diff encyclopedia_searchtolib.xml @ 5:b9c8e02d1405 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"

--- a/encyclopedia_searchtolib.xml	Tue Jul 07 11:57:09 2020 -0400
+++ b/encyclopedia_searchtolib.xml	Wed Aug 19 08:40:05 2020 -0400
@@ -13,7 +13,7 @@
         for SCAN_FILE in `ls -1 inputs/*`; do 
         echo "\$SCAN_FILE" &&
         EncyclopeDIA -Djava.awt.headless=true -Xmx20g 
-        #if not $l
+        #if not $library
             -walnut
         #end if
         -i \$SCAN_FILE
@@ -30,7 +30,7 @@
         ; done && 
         for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done &&
         EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport
-        #if not $l
+        #if not $library
             -pecan
         #end if
         @SCAN_INPUTS@
@@ -114,6 +114,19 @@
         </data>
         -->
     </outputs>
+    <tests>
+        <test>
+            <param name="scan_inputs" ftype="mzml" value="BCS_hela_narrow_3_1.mzML,BCS_hela_narrow_3_2.mzML"/>
+            <param name="library" ftype="dlib" value="small_pan_human_library.dlib"/>
+            <param name="fasta" ftype="fasta" value="uniprot_human.fasta"/>
+            <param name="select_outputs" value="log,elib,features,results"/>
+            <output name="results" ftype="tabular">
+                <assert_contents>
+                    <has_text text="QDSAAVGFDYK"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help><![CDATA[
 
 **SearchToLIB**