Mercurial > repos > galaxyp > openms_featurelinkerunlabeled

changeset 7:df7f4ac9a2c6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 12:59:10 -0500
parents 553b9cc3a1b2
children 93b88f7cb8cb
files FeatureLinkerUnlabeled.xml SKIP_TOOLS_FILE.txt macros.xml readme.md tools_blacklist.txt
diffstat 5 files changed, 25 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/FeatureLinkerUnlabeled.xml	Thu Jan 11 18:16:46 2018 -0500
+++ b/FeatureLinkerUnlabeled.xml	Mon Feb 12 12:59:10 2018 -0500
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Map Alignment]-->
-<tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.2.0">
+<tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.3.0">
   <description>Groups corresponding features from multiple maps.</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
@@ -19,6 +19,9 @@
 #if $param_out:
   -out $param_out
 #end if
+#if $param_design:
+  -design $param_design
+#end if
 #if $param_keep_subelements:
   -keep_subelements
 #end if
@@ -86,6 +89,7 @@
         </valid>
       </sanitizer>
     </param>
+    <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/>
     <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help="(-keep_subelements) "/>
     <param name="param_algorithm_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help="(-second_nearest_gap) "/>
     <param name="param_algorithm_use_identifications" display="radio" type="boolean" truevalue="-algorithm:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help="(-use_identifications) "/>
--- a/SKIP_TOOLS_FILE.txt	Thu Jan 11 18:16:46 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-OMSSAAdapter
-MyriMatchAdapter
-PepNovoAdapter
-SeedListGenerator
-SpecLibSearcher
-MapAlignerIdentification
-MapAlignerPoseClustering
-MapAlignerSpectrum
-MapAlignerRTTransformer
--- a/macros.xml	Thu Jan 11 18:16:46 2018 -0500
+++ b/macros.xml	Mon Feb 12 12:59:10 2018 -0500
@@ -2,10 +2,10 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="2.2">openms</requirement>
+      <requirement type="package" version="2.3">openms</requirement>
       <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>
+      <requirement type="package" version="2017.07.21">msgf_plus</requirement>
       <yield/>
     </requirements>
   </xml>
--- a/readme.md	Thu Jan 11 18:16:46 2018 -0500
+++ b/readme.md	Mon Feb 12 12:59:10 2018 -0500
@@ -53,29 +53,29 @@
  * clone or install CTD2Galaxy
 
     ```bash
-    git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
+    git clone https://github.com/WorkflowConversion/CTDConverter.git
     ```
     
- * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it.
+ * If you have CTDopts and CTDConverter installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. Further information can be found on the CTDConverter page.
 
     ```bash
-    python generator.py \ 
+    python convert.py galaxy \ 
     -i /PATH/TO/YOUR/CTD/*.ctd \
     -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \
     -d datatypes_conf.xml -g openms \
     -b version log debug test no_progress threads \
      in_type executable myrimatch_executable \
      fido_executable fidocp_executable \
-     omssa_executable pepnovo_executable \
+     omssa_executable pepnovo_e xecutable \
      xtandem_executable param_model_directory \
      java_executable java_memory java_permgen \
      r_executable rt_concat_trafo_out param_id_pool \
     -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
-    -s PATH/TO/SKIP_TOOLS_FILES.txt
+    -s PATH/TO/tools_blacklist.txt
     ```
 
 
- * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
+ * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. Some of these tools might already be deprecated and the files might not exist:
 
     ```
     sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml
@@ -171,8 +171,8 @@
     ```
     
 
- * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in
-   by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`:
+ * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in
+   by the automatic conversion step and are therefore in `tools_blacklist.txt`:
     * SeedListGenerator
     * SpecLibSearcher
     * MapAlignerIdentification
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools_blacklist.txt	Mon Feb 12 12:59:10 2018 -0500
@@ -0,0 +1,9 @@
+OMSSAAdapter
+MyriMatchAdapter
+PepNovoAdapter
+SeedListGenerator
+SpecLibSearcher
+MapAlignerIdentification
+MapAlignerPoseClustering
+MapAlignerSpectrum
+MapAlignerRTTransformer