diff hmmemit.xml @ 3:7b7ff4d209f7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6

--- a/hmmemit.xml	Wed Apr 04 14:00:58 2018 -0400
+++ b/hmmemit.xml	Sat Apr 07 03:50:15 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hmmer_hmmemit" name="hmmemit" version="@WRAPPER_VERSION@.0">
+<tool id="hmmer_hmmemit" name="hmmemit" version="@TOOL_VERSION@">
   <description>sample sequence(s) from a profile HMM</description>
   <macros>
     <import>macros.xml</import>
@@ -23,18 +23,17 @@
 #else:
     -N $oformat.N_smp
     -p
-    #if $oformat.L:
+    #if str($oformat.L):
         -L $oformat.L
     #end if
     $oformat.emission_profiles
 #end if
 
-
 @SEED@
 
-$hmmfile
-> $output
-      ]]></command>
+'$hmmfile'
+> '$output'
+  ]]></command>
   <inputs>
     <expand macro="input_hmm" />
 
@@ -47,25 +46,24 @@
             <option value="sample">Sample sequences from profile, not core model</option>
         </param>
         <when value="fasta">
-            <param name="N_fa" type="integer" value="1" min="1" help="(-N)"
+            <param name="N_fa" argument="-N" type="integer" min="1" value="1"
                 label="Number of sequences to generate"/>
         </when>
         <when value="aln">
-            <param name="N_aln" type="integer" value="1" min="1" help="(-N)"
+            <param name="N_aln" argument="-N" type="integer" min="1" value="1"
                 label="Number of sequences to generate"/>
         </when>
-        <when value="mrcs">
-        </when>
+        <when value="mrcs" />
         <when value="mrcsf">
-            <param name="minl" type="float" value="0.7" help="(--minl)"
+            <param argument="--minl" type="float" value="0.7"
                 label="show consensus as 'any' (X/N) unless >= this fraction"/>
-            <param name="minu" type="float" value="0.2" help="(--minu)"
+            <param argument="--minu" type="float" value="0.2"
                 label="show consensus as upper case if >= this fraction"/>
         </when>
         <when value="sample">
-            <param name="N_smp" type="integer" value="1" min="1" help="(-N)"
+            <param name="N_smp" argument="-N" type="integer" min="1" value="1"
                 label="Number of sequences to generate"/>
-            <param name="L" type="integer" optional="True" help="(-L)"
+            <param argument="-L" type="integer" optional="true"
                 label="Expected length of profile"/>
 
             <param name="emission_profiles" type="select" label="Emission profile options">
@@ -81,7 +79,7 @@
     <expand macro="seed"/>
   </inputs>
   <outputs>
-    <data format="fasta" name="output" label="Sequences generated from $hmmfile.name">
+    <data name="output" format="fasta" label="Sequences generated from $hmmfile.name">
       <change_format>
         <when input="oformat_select" value="aln" format="stockholm"/>
         <!-- the rest are fasta -->
@@ -170,6 +168,6 @@
 mode, and the target sequence length is configured for L=400.
 
 @ATTRIBUTION@
-]]></help>
+  ]]></help>
   <expand macro="citation"/>
 </tool>