diff interproscan5/ipsfaux.xml @ 3:74cf3f49f10c draft

Better HTML index.

--- a/interproscan5/ipsfaux.xml	Fri Jan 29 18:41:29 2016 -0500
+++ b/interproscan5/ipsfaux.xml	Tue Feb 02 12:27:19 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="ipsfaux" name="Faux Interproscan" version="1.0.0a">
+<tool id="ipsfaux" name="Faux Interproscan" version="1.0.1a">
     <description>Interproscan functional predictions of ORFs (faux). Input file and computation options are
     ignored (other than the types of outputs). The same precomputed results are produced every time.</description>
     <requirements>
@@ -12,8 +12,7 @@
 
     <command>
         #import os
-        echo "output_types=$output_types";
-
+        echo "Start timestamp: \$(date)";
         python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/fake_ips.py
             ## disables the precalculated lookup service, all calculation will be run locally
             -dp
@@ -21,7 +20,6 @@
             --seqtype $seqtype
             -f $output_types
             --applications $appl
-            --tempdir \$TEMP
 
             $pathways
             $goterms
@@ -30,9 +28,7 @@
             --output-file-base __base__
             2>&#38;1;
 
-        #if 'tsv' in str($output_types):
-            mv __base__.tsv $tsv_file;
-        #end if
+        mv __base__.tsv $tsv_file;
 
         #if 'gff3' in str($output_types):
             mv __base__.gff3 $gff3_file;
@@ -46,7 +42,11 @@
             mkdir -p $html_file.files_path;
             #set temp_archive_file = '__base__.html.tar.gz'
             tar -C $html_file.files_path -xvmzf $temp_archive_file;
-            python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $html_file $html_file.files_path;
+            #if str($seqtype) == 'p' and not str($getorfed):
+                python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $html_file $html_file.files_path;
+            #else
+                python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $html_file $html_file.files_path;
+            #end if
             rm $temp_archive_file;
         #end if
 
@@ -54,11 +54,15 @@
             mkdir -p $svg_file.files_path;
             #set temp_archive_file = '__base__.svg.tar.gz'
             tar -C $svg_file.files_path -xvmzf $temp_archive_file;
-            python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path;
+            #if str($seqtype) == 'p' and not str($getorfed):
+                python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $svg_file $svg_file.files_path;
+            #else
+                python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $svg_file $svg_file.files_path;
+            #end if
             rm $temp_archive_file;
         #end if
 
-        echo "End of ipsfaux"
+        echo "End timestamp: \$(date)"
     </command>
 
     <inputs>
@@ -69,6 +73,10 @@
             <option value="n">DNA / RNA</option>
         </param>
 
+        <param name="getorfed" type="boolean" label="DNA/RNA was externally processed by getorf?" help="Ignored for DNA inputs."
+               truevalue="getorfed"
+               falsevalue=""/>
+
         <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."
                truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"
                falsevalue=""/>
@@ -111,9 +119,8 @@
                label="Provide additional mappings"
                help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>
 
-        <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats"
+        <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats (in addition to TSV)"
                help="Select the output formats to generate (at least one)">
-            <option value="tsv" selected="true">Raw (TSV)</option>
             <option value="html" selected="true">HTML (Graphical)</option>
             <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option>
             <option value="gff3" selected="true">GFF3</option>
@@ -122,9 +129,7 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}">
-            <filter>'tsv' in output_types</filter>
-        </data>
+        <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}"/>
         <data format="html" name="html_file" label="Interproscan HTML on ${on_string}">
             <filter>'html' in output_types</filter>
         </data>