diff mixomics_plotindiv.xml @ 2:c8533e9298e5 draft

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

--- a/mixomics_plotindiv.xml	Thu Oct 15 12:22:25 2020 +0000
+++ b/mixomics_plotindiv.xml	Fri Oct 23 10:15:56 2020 +0000
@@ -1,26 +1,29 @@
-<tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="6.12+galaxy0" profile="16.04" workflow_compatible="true">
+<tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">
 
     <description>provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA)</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_plotindiv_script.R
+        @COMMAND_RSCRIPT@/mixomics_plotindiv.R
+
         --input_rdata $input_rdata
+
         $adv.legend
         $adv.ellipse
+
         --output_pdf $output_pdf
-        ]]>
-    </command>
+
+        @COMMAND_LOG_EXIT@
+
+    ]]></command>
 
     <inputs>
         <param name="input_rdata" type="data" format="rdata"
@@ -45,22 +48,9 @@
         </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 plotIndiv
@@ -73,6 +63,20 @@
 The plotIndiv function is part of the mixOmics package for exploration and integration of Omics datasets.
 Provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA).
 
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+======================= =================================== ========
+Name                    Output file                         Format
+======================= =================================== ========
+mixOmics.block.splsda   mixomics_blocksplsda_output.RData   rdata
+======================= =================================== ========
+
+---------------------------------------------------
+
 -----------
 Input files
 -----------
@@ -94,6 +98,9 @@
 
 Plot ellipse plots
 
+
+@HELP_MANUAL@
+
 ------------
 Output files
 ------------
@@ -101,11 +108,8 @@
 plotIndiv.pdf
     A pdf file with scatter plots for individuals
 
-        ]]>
-    </help>
+    ]]></help>
 
-    <citations>
-        <citation type="doi">10.1371/journal.pcbi.1005752</citation>
-    </citations>
+    <expand macro="citations" />
 
 </tool>
\ No newline at end of file