diff visualize_pore_diameter_aqp.xml @ 0:113c9904d083 draft

"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/visualize_pore_diameter_aqp.xml	Wed May 25 09:02:50 2022 +0000
@@ -0,0 +1,105 @@
+<tool id="visualize_pore_diameter_aqp" name="visualize pore diameter of AQP" version="0.1.0" python_template_version="3.5" profile="@GALAXY_VERSION@">
+    <macros>
+        <token name="@GALAXY_VERSION@">21.05</token>
+    </macros>
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' '$input_file.element_identifier' &&
+        Rscript '$__tool_directory__/visualize_pore_diameter_aqp.R'
+            -i '$input_file.element_identifier'
+            #if 'aqp' in $select_graph:
+                -a TRUE
+            #else:
+                -a FALSE
+            #end if
+            #if 'protomer' in $select_graph:
+                -p TRUE
+            #else:
+                -p FALSE
+            #end if
+            #if 'all' in $select_graph :
+                -d TRUE
+            #else:
+                -d FALSE
+            #end if
+            #if $pdf == 'yes' :
+                -f TRUE
+            #else:
+                -f FALSE
+            #end if
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="tabular" label="Aquaporin pore diameter table" help="Put your table containing the means and standard deviations of aquaporins pore diameter"/>
+        <param name="select_graph" type="select" multiple="true" display="checkboxes" label="Choose which graphics you want to get">
+            <option value="aqp" selected="true">Distance distribution by aquaporin</option>
+            <option value="protomer" selected="true">Distance distribution by protomer</option>
+            <option value="all" selected="true">Distance distribution by aquaporin and by protomer</option>
+        </param>
+        <param name="pdf" type="select" label="Do you want a pdf file that contains all the selected graphics?">
+            <option value="yes" selected="true">Yes</option>
+            <option value="no">No</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="png" from_work_dir="./Distance_distribution_by_aquaporin.png" label="Distance_distribution_by_aquaporin.png">
+            <filter>"aqp" in select_graph</filter>
+        </data>
+        <data name="out_file2" format="png" from_work_dir="./Distance_distribution_by_protomer.png" label="Distance_distribution_by_protomer.png">
+            <filter>"protomer" in select_graph</filter>
+        </data>
+        <data name="out_file3" format="png" from_work_dir="./Distance_distribution_on_all_protomers.png" label="Distance_distribution_on_all_protomers.png">
+            <filter>"all" in select_graph</filter>
+        </data>
+        <data name="out_file4" format="pdf" from_work_dir="./*.pdf" label="Distance distribution (PDF)">
+            <filter>pdf == "yes"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="table_sort_pore_diameter_aqp.tabular" ftype="tabular"/>
+            <param name="select_graph" value="aqp,protomer,all"/>
+            <param name="pdf" value="yes"/>
+            <output name="out_file" file="Distance_distribution_by_aquaporin.png"/>
+            <output name="out_file2" file="Distance_distribution_by_protomer.png"/>
+            <output name="out_file3" file="Distance_distribution_on_all_protomers.png"/>
+            <output name="out_file4" file="all_graphics_distribution.pdf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+This tool allows to visualize the pore diameter of an aquaporin over time.
+
+_____
+
+.. class:: infomark
+
+**Inputs**
+
+    - Aquaporin pore diameter table : table containing the average distance and standard deviation of each subpath for a complete trajectory
+    - Choose which graphics you want to get :
+        - Distance distribution by aquaporin : for each aquaporin, a ribbon graph is created showing the distance distribution over time
+        - Distance distribution by protomer : for each protomer, a ribbon graph is created showing the distance distribution over time
+        - Distance distribution by aquaporin and by protomer : for each protomer of each aquaporin, a ribbon graph is created showing the distribution of the distance over time
+    - Do you want a pdf file that contains all the selected graphics? :
+        - Yes : a PDF file containing all the selected graphics will be created in addition to the PNG files of the graphics
+        - No : only PNG files of the graphics will be created
+
+_____
+
+.. class:: infomark
+
+**Outputs**
+
+    - PNG file for each selected graphic type
+    - PDF file containing all selected graphics
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btz107</citation>
+    </citations>
+</tool>