diff emboss_epestfind.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_epestfind.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,58 @@
+<tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0.1">
+  <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' epestfind -sequence '$input1' -goutfile '$ofile2' -outfile '$ofile1' -window $window -order $order -potential $potential -poor $poor
+  -invalid $invalid -map $map -graph png -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="Sequence" />
+    <param name="window" type="integer" value="10" label="Minimal distance between positively charged amino acids" />
+    <param name="order" type="select" label="Sort by">
+      <option value="3">Score</option>
+      <option value="1">Length</option>
+      <option value="2">Position</option>
+    </param>
+    <param name="threshold" type="float" value="5.0" label="Threshold value to discriminate weak from potential PEST motifs" />
+    <param name="potential" type="select" label="Decide whether potential PEST motifs should be printed">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="poor" type="select" label="Decide whether poor PEST motifs should be printed">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="invalid" type="select" label="Decide whether invalid PEST motifs should be printed">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="map" type="select" label="Decide whether PEST motifs should be mapped to sequence">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="ofile2" format="png" />
+    <data name="ofile1" format="epestfind" />
+  </outputs>
+<!--    <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="window" value="10"/>
+      <param name="order" value="3"/>
+      <param name="threshold" value="5.0"/>
+      <param name="potential" value="yes"/>
+      <param name="poor" value="yes"/>
+      <param name="invalid" value="no"/>
+      <param name="map" value="yes"/>
+      <output name="ofile1" file="emboss_epestfind_out.epestfind"/>
+    </test>
+  </tests>  output file contains file location info  -->
+  <help>
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/epestfind.html
+  </help>
+  <expand macro="citations" />
+</tool>