Mercurial > repos > mytest > ngsap2
diff all_de_steps.xml @ 0:cc71440b759f draft default tip
Uploaded
| author | mytest |
|---|---|
| date | Tue, 22 Sep 2015 01:58:00 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_de_steps.xml Tue Sep 22 01:58:00 2015 -0400 @@ -0,0 +1,94 @@ +<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" > $output_log 2>&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 "" >> $output_log 2>&1; +echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1; +echo -e "\#\# Step 1: abundance_estimates_to_matrix" >> $output_log 2>&1; +echo -e "" >> $output_log 2>&1; + + +perl \$TRINITY_HOME/util/abundance_estimates_to_matrix.pl + --est_method $est_method + #for $i in $isoform_sample: + $i.sample_name + #end for + >> $output_log 2>&1; + + +## Step 2: run_DE_analysis +echo -e "" >> $output_log 2>&1; +echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1; +echo -e "\#\# Step 2: run_DE_analysis" >> $output_log 2>&1; +echo -e "" >> $output_log 2>&1; + +perl \$TRINITY_HOME/Analysis/DifferentialExpression/run_DE_analysis.pl + --matrix matrix.counts.matrix + --method $method + --output result_dir + >> $output_log 2>&1; + +## Step 3: analyze_diff_expr +echo -e "" >> $output_log 2>&1; +echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1; +echo -e "\#\# Step 3: analyze_diff_expr" >> $output_log 2>&1; +echo -e "" >> $output_log 2>&1; + +cd result_dir && perl \$TRINITY_HOME/Analysis/DifferentialExpression/analyze_diff_expr.pl + + --matrix ../matrix.TMM.fpkm.matrix + + >> $output_log 2>&1; + +pwd; +cd .. && zip -r results.zip result_dir; +</command> + +<inputs> + <!-- Required --> + + <param name='est_method' type='select' display="radio" label='Select est_method'> + <option value="RSEM" selected='true'>RSEM</option> + <option value="eXpress">eXpress</option> + </param> + + + <repeat name="isoform_sample" title="Isoform Sample" min="2"> + <param name="sample_name" type="text" label="Sample Name" help="Only alpha-numerical name without space."> + <validator type="empty_field" message="don't leave the field empty!"/> + </param> + <param format="tabular" name="isoform_sample_matrix" type="data" label="Isoform Sample Matrix"/> + </repeat> + + <param name='method' type="select" label="Select Method" > + <option value="edgeR">edgeR</option> + <option value="DESeq">DESeq</option> + <option value="DESeq2">DESeq2</option> + </param> + + + + <!-- Optional --> + +</inputs> +<outputs> + <data name='de_output' format='zip' label="${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>