diff encyclopedia_library_to_blib.xml @ 0:d37d900794f6 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/encyclopedia_library_to_blib.xml	Fri Jun 19 14:03:15 2020 +0000
@@ -0,0 +1,40 @@
+<tool id="encyclopedia_library_to_blib" name="ConvertLibraryToBlib" version="@VERSION@.0" python_template_version="3.5">
+    <description>Convert EncyclopeDIA Library to BLIB for Skyline</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        EncyclopeDIA -convert -libtoblib
+        -i '$i'
+        -o '$output'
+        #if $istest == 'yes'
+        && sqlite3 -readonly '$output' 'SELECT distinct peptideSeq FROM RefSpectra;' > '$test_output'
+        #end if
+    ]]></command>
+    <inputs>
+        <param argument="-i" type="data" format="elib,dlib" label="Library: Chromatagram .ELIB or Spectrum .DLIB"/>
+        <param name="istest" type="hidden" value="no"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="blib" label="${i.name} blib"/>
+        <data name="test_output" format="txt" >
+            <filter>istest == 'yes'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="i" ftype="dlib" value="PrositLib.dlib"/>
+            <param name="istest" value="yes"/>
+            <output name="test_output" ftype="txt">
+                <assert_contents>
+                    <has_text text="AGGVLHDDENLWSFGK"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Convert EncyclopeDIA Library to BLIB for Skyline.
+    ]]></help>
+    <expand macro="citations" />
+</tool>