--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/external_sample_status_prediction.xml	Wed Dec 16 23:30:03 2020 +0000
@@ -0,0 +1,65 @@
+<tool id="pancancer_external_sample_status_prediction" name="PAPAA: PanCancer external sample status prediction" version="@VERSION@">
+    <description>external sample status</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <version_command><![CDATA['papaa_external_sample_pred_targene_classifier.py' --version]]></version_command>
+    <command><![CDATA[
+        mkdir 'classifier' &&
+        mkdir -p 'classifier/figures' &&
+        ln -s '${classifier_summary}' 'classifier/classifier_summary.txt' &&
+        ln -s '${pancan_classifier_coefficients}' 'classifier/classifier_coefficients.tsv' &&
+        papaa_external_sample_pred_targene_classifier.py
+        --classifier_summary 'classifier'
+        #if $ex_vlog and str($ex_vlog):
+        --expression_file '$ex_vlog'
+        #end if
+        #if $sign and str($sign):
+        --status_sign '$sign'
+        #end if
+        --figure1 '${figure1}'
+        --figure2 '${figure2}'
+        > '${log}'
+        ]]>
+    </command>
+    <inputs>
+        <param argument="--classifier_summary" label="Classifier data" name="classifier_summary" optional="false" type="data" format="txt" help="classifer_summary.txt"/>
+        <param label="pancancer classifier coefficients" name="pancan_classifier_coefficients" optional="false" type="data" format="tabular" help="classifier_coefficients.tsv"/>
+        <param argument="--expression_file" label="external sample gene expression data" name="ex_vlog" optional="false" type="data" format="csv" help="data/vlog_trans.csv" />
+        <param argument="--status_sign" label="given mutational status" name="sign" optional="false" type="data" format="txt" help="data/sign.txt" />
+    </inputs>
+    <outputs>
+        <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)" />
+        <data format="pdf" name="figure1" label="${tool.name} on ${on_string} (Figure 1)" />
+        <data format="pdf" name="figure2" label="${tool.name} on ${on_string} (Figure 2)" />
+    </outputs>
+    <tests>
+        <test>
+          <param name="classifier_summary" value="classifier_summary.txt" ftype="txt"/>
+          <param name="pancan_classifier_coefficients" value="classifier_coefficients.tsv" ftype="tabular"/>
+          <param name="ex_vlog" value="vlog_trans.csv.gz" ftype="csv"/>
+          <param name="sign" value="sign.txt" ftype="txt"/>
+          <output name="log" file="external_sample_status_prediction_Log.txt" />
+          <output name="figure1" file="Figure_1.pdf" compare="sim_size" delta="50"/>
+          <output name="figure2" file="Figure_2.pdf" compare="sim_size" delta="50"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+      **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_external_sample_pred_targene_classifier.py:**
+        
+        **Inputs:**
+          --classifier_summary  String of the location of classifier scores file
+
+          --expression_file   File path for external sample expression data file (fpkm/rpkm/rlog/vlog/nlog values)
+
+          --status_sign   Provide sign for tumor/mutant [1] or normal/WT [-1] along with sorted sample names
+      
+        **Outputs:**
+          Model based classification scores distribution Plots for external normal and tumor samples   ("targene_external_sample_predictions.pdf and targene_external_sample_predictions_1.pdf")  ]]>
+      
+    </help>
+    <expand macro="citations" />
+</tool>