view all_de_steps.xml @ 0:cc71440b759f draft default tip

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<tool id='differential_expression' name='Differential Expression' version='1.0'>
<description>Generates results for DE </description>
<!--requirement></requirement-->
<requirements>
        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
        <requirement type="set_environment">TRINITY_HOME</requirement>

</requirements>
<command>

echo  -e "Differential Expression Log File" &gt; $output_log 2&gt;&amp;1;
	
## Step 0: preprocess  input_file preparaton

	#for $i in $isoform_sample:
		cp -s $i.isoform_sample_matrix $i.sample_name;
	#end for;
	

## Step 1: abundance_estimates_to_matrix
echo -e "" &gt;&gt;  $output_log  2&gt;&amp;1;
echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" &gt;&gt;  $output_log  2&gt;&amp;1;
echo -e "\#\# Step 1: abundance_estimates_to_matrix" &gt;&gt;  $output_log  2&gt;&amp;1;
echo -e "" &gt;&gt;  $output_log  2&gt;&amp;1;


perl \$TRINITY_HOME/util/abundance_estimates_to_matrix.pl 	
	--est_method $est_method  
	#for $i in $isoform_sample:
		$i.sample_name
	#end for
	&gt;&gt; $output_log 2&gt;&amp;1;


## Step 2: run_DE_analysis 
echo -e "" &gt;&gt;  $output_log  2&gt;&amp;1;
echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" &gt;&gt;  $output_log  2&gt;&amp;1;
echo -e "\#\# Step 2: run_DE_analysis" &gt;&gt;  $output_log  2&gt;&amp;1;
echo -e "" &gt;&gt;  $output_log  2&gt;&amp;1;

perl \$TRINITY_HOME/Analysis/DifferentialExpression/run_DE_analysis.pl
        --matrix matrix.counts.matrix
        --method $method
        --output result_dir
        &gt;&gt; $output_log 2&gt;&amp;1;

## Step 3: analyze_diff_expr
echo -e "" &gt;&gt;  $output_log  2&gt;&amp;1;
echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" &gt;&gt;  $output_log  2&gt;&amp;1;
echo -e "\#\# Step 3: analyze_diff_expr" &gt;&gt;  $output_log  2&gt;&amp;1;
echo -e "" &gt;&gt;  $output_log  2&gt;&amp;1;

cd result_dir &amp;&amp; perl \$TRINITY_HOME/Analysis/DifferentialExpression/analyze_diff_expr.pl

	--matrix ../matrix.TMM.fpkm.matrix

        &gt;&gt; $output_log 2&gt;&amp;1;

pwd;
cd .. &amp;&amp; zip -r results.zip result_dir;
</command>

<inputs>
 <!-- Required -->

  <param name='est_method' type='select' display="radio"  label='Select est_method'>
  	<option value="RSEM" selected='true'>RSEM</option>
  	<option value="eXpress">eXpress</option>
  </param>


  <repeat name="isoform_sample" title="Isoform Sample" min="2">
         <param name="sample_name" type="text" label="Sample Name" help="Only alpha-numerical name without space."> 
	 	<validator type="empty_field" message="don't leave the field empty!"/> 
	 </param>	
	<param format="tabular" name="isoform_sample_matrix" type="data" label="Isoform Sample Matrix"/>	
  </repeat>

  <param name='method' type="select" label="Select Method" >
         <option value="edgeR">edgeR</option>
         <option value="DESeq">DESeq</option>
         <option value="DESeq2">DESeq2</option>
  </param>



 <!-- Optional -->

</inputs>
<outputs>
	<data name='de_output' format='zip' label="${tool.name} on ${on_string}: compressed_output" from_work_dir="results.zip"/>
	<data name='output_log' format='txt' label="${tool.name} on ${on_string} : matrix_log"/>
</outputs>
</tool>