# HG changeset patch
# User galaxyp
# Date 1508354150 14400
# Node ID 55344a50655c6e4b23feb97bd7703ff5ecdd7433
# Parent  1dc8550349ddff6bccc913ce2412490fd246a028
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64

diff -r 1dc8550349dd -r 55344a50655c FileMerger.xml
--- a/FileMerger.xml	Wed Aug 09 09:07:38 2017 -0400
+++ b/FileMerger.xml	Wed Oct 18 15:15:50 2017 -0400
@@ -26,16 +26,6 @@
   -rt_concat:gap $param_rt_concat_gap
 #end if
 
-#if $rep_param_rt_concat_trafo_out:
--rt_concat:trafo_out
-  #for token in $rep_param_rt_concat_trafo_out:
-    #if " " in str(token):
-      "$token.param_rt_concat_trafo_out"
-    #else
-      $token.param_rt_concat_trafo_out
-    #end if
-  #end for
-#end if
 #if $param_raw_rt_auto:
   -raw:rt_auto
 #end if
@@ -74,8 +64,8 @@
     <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help="(-annotate_file_origin) "/>
     <param name="param_rt_concat_gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="(-gap) RT concatenation is enabled if a value &gt; 0 is set"/>
     <param name="param_raw_rt_auto" display="radio" type="boolean" truevalue="-raw:rt_auto" falsevalue="" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto) "/>
-    <repeat name="rep_param_raw_rt_custom" min="0" max="1" title="param_raw_rt_custom">
-      <param name="param_raw_rt_custom" type="text" size="30" value="0" label="List of custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files">
+    <repeat name="rep_param_raw_rt_custom" min="0" title="param_raw_rt_custom">
+      <param name="param_raw_rt_custom" type="text" size="30" value="0" label="Custom retention times that are assigned to the files" help="(-rt_custom) The number of given retention times must be equal to the number of input files">
         <sanitizer>
           <valid initial="string.printable">
             <remove value="'"/>
@@ -91,8 +81,7 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="featurexml"/>
-    <data name="param_rt_concat_trafo_out" format="trafoxml"/>
+    <data name="param_out" format="mzml"/>
   </outputs>
   <help>Merges several MS files into one file.
 
diff -r 1dc8550349dd -r 55344a50655c macros.xml
--- a/macros.xml	Wed Aug 09 09:07:38 2017 -0400
+++ b/macros.xml	Wed Oct 18 15:15:50 2017 -0400
@@ -6,6 +6,7 @@
       <requirement type="package" version="15.12.15.2">xtandem</requirement>
       <requirement type="package" version="1.0">fido</requirement>
       <requirement type="package" version="2016.10.26">msgf_plus</requirement>
+      <yield/>
     </requirements>
   </xml>
   <xml name="stdio">
diff -r 1dc8550349dd -r 55344a50655c readme.md
--- a/readme.md	Wed Aug 09 09:07:38 2017 -0400
+++ b/readme.md	Wed Oct 18 15:15:50 2017 -0400
@@ -69,6 +69,7 @@
      omssa_executable pepnovo_executable \
      xtandem_executable param_model_directory \
      java_executable java_memory java_permgen \
+     r_executable rt_concat_trafo_out \
     -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
     -s PATH/TO/SKIP_TOOLS_FILES.txt
     ```
@@ -77,8 +78,8 @@
  * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
 
     ```
-    sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml
-    sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml
+    sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml
+    sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml
     sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
     sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
     sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
@@ -117,6 +118,14 @@
     ]]>
     ```
     
+ * In `MetaProSIP.xml` add `R` as a requirement:
+ 
+   ```
+   <expand macro="requirements">
+       <requirement type="package" version="3.3.1">r-base</requirement>
+   </expand>
+   ```
+   
  * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
  
    ```
diff -r 1dc8550349dd -r 55344a50655c repository_dependencies.xml
--- a/repository_dependencies.xml	Wed Aug 09 09:07:38 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Required proteomics dependencies.">
-  <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
-</repositories>