diff fasta_merge_files_and_filter_unique_sequences.xml @ 2:379c41d859aa draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences commit 240d1baaa04767c7d6ad6e36c854c2b54093e92f

--- a/fasta_merge_files_and_filter_unique_sequences.xml	Fri Dec 16 05:19:27 2016 -0500
+++ b/fasta_merge_files_and_filter_unique_sequences.xml	Wed Feb 01 13:24:16 2017 -0500
@@ -5,13 +5,17 @@
     </requirements>
     <command>
         python '$__tool_directory__/fasta_merge_files_and_filter_unique_sequences.py'
-        '$output'
+        '$output' $uniqueness_criterion
         #for $input in $inputs:
             '$input'
         #end for
     </command>
     <inputs>
         <param name="inputs" format="fasta" multiple="True" type="data" label="Input FASTA files"/>
+        <param name="uniqueness_criterion" type="select" label="How are sequences judged to be unique?">
+            <option value="sequence" selected="true">Accession and Sequence</option>
+            <option value="accession">Accession Only</option>
+        </param>
     </inputs>
     <outputs>
         <data format="fasta" name="output" label="Merged and Filtered FASTA from ${on_string}"/>
@@ -19,7 +23,21 @@
     <tests>
         <test>
           <param name="inputs" value="1.fa,2.fa" ftype="fasta" />
-          <output name="output" file="res.fa" ftype="fasta" />
+          <param name="uniqueness_criterion" value="sequence" />
+          <output name="output" file="res-sequence.fa" ftype="fasta" />
+          <assert_stdout>
+            <has_line line="Skipping protein '&gt;one_2' with duplicate sequence (first seen as '&gt;one')" />
+            <has_line line="Skipping protein '&gt;two_2' with duplicate sequence (first seen as '&gt;two')" />
+            <has_line line="Skipping protein '&gt;three_2' with duplicate header" />
+          </assert_stdout>
+        </test>
+        <test>
+          <param name="inputs" value="1.fa,2.fa" ftype="fasta" />
+          <param name="uniqueness_criterion" value="accession" />
+          <output name="output" file="res-accession.fa" ftype="fasta" />
+          <assert_stdout>
+            <has_line line="Skipping protein '&gt;three_2' with duplicate header" />
+          </assert_stdout>
         </test>
     </tests>
     <help>
@@ -27,7 +45,11 @@
 **What it does**
 
 Concatenate FASTA database files together.
-Only first appearence of each unique sequence will appear in output.
+
+If the uniqueness criterion is "Accession and Sequence", only the first appearence of each unique sequence will appear in the output.
+Otherwise, duplicate sequences are allowed, but only the first appearance of each accession will appear in the output.
+
+In the context of this script, the accession is the entire header line.
 
 ------