diff signature_score.xml @ 1:11ff7bd04308 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 987e0ceb55e8de1d2f09d0f2ae48ff7cd3e82051

--- a/signature_score.xml	Mon Jun 24 07:22:06 2019 -0400
+++ b/signature_score.xml	Tue Jul 09 10:52:09 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="signature_score" name="Compute signature scores" version="0.9.0">
+<tool id="signature_score" name="Compute signature scores" version="0.9.1">
     <description>in single cell RNAseq</description>
     <requirements>
         <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
@@ -23,9 +23,11 @@
             --output '$output'
             --stats '$stats'
             --pdf '$pdf'
+            --correlations '$correlations'
+            --covariances '$covariances'
 ]]></command>
     <inputs>
-        <param name="input" type="data" format="txt" label="Raw counts of expression data"/>
+        <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data"/>
         <param name="sep" type="select" label="Indicate column separator">
             <option value="tab" selected="true">Tabs</option>
             <option value="comma">Comma</option>
@@ -36,9 +38,11 @@
                help="signature gene that are not expressed in at least this percentage of cells will not be kept to compute the effective signature" />
     </inputs>
     <outputs>
-        <data name="pdf" format="pdf" label="Plots from ${on_string}" />
+        <data name="pdf" format="pdf" label="Signatures plots from ${on_string}" />
         <data name="output" format="tabular" label="signature scores from ${on_string}" />
-        <data name="stats" format="tabular" label="genes statistics in ${on_string}" />
+        <data name="stats" format="tabular" label="genes statistics from ${on_string}" />
+        <data name="correlations" format="tabular" label="Signature genes correlations" />
+        <data name="covariances" format="tabular" label="Signature genes covariances" />
     </outputs>
     <tests>
         <test>
@@ -48,6 +52,8 @@
             <output name="pdf" file="signature.pdf" ftype="pdf" compare="sim_size" delta="200" />
             <output name="output" file="signature.tsv" ftype="tabular"/>
             <output name="stats" file="gene_stats.tsv" ftype="tabular"/>
+            <output name="correlations" file="correlations.tsv" ftype="tabular"/>
+            <output name="covariances" file="covariances.tsv" ftype="tabular"/>
         </test>
     </tests>
     <help>