diff macros.xml @ 2:c956182d4e2c draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"

--- a/macros.xml	Thu Apr 09 08:13:00 2020 -0400
+++ b/macros.xml	Thu Apr 16 05:32:53 2020 -0400
@@ -1,73 +1,105 @@
 <macros>
     <token name="@CP_VERSION@">3.1.9</token>
-    <token name="@PY_VERSION@">2.7.16</token>
+    <token name="@PY_VERSION@">3.7</token>
     <token name="@FORMATS@">jpg,png,tiff,bmp,gif,pcx,ppm,psd,pbm,pgm,eps</token>
+    <token name="@SPACES@">"    "</token>
+    <!-- four spaces needed for CP pipeline file -->
+    <token name="@COMMON_HELP@">
+        .. class:: infomark
 
-    <token name="@SPACES@">"    "</token> <!-- four spaces needed for CP pipeline file -->
+        **Input**
+
+        Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
+
+        .. class:: infomark
+
+        **Output**
+
+        The input CellProfiler pipeline file *(.cppipe)* in addition to the settings of this module.
+
+        .. class:: warningmark
+
+        **IMPORTANT**
+
+        The first tool in a CellProfiler workflow has to be **Starting modules** and the last one **CellProfiler**. You can also execute the entire pipeline with the final CellProfiler tool, in which you feed in the images you want to process as well.
+    </token>
+
 
     <xml name="output_pipeline_macro">
-        <data name="out_file" from_work_dir="output" format="txt" label="Output pipeline" />
+        <data name="out_file" from_work_dir="output" format="txt"/>
     </xml>
 
+
     <xml name="input_pipeline_macro">
-        <param name="input_pipeline" type="data" format="data" label="Pipeline to select"/>
+        <param name="input_pipeline" type="data" format="data" label="Select the input CellProfiler pipeline"/>
     </xml>
 
+
     <xml name="cp_requirements">
         <requirements>
             <requirement type="package" version="@CP_VERSION@">cellprofiler</requirement>
         </requirements>
     </xml>
 
+
     <xml name="py_requirements">
         <requirements>
             <requirement type="package" version="@PY_VERSION@">python</requirement>
         </requirements>
     </xml>
 
+
     <xml name="citations">
         <citations>
             <citation type="bibtex">
-            @misc{galaxytoolscellprofiler,
-            author = {Sun, Yi},
-            year = {2020},
-            title = {Cellprofiler Galaxy tools},
-            publisher = {Github},
-            journal = {Github repository},
-            url = {https://github.com/bgruening/galaxytools/tools/cellrprofiler},
-            }
+                @article{McQuin_2018,
+                title = {CellProfiler 3.0: Next-generation image processing for biology},
+                author = {McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE},
+                year = {2018},
+                volume = {16(7):e2005970},
+                DOI = {10.1371/journal.pbio.2005970},
+                journal = {PLoS Biol.},
+                url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005970},
+                }
             </citation>
         </citations>
     </xml>
 
+
     <xml name="cmd_modules">
-        <command detect_errors="aggressive"><![CDATA[
-            python '$script_file' '$inputs' '$input_pipeline'
-        ]]></command>
+        <command detect_errors="aggressive">
+            <![CDATA[
+                python '$script_file' '$inputs' '$input_pipeline'
+                ]]>
+        </command>
     </xml>
 
+
     <xml name="text_validator">
         <validator type="regex" message="Only numbers, letters, hyphen, underscore and spaces are allowed">^[A-Za-z0-9 _-]*$</validator>
     </xml>
 
+
     <xml name="test_input_pipeline_param">
         <param name="input_pipeline" value="common.txt" />
     </xml>
 
+
     <xml name="test_out_file" token_file="common.txt">
         <output name="out_file" ftype="txt" file="@FILE@" lines_diff="0"/>
     </xml>
-    
+
+
     <xml name="help" token_module="common">
-       <help>
-           This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe)
+        <help>
+            This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe)
 
-           Input: existing pipeline file
+            Input: existing pipeline file
 
-           Output: new pipeline file
+            Output: new pipeline file
 
-           Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone.
-       </help>
-   </xml>
+            Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone.
+        </help>
+    </xml>
 </macros>