diff macros.xml @ 0:4395ea2a01f4 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat Feb 06 10:00:10 2021 +0000
@@ -0,0 +1,93 @@
+<macros>
+    <token name="@CP_VERSION@">3.1.9</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
+
+        **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_param">
+        <data name="output_pipeline" from_work_dir="output.cppipe" format="txt"/>
+    </xml>
+
+
+    <xml name="input_pipeline_param">
+        <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">
+                @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' '$input_pipeline'
+                ]]>
+        </command>
+    </xml>
+
+
+    <xml name="text_validator">
+        <validator type="regex" message="Only numbers, letters, hyphen, underscore and spaces are allowed">^[A-Za-z0-9 _-]*$</validator>
+    </xml>
+
+
+    <xml name="test_input_pipeline_param">
+        <param name="input_pipeline" value="common.cppipe" />
+    </xml>
+
+
+    <xml name="test_out_file" token_file="common.cppipe">
+        <output name="output_pipeline" ftype="txt" file="@FILE@" lines_diff="0"/>
+    </xml>
+    
+</macros>
+