Mercurial > repos > caleb-easterly > peca

changeset 6:e16cd77cf9f7 draft

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planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
author caleb-easterly
date Mon, 26 Feb 2018 16:07:30 -0500
parents 5a39fa8a235a
children 6ea067ed77ac
files peca.R peca.xml test.xml
diffstat 3 files changed, 20 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/peca.R	Thu Feb 22 11:45:43 2018 -0500
+++ b/peca.R	Mon Feb 26 16:07:30 2018 -0500
@@ -36,7 +36,6 @@
     results <- PECA_df(quant_file,
                 group1_names,
                 group2_names,
-                type=ttype,
                 id = df_names[1])
 
     # put add protein names column
--- a/peca.xml	Thu Feb 22 11:45:43 2018 -0500
+++ b/peca.xml	Mon Feb 26 16:07:30 2018 -0500
@@ -1,4 +1,5 @@
-<tool id="peca" name="PECA: Probe-level expression change averaging" version="0.1.0">
+<tool id="peca" name="PECA" version="0.1.0">
+    <description>probe-level expression change averaging</description>
     <requirements>
         <requirement type="package" version="1.14.0">bioconductor-peca</requirement>
         <requirement type="package" version="0.7">r-dbi</requirement>
@@ -17,7 +18,7 @@
             <option value="t" selected="true">Standard t-test</option>
             <option value="modt">Modified t-test</option>
             <option value="rots">Reproducibility-optimized test statistic</option>
-        <param>
+        </param>
     </inputs>
     <outputs>
         <data format="tabular" name="output"/>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test.xml	Mon Feb 26 16:07:30 2018 -0500
@@ -0,0 +1,17 @@
+<tool id="peca" name="PECA: Probe-level expression change averaging" version="0.1.0">
+    <command detect_errors="exit_code"><![CDATA[
+        ## write groups to file
+        echo '$group1' > group1.txt &&
+        echo '$group2' > group2.txt 
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular"/>
+        <param name="group1" type="data_column" data_ref="input" multiple="true"/>
+        <param name="group2" type="data_column" data_ref="input" multiple="true"/> 
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output"/>
+    </outputs>
+    <help><![CDATA[
+    ]]></help>
+</tool>