diff example2.xml @ 0:47e1dc8b27f8 draft

Uploaded example2 first

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+++ b/example2.xml	Wed Dec 02 22:49:57 2015 -0500
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+<tool id="formatplotfasta" name="Adjust fasta line length and plot content" version="0.0.1" force_history_refresh="True">
+  
+  <description>Change the number of nucleotides per line in the input fasta and plot nt content </description>
+  
+  <requirements>
+      <requirement type="package" version="1.4"> matplotlib </requirement>
+  </requirements>
+
+  <command interpreter="python"> example2.py "${infasta}" $linesize $formatted_fasta $plot </command>
+  
+  <inputs>
+    <param name="infasta" format="fasta" type="data" label="input fasta" help="no help"/>
+    <param name="linesize" type="integer" value="50" label="number of nt per line" help=" be reasonable!"/>
+  </inputs>
+
+  <outputs>
+    <data name="formatted_fasta" format="fasta" label="${tool.name} on ${on_string}: formatted fasta"/>
+    <data name="plot" format="pdf" label="${tool.name} on ${on_string}: plot"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="infasta" value="mouse_reference_mtDNA.fasta"/>
+      <param name="linesize" value="200"/>
+      <output name="formatted_fasta" file="adjusted_200_mouse_reference_mtDNA.fasta"/>
+      <output name="plot" file="mouse_reference_mtDNA.fasta_nt_counts.pdf"/>
+    </test>
+  </tests>
+
+  <help>
+    
+<![CDATA[
+Short description.
+
+-----
+
+.. class:: infomark
+
+**What it does**
+
+Longer description. 
+
+-----
+
+.. class:: warningmark
+
+**Note**
+
+Some warining, if needed:
+
+-----
+
+.. class:: infomark
+
+**Formats**
+
+**FASTA multiple alignment** 
+
+See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format
+
+-----
+
+**Example**
+
+
+-----
+
+**Citation**
+
+(boris-at-bx.psu.edu) ]]>
+
+  </help>
+</tool>
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