--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compare_within_models.xml	Wed Dec 16 23:29:26 2020 +0000
@@ -0,0 +1,120 @@
+<tool id="pancancer_compare_within_models" name="PAPAA: PanCancer compare within models" version="@VERSION@">
+    <description>compare within models</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <version_command><![CDATA['papaa_compare_within_models.R' --version 2>&1 | grep PAPAA]]></version_command>
+    <command><![CDATA[
+        mkdir 'classifier' &&
+        mkdir -p 'classifier/figures' &&
+        ln -s '${pancan_classifier_summary}' 'classifier/classifier_summary.txt' &&
+        ln -s '${pancan_classifier_coefficients}' 'classifier/classifier_coefficients.tsv' &&
+        #for $within_summary in $pancan_within_classifier_summary:
+            mkdir -p 'classifier/within_disease/${within_summary.element_identifier}' &&
+            ln -s '${within_summary}' 'classifier/within_disease/${within_summary.element_identifier}/classifier_summary.txt' &&
+        #end for
+        #for $within_coefficient in $pancan_within_classifier_coefficients:
+            mkdir -p 'classifier/within_disease/${within_coefficient.element_identifier}' &&
+            ln -s '${within_coefficient}' 'classifier/within_disease/${within_coefficient.element_identifier}/classifier_coefficients.tsv' &&
+        #end for
+        #if $include_alt.include_alt_select == 'true':
+        mkdir 'alt_classifier' &&
+        ln -s '${include_alt.alt_pancan_classifier_summary}' 'alt_classifier/classifier_summary.txt' &&
+        ln -s '${include_alt.alt_pancan_classifier_coefficients}' 'alt_classifier/classifier_coefficients.tsv' &&
+        #for $within_summary in $include_alt.alt_pancan_within_classifier_summary:
+            mkdir -p 'alt_classifier/within_disease/${within_summary.element_identifier}' &&
+            ln -s '${within_summary}' 'alt_classifier/within_disease/${within_summary.element_identifier}/classifier_summary.txt' &&
+        #end for
+        #for $within_coefficient in $include_alt.alt_pancan_within_classifier_coefficients:
+            mkdir -p 'alt_classifier/within_disease/${within_coefficient.element_identifier}' &&
+            ln -s '${within_coefficient}' 'alt_classifier/within_disease/${within_coefficient.element_identifier}/classifier_coefficients.tsv' &&
+        #end for
+        #end if
+        ls -lahR &&
+        papaa_compare_within_models.R
+        --pancan_model 'classifier'
+        #if $include_alt.include_alt_select == 'true':
+        --alt_model 'alt_classifier'
+        #end if
+        > '${log}'
+        ]]>
+    </command>
+    <inputs>
+        <param argument="--pancan_model" label="pancancer classifier summary" name="pancan_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 label="pan_within classifier summary" name="pancan_within_classifier_summary" optional="false" type="data" format="txt" multiple="true" help="multiple classifer_summary.txt"/>
+        <param label="pan_within classifier coefficients" name="pancan_within_classifier_coefficients" optional="false" type="data" format="tabular" multiple="true" help="multiple classifier_coefficients.tsv"/>
+        <conditional name="include_alt">
+          <param name="include_alt_select" type="select" label="Would you want to compare given model with alt gene model?" help="output of pancancer classifier and pancancer within disease for alt gene">
+            <option value="false" selected="true">do not do alt gene</option>
+            <option value="true">do alt gene</option>
+          </param>
+          <when value="true">
+                <param argument="--alt_model" label="pancancer classifier summary" name="alt_pancan_classifier_summary" optional="false" type="data" format="txt" help="alt classifer_summary.txt"/>
+                <param label="pancancer classifier coefficients" name="alt_pancan_classifier_coefficients" optional="false" type="data" format="tabular" help="alt classifier_coefficients.tsv"/>
+                <param argument="pan_within classifier summary" label="alt_pancan_within_classifier_summary" name="alt_pancan_within_classifier_summary" optional="true" type="data" format="txt" multiple="true" help="multiple alt classifer_summary.txt"/>
+                <param label="alt_pancan_within classifier coefficients" name="alt_pancan_within_classifier_coefficients" optional="true" type="data" format="tabular" multiple="true" help="multiple alt classifier_coefficients.tsv"/>
+            </when>
+            <when value="false">
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)" />
+        <data format="pdf" name="aupr_comparison" label="${tool.name} on ${on_string} (aupr_comparison.pdf)" from_work_dir="classifier/figures/aupr_comparison.pdf"/>
+        <data format="pdf" name="auroc_comparison" label="${tool.name} on ${on_string} (auroc_comparison.pdf)" from_work_dir="classifier/figures/auroc_comparison.pdf"/>
+        <data format="pdf" name="alt_gene_aupr_comparison" label="${tool.name} on ${on_string} (alt_gene_aupr_comparison.pdf)" from_work_dir="classifier/figures/alt_gene_aupr_comparison.pdf" >
+          <filter>include_alt['include_alt_select'] == 'true' </filter> 
+        </data>
+        <data format="pdf" name="alt_gene_auroc_comparison" label="${tool.name} on ${on_string} (alt_gene_auroc_comparison.pdf)" from_work_dir="classifier/figures/alt_gene_auroc_comparison.pdf" >
+          <filter>include_alt['include_alt_select'] == 'true' </filter> 
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="pancan_classifier_summary" value="classifier_summary.txt" ftype="txt"/>
+            <param name="pancan_classifier_coefficients" value="classifier_coefficients.tsv" ftype="tabular"/>
+            <param name="pancan_within_classifier_summary" value="classifier_summary/GBM" > <!--
+                <collection type="list">
+                    <element name="GBM" value="GBM_100.txt" ftype="txt"/>
+                </collection> -->
+            </param>
+            <param name="pancan_within_classifier_coefficients" value="classifier_coefficients/GBM"> <!--
+                <collection type="list">
+                    <element name="GBM" value="GBM_99.tabular" ftype="tabular"/>
+                </collection> -->
+            </param>
+            <param name="include_alt_select" value="false"/>
+            <!--
+            <conditional name="include_alt">
+              <param name="include_alt_select" value="false"/>
+                <param name="alt_pancan_summary" value="alt_pancan_summary.txt" ftype="txt"/>
+                <param name="alt_pancan_classifier_coefficients" value="alt_pancan_classifier_coefficients.tsv" ftype="tabular"/>
+                <param name="alt_pan_within_classifier_summary" value="alt_pan_within_classifier_summary.txt" ftype="txt"/>
+                <param name="alt_pan_within_classifier_coefficients" value="alt_pan_within_classifier_coefficients.tsv" ftype="tabular"/> 
+            </conditional>
+            -->
+            <output name="log" file="compare_within_models_Log.txt"/>
+            <output name="aupr_comparison" file="aupr_comparison.pdf" compare="sim_size" delta="50"/>
+            <output name="auroc_comparison" file="auroc_comparison.pdf" compare="sim_size" delta="50"/>
+
+        </test>
+    </tests>
+    <help><![CDATA[
+
+        **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_compare_within_models.R:**
+            
+            **Inputs:**
+                --pancan_model      String of the Directory: location of Pan classifier summary file
+                --alt_model         String of the Directory: location of Alt gene classifier summary file
+            
+            **Outputs:**
+                Comparison plots for Pan and Pan_within models ("auroc_comparison.pdf" and "aupr_comparison.pdf")  
+
+                Comparison plots for altgene, alt_within, Pan_alt models ("alt_gene_auroc_comparison.pdf" and "alt_gene_aupr_comparison.pdf")  ]]>
+            
+    </help>
+    <expand macro="citations" />
+</tool>