Mercurial > repos > jjohnson > encyclopedia_encyclopedia

diff encyclopedia_encyclopedia.xml @ 5:aeda6093dd40 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
author jjohnson
date Wed, 19 Aug 2020 08:35:54 -0400
parents e191adb34d04
children 61692bb2c78f
line wrap: on
line diff
--- a/encyclopedia_encyclopedia.xml	Tue Jul 07 11:55:15 2020 -0400
+++ b/encyclopedia_encyclopedia.xml	Wed Aug 19 08:35:54 2020 -0400
@@ -29,15 +29,15 @@
         <param name="select_outputs" type="select" label="Select outputs" multiple="true">
             <option value="log" selected="true">log</option>
             <option value="elib" selected="true">elib</option>
-            <option value="first_delta_rt_pdf" selected="true">encyclopedia.txt.first.delta_rt.pdf</option>
-            <option value="first_rt_fit_pdf" selected="true">encyclopedia.txt.first.rt_fit.pdf</option>
-            <option value="first_rt_fit_txt" selected="true">encyclopedia.txt.first.rt_fit.txt</option>
-            <option value="final_delta_rt_pdf" selected="true">encyclopedia.txt.final.delta_rt.pdf</option>
-            <option value="final_rt_fit_pdf" selected="true">encyclopedia.txt.final.rt_fit.pdf</option>
-            <option value="final_rt_fit_txt" selected="true">encyclopedia.txt.final.rt_fit.txt</option>
+            <option value="first_delta_rt_pdf" selected="false">encyclopedia.txt.first.delta_rt.pdf</option>
+            <option value="first_rt_fit_pdf" selected="false">encyclopedia.txt.first.rt_fit.pdf</option>
+            <option value="first_rt_fit_txt" selected="false">encyclopedia.txt.first.rt_fit.txt</option>
+            <option value="final_delta_rt_pdf" selected="false">encyclopedia.txt.final.delta_rt.pdf</option>
+            <option value="final_rt_fit_pdf" selected="false">encyclopedia.txt.final.rt_fit.pdf</option>
+            <option value="final_rt_fit_txt" selected="false">encyclopedia.txt.final.rt_fit.txt</option>
             <option value="features" selected="true">features.txt</option>
             <option value="encyclopedia" selected="true">encyclopedia.txt</option>
-            <option value="encyclopedia_decoy" selected="true">encyclopedia.decoy.txt</option>
+            <option value="encyclopedia_decoy" selected="false">encyclopedia.decoy.txt</option>
         </param>
     </inputs>
     <outputs>
@@ -90,6 +90,24 @@
             </actions>
         </data>
     </outputs>
+    <tests>
+        <test>
+            <param name="scan_input" ftype="mzml" value="BCS_hela_wide_500_900_1.mzML"/>
+            <param name="library" ftype="elib" value="BCS_hela.elib"/>
+            <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
+            <output name="features" ftype="tabular">
+                <assert_contents>
+                    <has_text text="ESYDDVSSFR"/>
+                </assert_contents>
+            </output>
+            <output name="encyclopedia" ftype="tabular">
+                <assert_contents>
+                    <has_text text="ESYDDVSSFR"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
     <help><![CDATA[
 **EncyclopeDIA**
 
@@ -112,6 +130,7 @@
 
   - A log file
   - The identified features in tabular format 
+  - The identified proteins in tabular format 
 
     ]]></help>
     <expand macro="citations" />