diff unafold.xml @ 1:37198dc9311c draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 3d01452f19416679047a05e4c0a05c15d11f34ea

--- a/unafold.xml	Tue Jun 16 11:21:12 2015 -0400
+++ b/unafold.xml	Wed Feb 24 11:46:54 2016 -0500
@@ -1,34 +1,54 @@
 <?xml version="1.0"?>
-<tool id="unafold" name="UNAFold" version="1.0.0">
+<tool id="unafold" name="UNAFold" version="1.1.0">
     <description>UNAFold RNA and DNA structure prediction</description>
-    
+
     <requirements>
         <requirement type="package" version="3.8">unafold</requirement>
     </requirements>
-    
+
     <stdio>
         <regex match="mv: cannot stat ..: No such file or directory" source="stderr" level="fatal" description="Could not find CT output file\n" />
     </stdio>
-    
+
     <version_command>UNAFold.pl --version</version_command>
-    
-    <command>
+
+    <command><![CDATA[
+        #if str($input_source.select_fasta) == "false"
+            echo ">Sequence"                      >  "input.fasta" &&
+            echo "${input_source.input_sequence}" >> "input.fasta" &&
+        #end if
+        
         UNAFold.pl
             -n $n.a
             -t $temp
-            
             #if $n.a == "DNA"
                 -N $sodium
                 -M $magnesium
             #end if
+            
+            #if str($input_source.select_fasta) == "false"
+                "input.fasta"
+            #else
+                "${input_source.input_file}"
+            #end if
+            &&
         
-        $input_file &amp;&amp;
-        output=\$(ls | grep &#92;.ct | sort -r | head -n 1) &amp;&amp;
+        output=\$(ls | grep \.ct | sort -r | head -n 1) &&
+        
         mv "\$output" "$output_ct"
-    </command>
-    
+    ]]></command>
+
     <inputs>
-        <param format="fasta" name="input_file" type="data" label="Input sequence (FASTA)"/>
+        <conditional name="input_source">
+            <param name="select_fasta" type="boolean" truevalue="true" falsevalue="false" label="Input from FASTA file" selected="false" />
+            
+            <when value="true">
+                <param format="fasta" name="input_file" type="data" label="Input sequence (FASTA)"/>
+            </when>
+            <when value="false">
+                <param name="input_sequence" type="text" label="Input sequence"/>
+            </when>
+        </conditional>
     
         <conditional name="n">
             <param name="a" type="select" label="Nucleic Acid Type">
@@ -46,55 +66,87 @@
         
         <param name="temp" type="integer" size="3" value="37" min="0" max="100" label="Temperature (&#176;C)"/>
     </inputs>
-    
+
     <outputs>
-        <data format="ct" name="output_ct" label="${tool.name} on ${input_file.hid}: ${input_file.name}"/>
+        <data format="ct" name="output_ct" label="${tool.name}"/>
     </outputs>
-    
+
     <tests>
         <test>
+            <param name="select_fasta" value="true" />
             <param name="input_file" value="test1_input.fa" ftype="fasta" />
             <param name="temp" value="37" />
             
             <output name="output_ct" file="test1_output.ct" />
         </test>
+        <test>
+            <param name="select_fasta" value="false" />
+            <param name="input_sequence" value="GGGGGaaaCCCCC" />
+            <param name="temp" value="37" />
+            
+            <output name="output_ct" file="test1_output.ct" lines_diff="2" /><!-- Sequence name (header) differs -->
+        </test>
     </tests>
 
-    <help>
-        Usage: UNAFold.pl [options] file [file]
+    <help><![CDATA[
+``Usage: UNAFold.pl [options] file [file]``
+
+``Options:``
+``-V, --version``
+
+``-h, --help``
+
+``-n, --NA=(RNA | DNA) (defaults to RNA)``
+
+``-t, --temp=<temperature> (defaults to 37)``
+
+``-N, --sodium=<[Na+] in M> (defaults to 1)``
+
+``-M, --magnesium=<[Mg++] in M> (defaults to 0)``
+
+``-p, --polymer``
+
+``-C, --Ct=<total strand concentration>``
+
+``-I, --noisolate``
+
+``-m, --maxbp=<maximum basepair distance>``
+
+``-c, --constraints=<name of constraints file> (defaults to prefix.aux)``
+
+``-P, --percent=<energy increment percent> (defaults to 5)``
+
+``-W, --window=<window size> (default set by sequence length)``
 
-        Options:
-        -V, --version
-        -h, --help
-        -n, --NA=(RNA | DNA) (defaults to RNA)
-        -t, --temp=&lt;temperature&gt; (defaults to 37)
-        -N, --sodium=&lt;[Na+] in M&gt; (defaults to 1)
-        -M, --magnesium=&lt;[Mg++] in M&gt; (defaults to 0)
-        -p, --polymer
-        -C, --Ct=&lt;total strand concentration&gt;
-        -I, --noisolate
-        -m, --maxbp=&lt;maximum basepair distance&gt;
-        -c, --constraints=&lt;name of constraints file&gt; (defaults to prefix.aux)
-        -P, --percent=&lt;energy increment percent&gt; (defaults to 5)
-        -W, --window=&lt;window size&gt; (default set by sequence length)
-        -X, --max=&lt;maximum number of foldings&gt; (defaults to 100)
-            --ann=(none | p-num | ss-count) (defaults to none)
-            --mode=(auto | bases | lines) (defaults to auto)
-            --label=&lt;base numbering frequency&gt;
-            --rotate=&lt;structure rotation angle&gt;
-            --run-type=(text | html) (defaults to text)
-            --model=(EM | PF) (defaults to EM)
-            --circular
-        Obscure options:
-            --allpairs
-            --maxloop=&lt;maximum bulge/interior loop size&gt; (defaults to 30)
-            --nodangle
-            --simple
-            --prefilter=&lt;filter value&gt;
+``-X, --max=<maximum number of foldings> (defaults to 100)``
+
+``--ann=(none | p-num | ss-count) (defaults to none)``
+
+``--mode=(auto | bases | lines) (defaults to auto)``
+
+``--label=<base numbering frequency>``
+
+``--rotate=<structure rotation angle>``
+
+``--run-type=(text | html) (defaults to text)``
+
+``--model=(EM | PF) (defaults to EM)``
 
-        Report bugs to [e-mail]
-    </help>
-    
+``--circular``
+
+``Obscure options:``
+
+``--allpairs``
+
+``--maxloop=<maximum bulge/interior loop size> (defaults to 30)``
+
+``--nodangle``
+
+``--simple``
+
+``--prefilter=<filter value>``
+    ]]></help>
+
     <citations>
         <citation type="doi">10.1007/978-1-60327-429-6_1</citation>
     </citations>