changeset 1:8057fdd27860 draft default tip

planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty

--- a/rpviz.xml	Mon Dec 13 17:40:42 2021 +0000
+++ b/rpviz.xml	Fri Nov 18 16:39:23 2022 +0000
@@ -1,28 +1,32 @@
-<tool id="rpviz" name="Visualize pathways" version="5.10.0">
+<tool id="rpviz" name="Visualize pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
     <description>Visualize pathways from the RetroPath Suite</description>
+    <macros>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@TOOL_VERSION@">6.0.1</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="5.10.0">rptools</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #set input_folder="input_folder"
-        mkdir -p '$input_folder';
+        mkdir -p '$input_folder' &&
         #if str($input_type_conditional.input_type) == "sbml":
             #for $input in $input_type_conditional.input_sbml.keys():
-                ln -sf $input_type_conditional.input_sbml[$input] '$input_folder/${input}.xml';
+                ln -sf $input_type_conditional.input_sbml[$input] '$input_folder/${input}.xml' &&
             #end for
             python -m rptools.rpviz '$input_folder'
         #elif str($input_type_conditional.input_type) == "tar":
             python -m rptools.rpviz '${input_type_conditional.input_tar}'
         #elif str($input_type_conditional.input_type) == "single_sbml":
-            ln -sf '$input_type_conditional.input_single_sbml' '$input_folder/${input_type_conditional.input_single_sbml.name}';
+            ln -sf '$input_type_conditional.input_single_sbml' '$input_folder/${input_type_conditional.input_single_sbml.name}' &&
             python -m rptools.rpviz '$input_folder'
         #end if
         'out'
         #if $adv.cofactor_file
             --cofactor '$adv.cofactor_file'
         #end if
-        --autonomous_html '$html_file';
-        rm -fr '$input_folder';
+        --autonomous_html '$html_file' &&
+        rm -fr '$input_folder'
     ]]></command>
     <inputs>
         <conditional name="input_type_conditional">
@@ -35,14 +39,14 @@
                 <param name="input_tar" type="data" format="tar" label="Source SBML" />
             </when>
             <when value="sbml">
-                <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" />
+                <param name="input_sbml" type="data_collection" format="sbml" collection_type="list" label="Source SBML" />
             </when>
             <when value="single_sbml">
-                <param name="input_single_sbml" type="data" format="xml" label="Source SBML" />
+                <param name="input_single_sbml" type="data" format="sbml" label="Source SBML" />
             </when>
         </conditional>
         <section name="adv" title="Advanced Options" expanded="false">
-            <param name="cofactor_file" type="data" format="tsv" optional="true" label="cofactor file" />
+            <param name="cofactor_file" type="data" format="tsv" optional="true" label="Cofactor file" help="File listing structures to consider as cofactors."/>
         </section>
     </inputs>
     <outputs>
@@ -55,7 +59,11 @@
                 <param name="input_type" value="single_sbml"/>
                 <param name="input_single_sbml" value="lycopene_CrtEBI_from_selenzy.xml" />
             </conditional>
-            <output name="html_file" file="rpviz_single_output.html" compare="sim_size"/>
+            <output name="html_file" >
+                <assert_contents>
+                    <has_size value="1296252" delta="100" />
+                </assert_contents>
+            </output>
         </test>
         <test>
         <!-- test 2: check if identical html output is produced (tar input) --> 
@@ -63,39 +71,47 @@
                 <param name="input_type" value="tar"/>
                 <param name="input_tar" value="as_tar_inputs.tgz" />
             </conditional>
-            <output name="html_file" file="rpviz_tar_output.html" compare="sim_size"/>
+            <output name="html_file" >
+                <assert_contents>
+                    <has_size value="1604488" delta="100" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
 RPVIZ
 ================
-Visualize pathways from the RetroPath Suite
+
+Visualize pathways from the `RetroPath Suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.
 
 Input
 -----
 
-* **input_rpSBMLs**\ : (string) Input file containing rpSBML files in a tar archive or a folder.
-                             
+Required:
+
+* **Source SBML**\ : Input file containing rpSBML files in a tar archive, collection or single file.
+
+Optional:
+
+* **Cofactor file**\ : File listing structures to consider as cofactors.
+
 Output
 ------
 
-* **output_folder**\ : (string) Output folder to be used. If it does not exist, an attempt will be made to create it.It the creation of the folder fails, IOError will be raised.
-* **autonomous_html**\ : (string) Optional file path, if provided will output an autonomous HTML containing all dependancies.
+* **Pathways Visualization**\ : HTML output for pathway's visualization.
 
 Project Links
 ------------------
 
 * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpviz>`_
 
-Version
-----------
-
-5.10.0
-
 License
 -------
 
 * `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
 
     ]]></help>
+    <creator>
+        <person givenName="Thomas" familyName="Duigou" email="[e-mail]" identifier="https://orcid.org/0000-0002-2649-2950" />
+    </creator>
 </tool>
\ No newline at end of file