diff peptide_shaker.xml @ 26:3ef5a7dd1a36 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty

--- a/peptide_shaker.xml	Sun Feb 21 11:13:24 2016 -0500
+++ b/peptide_shaker.xml	Tue May 10 06:33:08 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.1.1">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.10.0">
     <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="1.1">peptide_shaker</requirement>
+        <requirement type="package" version="1.10">peptide_shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -47,9 +47,9 @@
 
             ##Optional processing parameters:
             #if $processing_options.processing_options_selector == "yes"
-                -protein_FDR "${processing_options.protein_fdr}"
-                -peptide_FDR "${processing_options.peptide_fdr}"
-                -psm_FDR "${processing_options.psm_fdr}"
+                -protein_fdr "${processing_options.protein_fdr}"
+                -peptide_fdr "${processing_options.peptide_fdr}"
+                -psm_fdr "${processing_options.psm_fdr}"
                 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
                 #if $processing_options.ptm_score.ptm_score_selector == 1
                     -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
@@ -62,10 +62,10 @@
 
            ##Optional filtering parameters:
             #if $filtering_options.filtering_options_selector == "yes":
-                -min_peptide_length "${filtering_options.min_peptide_length}"
-                -max_peptide_length "${filtering_options.max_peptide_length}"
-                -max_precursor_error "${filtering_options.max_precursor_error}"
-                -max_precursor_error_type "${filtering_options.max_precursor_error_type}"
+                -import_peptide_length_min "${filtering_options.min_peptide_length}"
+                -import_peptide_length_max "${filtering_options.max_peptide_length}"
+                -import_precurosor_mz "${filtering_options.max_precursor_error}"
+                -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
                 ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
                 ##-max_omssa_e "${filtering_options.max_omssa_e}"
                 ##-max_mascot_e "${filtering_options.max_mascot_e}"
@@ -493,8 +493,8 @@
                 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10"
                     help="Next option specifies units (Da or ppm)" />
                 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
-                    <option value="0">ppm</option>
-                    <option value="1">Daltons</option>
+                    <option value="1">ppm</option>
+                    <option value="0">Daltons</option>
                 </param>
                 <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /-->
                 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->