Repository 'openms_xtandemadapter'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter

Changeset 2:22e9bb7d151a (2017-10-18)
Previous changeset 1:cd0746ee4796 (2017-08-09) Next changeset 3:61bc5fb43781 (2017-10-28)
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
modified:
XTandemAdapter.xml
macros.xml
readme.md
removed:
repository_dependencies.xml
b
diff -r cd0746ee4796 -r 22e9bb7d151a XTandemAdapter.xml
--- a/XTandemAdapter.xml Wed Aug 09 09:18:43 2017 -0400
+++ b/XTandemAdapter.xml Wed Oct 18 15:22:33 2017 -0400
b
@@ -132,7 +132,7 @@
     </param>
     <param name="param_max_precursor_charge" type="integer" min="0" optional="True" value="4" label="Maximum precursor charge ('0' to use X! Tandem default)" help="(-max_precursor_charge) "/>
     <param name="param_no_isotope_error" display="radio" type="boolean" truevalue="-no_isotope_error" falsevalue="" checked="false" optional="True" label="By default, misassignment to the first and second isotopic 13C peak are also considered" help="(-no_isotope_error) Set this flag to disable"/>
-    <repeat name="rep_param_fixed_modifications" min="0" max="1" title="param_fixed_modifications">
+    <repeat name="rep_param_fixed_modifications" min="0"  title="param_fixed_modifications">
       <param name="param_fixed_modifications" type="select" optional="True" label="Fixed modifications, specified using Unimod (www.unimod.org) terms," help="(-fixed_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
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diff -r cd0746ee4796 -r 22e9bb7d151a macros.xml
--- a/macros.xml Wed Aug 09 09:18:43 2017 -0400
+++ b/macros.xml Wed Oct 18 15:22:33 2017 -0400
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@@ -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">
b
diff -r cd0746ee4796 -r 22e9bb7d151a readme.md
--- a/readme.md Wed Aug 09 09:18:43 2017 -0400
+++ b/readme.md Wed Oct 18 15:22:33 2017 -0400
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@@ -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):
  
    ```
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diff -r cd0746ee4796 -r 22e9bb7d151a repository_dependencies.xml
--- a/repository_dependencies.xml Wed Aug 09 09:18:43 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -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>