length toponly bottomonly -->
+    <expand macro="seed"/>
+  </inputs>
+  <outputs>
+    <expand macro="output_dfam_alisc" tool="NHMMER"/>
+  </outputs>
+  <tests>
+    <test expect_num_outputs="4">
+      <param name="hmmfile" value="MADE1.hmm"/>
+      <param name="seqfile" value="dna_target.fa"/>
+      <expand macro="oformat_test" />
+      <param name="oformat" value="tblout,dfamtblout,aliscoresout"/>
+      <expand macro="seed_test" />
+      <output name="output" file="nhmmer.out" lines_diff="16">
+        <expand macro="assert_out" tool="nhmmer"/>
+      </output>
+      <output name="tblout" file="nhmmer.out.tblout" lines_diff="12">
+        <expand macro="assert_tblout" tool="nhmmer"/>
+      </output>
+      <output name="aliscoresout" file="nhmmer.out.aliscoresout" lines_diff="10"/>
+      <output name="dfamtblout" file="nhmmer.out.dfamtblout" lines_diff="10">
+        <assert_contents>
+          <has_line_matching expression="# hit scores"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="1">
+      <param name="hmmfile" value="MADE1.hmm"/>
+      <param name="seqfile" value="dna_target.fa"/>
+      <expand macro="oformat_test" />
+      <param name="oformat" value=""/>
+      <expand macro="seed_test" />
+      <output name="output" file="nhmmer.out" lines_diff="16">
+        <expand macro="assert_out" tool="nhmmer"/>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+nhmmer is used to search one or more nucleotide queries against a nucleotide
+sequence database. For each query in <queryfile>, use that query to search the
+target database of sequences in <seqdb>, and output a ranked list of the hits
+with the most significant matches to the query. A query may be either a profile
+model built using hmmbuild, a sequence alignment, or a single sequence.
+Sequence based queries can be in a number of formats (see --qformat), and can
+typically be autodetected. Note that only Stockholm format supports the use of
+multiple sequence-based queries.
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_N_HELP@
+@HSSI_HELP@
+@THRESHOLDS_NODOM_HELP@
+@CUT_HELP@
+@ACCEL_HEUR_HELP@
+@FORMAT_SELECTOR_HELP@
+@ADV_OPTS_HELP@
+@LENGTHS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+  ]]></help>
+  <expand macro="citation"/>
+</tool>