diff encyclopedia_prosit_csv_to_library.xml @ 0:8a9cef108b0c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/encyclopedia_prosit_csv_to_library.xml	Mon Sep 14 17:06:37 2020 +0000
@@ -0,0 +1,44 @@
+<tool id="encyclopedia_prosit_csv_to_library" name="ConvertPrositCSVToLibrary" version="@VERSION@.0" python_template_version="3.5">
+    <description>Convert Prosit/Spectronaut CSV to EncyclopeDIA DLIB library</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+        EncyclopeDIA -convert -prositcsvtolibrary
+        -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
+        -i '$i'
+        -f '$f'
+        -o '$output'
+        #if $istest == 'yes'
+        && sqlite3 -readonly '$output' 'select distinct ProteinAccession from peptidetoprotein;' > '$test_output'
+        #end if
+    ]]></command>
+    <inputs>
+        <param argument="-i" type="data" format="csv" label="Prosit output csv file"/>
+        <param argument="-f" type="data" format="fasta" label="Protein Fasta database"/>
+        <param name="istest" type="hidden" value="no"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="dlib" label="${i.name} DLIB"/>
+        <data name="test_output" format="txt" >
+            <filter>istest == 'yes'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="i" ftype="csv" value="PrositLib.csv"/>
+            <param name="f" ftype="fasta" value="YeastProteinFasta5.fasta"/>
+            <param name="istest" value="yes"/>
+            <output name="test_output" ftype="txt">
+                <assert_contents>
+                    <has_text text="PCL1_YEAST"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Convert Prosit/Spectronaut CSV to library DLIB
+    ]]></help>
+    <expand macro="citations" />
+</tool>