changeset 1:ddde82ae5dea draft

planemo upload

--- a/countmatrixforedger.xml	Fri Dec 09 10:52:35 2016 -0500
+++ b/countmatrixforedger.xml	Sun Dec 11 18:57:58 2016 -0500
@@ -9,7 +9,6 @@
                 echo -e ${s.sample_data}"\t"${s.sample_name}"\t"${s.sample_group} >> script.data;
             #end for#
 
-            cat script.data > /tmp/script.data;
             $__tool_directory__/tools/scrsh.sh script.data;
 
             cat count.matrix > $count_matrix;
@@ -27,29 +26,12 @@
         </repeat>
     </inputs>
     <outputs>
-<!--        <data name="output" format="data" /> -->
         <data name="count_matrix" format="data" />
         <data name="annotation" format="data" />
         <data name="log" format="data" />
         <data name="error_log" format="data" />
     </outputs>
     <tests>
-<!--         <test>
-            <param name="sample_0|sample_data" value="data1" />
-            <param name="sample_1|sample_data" value="data2" />
-            <param name="sample_2|sample_data" value="data3" />
-            <param name="sample_3|sample_data" value="data4" />
-            <param name="sample_0|sample_name" value="sample1" />
-            <param name="sample_1|sample_name" value="sample2" />
-            <param name="sample_2|sample_name" value="sample3" />
-            <param name="sample_3|sample_name" value="sample4" />            
-            <param name="sample_0|sample_group" value="gr1" />
-            <param name="sample_1|sample_group" value="gr1" />
-            <param name="sample_2|sample_group" value="gr2" />
-            <param name="sample_3|sample_group" value="gr2" />
-            <output name="output" file="output"/>
-
-        </test> -->
         <test>
             <param name="sample_0|sample_data" value="data1" />
             <param name="sample_1|sample_data" value="data2" />
@@ -72,24 +54,10 @@
     </tests>
     <help>
         <![CDATA[ 
-
-tutaj cos bedzie
      ]]>
     </help>
         <citations>
-        <citation type="bibtex">
-            @article{Berenger2014,
-              doi = {10.1186/1758-2946-6-23},
-              url = {http://dx.doi.org/10.1186/1758-2946-6-23},
-              year  = {2014},
-              publisher = {Springer Nature},
-              volume = {6},
-              number = {1},
-              pages = {23},
-              author = {Francois Berenger and Arnout Voet and Xiao Lee and Kam YJ Zhang},
-              title = {A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening},
-              journal = {Journal of Cheminformatics}
-            }
+        <citation>
         </citation>
     </citations>
 </tool>

--- a/plotheatmap.xml	Fri Dec 09 10:52:35 2016 -0500
+++ b/plotheatmap.xml	Sun Dec 11 18:57:58 2016 -0500
@@ -1,5 +1,5 @@
-<tool id="plotheatmap" name="plotheatmap" version="1.0">
-    <description>Make a count matrix for edgeR</description>
+<tool id="plotheatmap" name="plotHeatmap" version="1.0">
+    <description>Plot heatmap</description>
     <stdio>
         <exit_code range="1:" />
     </stdio>
@@ -7,8 +7,6 @@
         <![CDATA[ 
             $__tool_directory__/tools/script.R $count_matrix $stats_matrix $log_fc $log_cpm $pvalue $fdr > $rscript_log 2> $rerror_log
 
-
-
         ]]>
     </command>
     <inputs>
@@ -21,7 +19,6 @@
 
     </inputs>
     <outputs>
-<!--        <data name="output" format="data" /> --> 
        <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" >
             <filter>(outftype == 'pdf')</filter>
         </data>
@@ -37,7 +34,6 @@
             <param name="log_cpm" value="2"/>
             <param name="pvalue" value="0.05"/>
             <param name="fdr" value="0.1"/>
-<!--             <output name="output" file="done"/> -->
             <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size" />
             <output name="rscript_log" file="rscript.log"/>
             <output name="rerror_log" file="rerror.log"/>
@@ -47,11 +43,8 @@
     </tests>
     <help>
         <![CDATA[ 
-
-tutaj cos bedzie
      ]]>
     </help>
     <citations>
-        
     </citations>
 </tool>
\ No newline at end of file