Mercurial > repos > artbio > cpm_tpm_rpk

diff cpm_tpm_rpk.xml @ 3:8b1020c25f0f draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
author artbio
date Fri, 12 Apr 2019 12:01:35 -0400
parents 563337e780ce
children be358a1ebf67
line wrap: on
line diff
--- a/cpm_tpm_rpk.xml	Wed Feb 06 19:31:57 2019 -0500
+++ b/cpm_tpm_rpk.xml	Fri Apr 12 12:01:35 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.3.0">
+<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.4.0">
     <description>from raw counts expression values</description>
     <requirements>
         <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
@@ -64,6 +64,7 @@
                     <option value="cpm" selected="true">CPM</option>
                     <option value="tpm">TPM</option>
                     <option value="rpk">RPK</option>
+                    <option value="none">NONE</option>
                 </param>
                 <when value="tpm">
                     <param name="gene_file" type="data" format="txt" label="Gene length file"/> 
@@ -97,6 +98,8 @@
                 </when>
                 <when value="cpm">
                 </when>
+                <when value="none">
+                </when>
             </conditional>
         <param name="log" type="select" label="Data should be log transformed ?">
             <option value="FALSE" selected="true">No</option>
@@ -108,10 +111,10 @@
                 <option value="yes" >t-SNE and PCA</option>
             </param>
             <when value="yes">
-                    <param name="seed" value="49.0" type="float" label="Seed value for reproducibility" help="Set to 49 as default" />
-                    <param name="perp" value="10.0" type="float" label="perplexity" help="should be less than ((nbre observations)-1)/3" /> 
-                    <param name="theta" value="1.0" type="float" label="theta"/>
-                    <param name="tsne_labels" type="select" label="Add labels to points in the t-SNE plot" >
+                    <param name="seed" value="49.0" type="float" label="Seed value for reproducibility of t-SNE" help="Set to 49 as default" />
+                    <param name="perp" value="10.0" type="float" label="perplexity (t-SNE)" help="should be less than ((nbre observations)-1)/3" /> 
+                    <param name="theta" value="1.0" type="float" label="theta (t-SNE)"/>
+                    <param name="tsne_labels" type="select" label="Add labels to points plots" >
                         <option value="no" selected="true">No Labels</option>
                         <option value="yes" >Label points</option>
                     </param>
@@ -136,6 +139,19 @@
     <tests>
         <!-- test t-SNE -->
         <test>
+            <param name="input" value="none.tab" ftype="tabular"/>
+            <param name="type_transfo" value="none"/>
+            <param name="log" value="FALSE"/>
+            <param name="visualisation" value="yes"/>
+            <param name="seed" value="49"/>
+            <param name="perp" value="10"/>
+            <param name="theta" value="1" />
+            <param name="tsne_labels" value="yes" />
+            <output name="output" file="none.tab" ftype="tabular"/>
+            <output name="tsne_out" file="none_tsne.pdf" ftype="pdf"/>
+            <output name="pca_out" file="none_pca.pdf" ftype="pdf"/>
+        </test>
+        <test>
             <param name="input" value="counts.tab" ftype="tabular"/>
             <param name="type_transfo" value="cpm"/>
             <param name="log" value="TRUE"/>