diff peptide_shaker.xml @ 21:dfaea053e32f draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c

--- a/peptide_shaker.xml	Sun May 31 09:05:57 2015 -0400
+++ b/peptide_shaker.xml	Tue Jun 16 23:43:39 2015 -0400
@@ -1,13 +1,13 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="0.38.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="0.40.0">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
-    <requirements>
-        <requirement type="package" version="0.38">peptide_shaker</requirement>
-    </requirements>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <requirements>
+        <requirement type="package" version="0.40">peptide_shaker</requirement>
+    </requirements>
     <expand macro="stdio" />
     <command>
 <![CDATA[
@@ -161,7 +161,7 @@
 ]]>
     </command>
     <inputs>
-        <param name="searchgui_input" format="searchgui_zip" type="data" label="Compressed SearchGUI results"
+        <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
             help="SearchGUI Results from History"/>
 
         <conditional name="species_type">
@@ -545,7 +545,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/>
+            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
             <param name="species_type_selector" value="no_species_type"/>
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="no"/>
@@ -555,13 +555,13 @@
             <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" />
         </test>
         <test>
-            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/>
+            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
             <param name="species_type_selector" value="no_species_type"/>
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="yes"/>
             <param name="min_peptide_length" value="1"/>
             <param name="outputs" value="0,1,2,3,4,5,6,7"/>
-            <output name="output_certificate" file="peptide_shaker_certificate_result2.tabular" ftype="tabular" lines_diff="4"/>
+            <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/>
             <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" />
             <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" />
             <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" />
@@ -571,7 +571,7 @@
             <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" />
         </test>
         <test>
-            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/>
+            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
             <param name="species_type_selector" value="Vertebrates"/>
             <param name="species" value="Human (Homo sapiens)"/>
             <param name="processing_options_selector" value="no"/>