diff idconvert.xml @ 2:edb33e8224c6 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292

--- a/idconvert.xml	Mon Aug 08 10:43:52 2016 -0400
+++ b/idconvert.xml	Sat Feb 23 06:21:11 2019 -0500
@@ -1,9 +1,8 @@
 <tool id="idconvert" name="idconvert" version="@VERSION@.0">
     <description>Convert mass spectrometry identification files</description>
-    <macros>
-        <import>msconvert_macros.xml</import>
-    </macros>
-    <expand macro="generic_requirements" />
+    <requirements>
+      <requirement type="package" version="3.0.9992">proteowizard</requirement>
+    </requirements>
     <stdio>
         <exit_code range="1:" />
         <regex match="Error"
@@ -15,15 +14,15 @@
 <![CDATA[
 #import os.path
 #set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')])
-ln -s "$from.input" "$input_name" &&
-idconvert $input_name 
+ln -s '$from.input' '$input_name' &&
+idconvert '$input_name'
 #if str($to_format) == 'pep.xml':
 --pepXML
 #elif str($to_format) == 'text':
 --text
 #end if
---outdir outdir 
-&& cp outdir/* $output
+--outdir 'outdir'
+&& cp outdir/* '$output'
 ]]>
     </command>
     <inputs> 
@@ -49,40 +48,40 @@
             <option value="pep.xml">pepXML (pepxml)</option>
             <option value="text">text</option>
         </param>
-  </inputs>
-  <outputs>
-      <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}">
-        <change_format>
-          <when input="to_format" value="pep.xml" format="pepxml" />
-          <when input="to_format" value="text" format="txt" />
-        </change_format>
-      </data>
-  </outputs>
-  <tests>
-      <test>
-          <param name="input" value="Rpal_01.pepXML" />
-          <param name="from_format" value="pepxml" />
-          <param name="to_format" value="mzid" />
-          <output name="output_psms">
-              <assert_contents>
-                  <has_text text="MzIdentML" />
-                  <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
-              </assert_contents>
-          </output>
-      </test>
-      <test>
-          <param name="input" value="Rpal_01.mzid" />
-          <param name="from_format" value="mzid" />
-          <param name="to_format" value="pep.xml" />
-          <output name="output_psms">
-              <assert_contents>
-                  <has_text text="msms_pipeline_analysis" />
-                  <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
-              </assert_contents>
-          </output>
-      </test>
-  </tests>
-  <help>
+    </inputs>
+    <outputs>
+        <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}">
+            <change_format>
+                <when input="to_format" value="pep.xml" format="pepxml" />
+                <when input="to_format" value="text" format="txt" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="Rpal_01.pepXML" />
+            <param name="from_format" value="pepxml" />
+            <param name="to_format" value="mzid" />
+            <output name="output">
+                <assert_contents>
+                    <has_text text="MzIdentML" />
+                    <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="Rpal_01.mzid" />
+            <param name="from_format" value="mzid" />
+            <param name="to_format" value="pep.xml" />
+            <output name="output">
+                <assert_contents>
+                    <has_text text="msms_pipeline_analysis" />
+                    <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
 <![CDATA[
 idconvert [options] [filemasks]
 Convert mass spec identification file formats.
@@ -118,6 +117,8 @@
 idconvert mascot.mzid --pepXML
 
 ]]>
-  </help>
-  <expand macro="citations" />
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btn323</citation>
+    </citations>
 </tool>