diff mixomics_plotvar.xml @ 2:c8533e9298e5 draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"

--- a/mixomics_plotvar.xml	Thu Oct 15 12:22:25 2020 +0000
+++ b/mixomics_plotvar.xml	Fri Oct 23 10:15:56 2020 +0000
@@ -1,26 +1,29 @@
-<tool id="mixomics_plotvar" name="mixOmics plotVar" version="6.12+galaxy0" profile="16.04" workflow_compatible="true">
+<tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">
 
     <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</description>
 
-    <requirements>
-        <requirement type="package" version="6.12">bioconductor-mixomics</requirement>
-        <requirement type="package" version="2.0">r-argparse</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_mixomics.xml</import>
+    </macros>
 
-    <stdio>
-        <!-- <exit_code range="1:" level="fatal" /> -->
-    </stdio>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command detect_errors="aggressive"><![CDATA[
 
-    <command detect_errors="aggressive">
-        <![CDATA[
-        Rscript
-        ${__tool_directory__}/mixomics_plotvar_script.R
+        @COMMAND_RSCRIPT@/mixomics_plotvar.R
+
         --input_rdata $input_rdata
+
         $adv.legend
         --cutoff $adv.cutoff
+
         --output_pdf $output_pdf
-        ]]>
-    </command>
+
+        @COMMAND_LOG_EXIT@
+
+    ]]></command>
 
     <inputs>
         <param name="input_rdata" type="data" format="rdata"
@@ -46,22 +49,9 @@
         </test>
     </tests>
 
-    <help>
-        <![CDATA[
-.. class:: infomark
-
-**Authors** Pierre Pericard ([e-mail])
-
----------------------------------------------------
+    <help><![CDATA[
 
-.. class:: infomark
-
-**Please cite**
-
-Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
-PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
-
----------------------------------------------------
+@HELP_AUTHORS@
 
 ================
 mixOmics plotVar
@@ -74,6 +64,20 @@
 The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets.
 Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA.
 
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+======================= =================================== ========
+Name                    Output file                         Format
+======================= =================================== ========
+mixOmics.block.splsda   mixomics_blocksplsda_output.RData   rdata
+======================= =================================== ========
+
+---------------------------------------------------
+
 -----------
 Input files
 -----------
@@ -95,18 +99,18 @@
 
 Cut-off
 
+
+@HELP_MANUAL@
+
 ------------
 Output files
 ------------
 
-plotIndiv.pdf
-    A pdf file with scatter plots for individuals
+plotVar.pdf
+    A pdf file with scatter plots for variables
 
-        ]]>
-    </help>
+    ]]></help>
 
-    <citations>
-        <citation type="doi">10.1371/journal.pcbi.1005752</citation>
-    </citations>
+    <expand macro="citations" />
 
 </tool>
\ No newline at end of file