# HG changeset patch
# User galaxyp
# Date 1485376651 18000
# Node ID ba5377754cce39af87655de65dbe3a5aa350d870
# Parent  515c835c2f077a8ec357043b44fdf5c0c64f78b7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d

diff -r 515c835c2f07 -r ba5377754cce macros.xml
--- a/macros.xml	Wed Jan 18 16:43:30 2017 -0500
+++ b/macros.xml	Wed Jan 25 15:37:31 2017 -0500
@@ -16,6 +16,8 @@
             ### multiple enzymes?
             -enzyme "${enzyme}"
             ### -specificity
+            ### value per enzyme
+            -mc $missed_cleavages
             #set $fixed_mods_str = $fixed_modifications or ''
             #set $variable_mods_str = $variable_modifications or ''
             #if $fixed_mods_str
@@ -26,10 +28,11 @@
             #end if
             -min_charge $min_charge
             -max_charge $max_charge
-            ### value per enzyme
-            -mc $missed_cleavages
             -fi $forward_ion
             -ri $reverse_ion
+            -min_isotope ${min_isotope} 
+            -max_isotope ${max_isotope} 
+
     </token>
     <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
     <token name="@SEARCHGUI_VERSION@">3.1.4</token>
@@ -106,6 +109,8 @@
             <option value="y" selected="true">y</option>
             <option value="z">z</option>
         </param>
+        <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
+        <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
     </xml>
 
     <xml name="citations">
diff -r 515c835c2f07 -r ba5377754cce peptide_shaker.xml
--- a/peptide_shaker.xml	Wed Jan 18 16:43:30 2017 -0500
+++ b/peptide_shaker.xml	Wed Jan 25 15:37:31 2017 -0500
@@ -337,8 +337,12 @@
             <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="600" />
-            <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" />
+            <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="900" />
+            <output name="output_psm">
+                <assert_contents>
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
@@ -346,14 +350,53 @@
             <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.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" />
-            <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" />
-            <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" />
-            <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" />
-            <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" />
+            <output name="output_certificate">
+                <assert_contents>
+                    <has_text text="Tolerance: 100" />
+                    <has_text text="Carbamidomethylation of C" />
+                </assert_contents>
+            </output>
+            <output name="output_hierarchical">
+                <assert_contents>
+                    <has_text_matching expression="1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2" />
+                </assert_contents>
+            </output>
+            <output name="output_psm">
+                <assert_contents>
+                    <not_has_text text="Phosphosite" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+            <output name="output_psm_phosphorylation">
+                <assert_contents>
+                    <has_text text="Phosphosite" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+            <output name="output_peptides">
+                <assert_contents>
+                    <has_text text="Modification" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+            <output name="output_peptides_phosphorylation">
+                <assert_contents>
+                    <has_text text="Phosphosite" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+            <output name="output_proteins">
+                <assert_contents>
+                    <has_text text="Modification" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+            <output name="output_proteins_phosphorylation">
+                <assert_contents>
+                    <has_text text="Phosphosite" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>
diff -r 515c835c2f07 -r ba5377754cce searchgui.xml
--- a/searchgui.xml	Wed Jan 18 16:43:30 2017 -0500
+++ b/searchgui.xml	Wed Jan 25 15:37:31 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
@@ -101,9 +101,7 @@
                 -omssa_remove_prec ${omssa.remove_precursor}
                 -omssa_scale_prec ${omssa.scale_precursor}
                 -omssa_estimate_charge ${omssa.estimate_charge}
-
                 -omssa_memory ${omssa.omssa_memory}
-                ## -omssa_isotopes ${omssa.omssa_isotopes} 
                 -omssa_neutron ${omssa.omssa_neutron} 
                 -omssa_low_intensity "${omssa.omssa_low_intensity}" 
                 -omssa_high_intensity ${omssa.omssa_high_intensity} 
@@ -148,8 +146,6 @@
                 -msgf_protocol ${msgf.msgf_protocol} 
                 -msgf_num_matches ${msgf.msgf_num_matches} 
                 -msgf_additional ${msgf.msgf_additional} 
-                -msgf_isotope_low ${msgf.msgf_isotope_low} 
-                -msgf_isotope_high ${msgf.msgf_isotope_high} 
             #end if
             
             #* Not working in tests
@@ -168,8 +164,6 @@
                 -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
                 -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass}
                 -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass}
-                -myrimatch_isotope_low ${myrimatch.myrimatch_isotope_low}
-                -myrimatch_isotope_high ${myrimatch.myrimatch_isotope_high}
                 -myrimatch_num_matches ${myrimatch.myrimatch_num_matches}
                 -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms}
                 -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation}
@@ -581,9 +575,7 @@
                 
                 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
                     label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
-                  <!-- param name="omssa_isotopes" type="integer" value="0" 
-                      label="OMSSA: Number of Isotopes" help="Number of isotopes to use (integer), 0 implies monoisotopic (default)" / -->
-                   <param name="omssa_neutron" type="float" value="1446.94" 
+                <param name="omssa_neutron" type="float" value="1446.94" 
                        label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
                 <param name="omssa_low_intensity" type="float" value="0.0" 
                     label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
@@ -712,8 +704,6 @@
                     <option value="0" selected="True">output basic scores only</option>
                     <option value="1" >output additional features</option>
                 </param>
-                <param name="msgf_isotope_low" label="MSGF: Lower Isotope Error Range" type="integer" value="0" help="Lower isotope error range" />
-                <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" /> 
             </when>
         </conditional>
 
@@ -864,10 +854,6 @@
                     label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" />
                 <param name="myrimatch_max_prec_mass"  type="float" value="10000.0"
                     label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" />
-                <param name="myrimatch_isotope_low"  type="integer" value="-1"
-                    label="MyriMatch: Lower Isotope Error Range" help="Lower isotope error ragne" />
-                <param name="myrimatch_isotope_high"  type="integer" value="2"
-                    label="MyriMatch: Upper Isotope Error Range" help="Upper isotope error range" />
                 <param name="myrimatch_num_matches"  type="integer" value="10"
                     label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
                 <param name="myrimatch_num_ptms"  type="integer" value="2"
@@ -1099,7 +1085,6 @@
             <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
             <param name="xtandem.xtandem_advanced" value="yes"/>
             <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
-
             <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> 
         </test>
         <!-- Test that search works with MSAmanda -->
@@ -1112,7 +1097,6 @@
             <param name="min_charge" value="1"/>
             <param name="max_charge" value="3"/>
             <param name="engines" value="MS_Amanda"/>
-
             <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> 
         </test>
     </tests>
diff -r 515c835c2f07 -r ba5377754cce test-data/tiny_searchgui_result1.zip
Binary file test-data/tiny_searchgui_result1.zip has changed