diff peptide_shaker.xml @ 33:bce45e9e6d70 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312

--- a/peptide_shaker.xml	Wed Jan 25 15:37:43 2017 -0500
+++ b/peptide_shaker.xml	Mon Feb 06 21:53:07 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.14.6">
     <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="1.13.6">peptide-shaker</requirement>
+        <requirement type="package" version="1.14.6">peptide-shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -82,7 +82,7 @@
             (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
                 --exec_dir="\$cwd/${bin_dir}"
                 -in \$cwd/peptideshaker_output.zip
-                -output_file output.mzid
+                -output_file \$cwd/output.mzid
                 #if $contact_options.contact_options_selector == "yes":
                     -contact_first_name "$contact_options.contact_first_name"
                     -contact_last_name "$contact_options.contact_last_name"
@@ -337,7 +337,7 @@
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="no"/>
             <param name="outputs" value="zip,3"/>
-            <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="900" />
+            <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
             <output name="output_psm">
                 <assert_contents>
                     <has_text text="cds.comp41779_c0_seq1" />
@@ -358,7 +358,7 @@
             </output>
             <output name="output_hierarchical">
                 <assert_contents>
-                    <has_text_matching expression="1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2" />
+                    <has_text_matching expression="1.1\tcds.comp" />
                 </assert_contents>
             </output>
             <output name="output_psm">