Mercurial > repos > vimalkumarvelayudhan > riboseqr_wrapper

diff triplet.xml @ 3:d7ce95ccf54f

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Change R data file format in xml wrappers (rda -> RData) Add test data, sample workflow. Updated README with instructions on testing.
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Wed, 22 Jul 2015 12:07:39 +0100
parents b2eb07000039
children
line wrap: on
line diff
--- a/triplet.xml	Tue Jul 21 15:40:22 2015 +0100
+++ b/triplet.xml	Wed Jul 22 12:07:39 2015 +0100
@@ -25,7 +25,7 @@
         --output_path "$html_file.files_path"
     </command>
     <inputs>
-        <param name="rdata_load" type="data" format="rda"
+        <param name="rdata_load" type="data" format="RData"
                label="Select prepared riboSeqR input (R data file)"
                multiple="false" optional="false"
                help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;findCDS
@@ -79,24 +79,24 @@
                       plot" help="Comma-separated values."/>
     </inputs>
     <outputs>
-        <data format="rda" name="rdata_save"
+        <data format="RData" name="rdata_save"
               label="Triplet periodicity (R data file)"/>
         <data format="html" name="html_file"
               label="Triplet periodicity (HTML report)"/>
     </outputs>
-    <tests>
-        <test>
-            <param name="rdata_load" value="Prepare riboSeqR input (R data file)" ftype="rda" />
-            <param name="fasta_file" value="rsem_chlamy236_deNovo.transcripts.fa" />
-            <param name="include_lengths" value="25:30" />
-            <param name="analyze_plot_lengths" value="26:30" />
-            <output name="rdata_save" file="Triplet periodicity (R data file)" ftype="rda" />
-            <output name="html_file" file="Triplet_periodicity_(HTML_report).html">
-                <extra_files type="file" name="Periodicity-plot.png" value="Periodicity-plot.png" ftype="png" />
-                <extra_files type="file" name="Periodicity-plot.pdf" value="Periodicity-plot.pdf" ftype="pdf" />
-            </output>
-        </test>
-    </tests>
+    <!--<tests>-->
+        <!--<test>-->
+            <!--<param name="rdata_load" value="Prepare riboSeqR input (R data file)" ftype="RData" />-->
+            <!--<param name="fasta_file" value="rsem_chlamy236_deNovo.transcripts.fa" />-->
+            <!--<param name="include_lengths" value="25:30" />-->
+            <!--<param name="analyze_plot_lengths" value="26:30" />-->
+            <!--<output name="rdata_save" file="Triplet periodicity (R data file)" ftype="RData" />-->
+            <!--<output name="html_file" file="Triplet_periodicity_(HTML_report).html">-->
+                <!--<extra_files type="file" name="Periodicity-plot.png" value="Periodicity-plot.png" ftype="png" />-->
+                <!--<extra_files type="file" name="Periodicity-plot.pdf" value="Periodicity-plot.pdf" ftype="pdf" />-->
+            <!--</output>-->
+        <!--</test>-->
+    <!--</tests>-->
     <help>
 Triplet Periodicity
 -------------------