# HG changeset patch
# User charles-bernard
# Date 1513881229 18000
# Node ID 5d745637f0450c76856e123fa1ed211eed860ef1
# Parent  f4b26211e3d885223b43416a753af0222125c726
Uploaded

diff -r f4b26211e3d8 -r 5d745637f045 alfa/.shed.yml
--- a/alfa/.shed.yml	Thu Dec 21 12:58:57 2017 -0500
+++ b/alfa/.shed.yml	Thu Dec 21 13:33:49 2017 -0500
@@ -4,7 +4,7 @@
 - Sequence Analysis
 - Visualization
 description: Plot the distribution of the genomic features captured by aligned reads
-long_description: |
+long_description:
 	ALFA provides a global overview of features distribution composing New Generation Sequencing dataset(s).
 	Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism.
 	https://github.com/biocompibens/ALFA
diff -r f4b26211e3d8 -r 5d745637f045 alfa/ALFA.xml
--- a/alfa/ALFA.xml	Thu Dec 21 12:58:57 2017 -0500
+++ b/alfa/ALFA.xml	Thu Dec 21 13:33:49 2017 -0500
@@ -79,8 +79,8 @@
 					</param>
 				</when>
 				<when value="index">
-					<param name="strandedIndex" type="data" format="index" label="Select your ALFA Stranded index file (index format)"/>
-					<param name="unstrandedIndex" type="data" format="index" label="Select your ALFA Unstranded index file (index format)"/>
+					<param name="strandedIndex" type="data" label="Select your ALFA Stranded index file (index format)"/>
+					<param name="unstrandedIndex" type="data" label="Select your ALFA Unstranded index file (index format)"/>
 				</when>
 				<when value="built_in_index">
 					<param name="built_in_index_prefix" type="select" label="Select Genome">
@@ -132,9 +132,9 @@
 				<option value="4">5’-UTR | start_codon | CDS | undescribed CDS | stop_codon | 3’-UTR | undescribed exons | intron | undescribed genes | intergenic | antisense</option>
 			</param>
 			<param name="plotFormat" type="select" label="Plot Options: Select graph format" help="Ignore if you did not choose the histograms output file">
-				<option value="pdf" selected="true">pdf</option>
+				<option value="png"  selected="true">png</option>
+				<!--<option value="pdf" selected="true">pdf</option>-->
 				<option value="svg">svg</option>
-				<option value="png">png</option>
 			</param>
 			<conditional name="plotThreshold">
 				<param name="plotThresholdChoice" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Plot Options: Modify y axis range of the normalized counts of bio-features" help="Ignore if you did not choose the histograms output file"/>
@@ -149,9 +149,11 @@
 	
 	<outputs>
 		<data name="logReport" format="txt" label="${projectName}-Log Report"/>
+		<!--
 		<data name="outputPdf" format="pdf" label="${projectName}-BioFeatures Distribution">
 			<filter>outputFiles['plot'] is True and outputOptions['plotFormat'] == 'pdf'</filter>
 		</data>
+		-->
 		<data name="outputCategoriesPng" format="png" label="${projectName}-Categories Distribution">
 			<filter>outputFiles['plot'] is True and outputOptions['plotFormat'] == 'png'</filter>
 		</data>
diff -r f4b26211e3d8 -r 5d745637f045 alfa/ALFA_wrapper.py
--- a/alfa/ALFA_wrapper.py	Thu Dec 21 12:58:57 2017 -0500
+++ b/alfa/ALFA_wrapper.py	Thu Dec 21 13:33:49 2017 -0500
@@ -147,6 +147,7 @@
     # Change into the tmp dir because ALFA produces files in the current dir
     curr_dir = os.getcwd()
     os.chdir(tmp_dir)
+    print(cmd)
     logging.info("__________________________________________________________________\n")
     logging.info("Alfa execution")
     logging.info("__________________________________________________________________\n")
@@ -164,11 +165,11 @@
     if args.output_pdf:
         shutil.move(plot_suffix + '.pdf', args.output_pdf[0])
     if args.output_png:
-        shutil.move(plot_suffix + '.categories.png', args.output_png[0])
-        shutil.move(plot_suffix + '.biotypes.png', args.output_png[1])
+        shutil.move(plot_suffix + '.Categories.png', args.output_png[0])
+        shutil.move(plot_suffix + '.Biotypes.png', args.output_png[1])
     if args.output_svg:
-        shutil.move(plot_suffix + '.categories.svg', args.output_svg[0])
-        shutil.move(plot_suffix + '.biotypes.svg', args.output_svg[1])
+        shutil.move(plot_suffix + '.Categories.svg', args.output_svg[0])
+        shutil.move(plot_suffix + '.Biotypes.svg', args.output_svg[1])
     if args.output_count:
         count_filename = merge_count_files(reads_labels)
         shutil.move(count_filename, args.output_count[0])