diff hmmbuild.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/hmmbuild.xml.orig	Tue Aug 31 08:43:59 2021 +0000
@@ -0,0 +1,114 @@
+<?xml version="1.0"?>
+<<<<<<< HEAD
+<tool id="hmmer_hmmbuild" name="hmmbuild" version="@TOOL_VERSION@+galaxy1">
+  <description>Build a profile HMM from an input multiple alignment</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+@ADDTHREADS@
+=======
+<tool id="hmmer_hmmbuild" name="hmmbuild" version="@TOOL_VERSION@">
+    <description>Build a profile HMM from an input multiple alignment</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)
+hmmbuild
+
+#if $hmmname:
+    -n '$hmmname'
+#end if
+
+@FORMAT_SELECTOR@
+@MCSS@
+@ARSWS@
+@AEEWS@
+@PRIOR@
+@HSSI@
+@EVAL_CALIB@
+
+@CPU@
+@SEED@
+
+@LENGTHS@
+#if str($maxinsertlen):
+    --maxinsertlen $maxinsertlen
+#end if
+
+'$hmmout'
+'$msafile'
+  ]]></command>
+  <inputs>
+    <expand macro="input_msa" />
+    <param name="hmmname" argument="-n" type="text" optional="true" label="Name for the HMM" />
+    <expand macro="format_selector"/>
+    <expand macro="mcss"/>
+    <expand macro="arsws"/>
+    <expand macro="aeews"/>
+    <expand macro="prior"/>
+    <expand macro="hssi"/>
+    <expand macro="eval_calib_xml"/>
+    <expand macro="seed"/>
+
+    <expand macro="lengths" />
+    <param argument="--maxinsertlen" type="integer" optional="true" label="Pretend all inserts are length &lt;= n" />
+  </inputs>
+  <outputs>
+    <data name="hmmout" format="hmm3" label="HMM profile from $msafile.name"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="msafile" value="globins4.sto"/>
+      <expand macro="seed_test" />
+      <output name="hmmout" file="globins4.hmm" compare="sim_size">
+          <assert_contents>
+              <has_line_matching expression="HMMER3/f.*"/>
+              <has_line_matching expression="ALPH  amino"/>
+              <has_line_matching expression="NSEQ  4"/>
+              <has_line_matching expression="//"/>
+          </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="msafile" value="MADE1.sto"/>
+      <param name="input_format_select" value="--dna"/>
+      <expand macro="seed_test" />
+      <output name="hmmout" file="MADE1.hmm" compare="sim_size">
+          <assert_contents>
+              <has_line_matching expression="HMMER3/f.*"/>
+              <has_line_matching expression="ALPH  DNA"/>
+              <has_line_matching expression="NSEQ  1997"/>
+              <has_line_matching expression="//"/>
+          </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+For each multiple sequence alignment in <msafile> build a profile HMM and save
+it to a new file <hmmfile out>.
+
+@HELP_PRE_OTH@
+
+@FORMAT_SELECTOR_HELP@
+@MCSS_HELP@
+@ARSWS_HELP@
+@AEEWS_HELP@
+@PRIOR_HELP@
+@HSSI_HELP@
+@EVAL_CALIB_HELP@
+@SEED_HELP@
+@LENGTHS_HELP@
+
+@ATTRIBUTION@
+  ]]></help>
+  <expand macro="citation"/>
+</tool>