diff peptide_shaker.xml @ 10:9d12b1d3c4ef draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 04b529c9366e6b77f45bfaa44c1a7fac5772f5b9

--- a/peptide_shaker.xml	Thu Jun 04 12:10:51 2015 -0400
+++ b/peptide_shaker.xml	Mon Jun 08 19:54:30 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="0.39.0">
+<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>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.39">peptide_shaker</requirement>
+        <requirement type="package" version="0.40">peptide_shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -561,7 +561,7 @@
             <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" />