changeset 10:f7136e93604b draft

planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit b9403b3ce2b7a41fa8ee1aa47909152de78cf641

--- a/fsd.py	Wed May 09 09:41:38 2018 -0400
+++ b/fsd.py	Tue May 15 13:49:34 2018 -0400
@@ -11,8 +11,7 @@
 # If only one file is provided, then a family size distribution, which is separated after SSCSs without a partner and DCSs, is produced.
 # Whereas a family size distribution with multiple data in one plot is produced, when more than one file (up to 4) is given.
 
-# USAGE: python FSD_Galaxy_1.4_commandLine_FINAL.py filename --inputFile2 filename2 --inputFile3 filename3 --inputFile4 filename4 /
-#        --title_file outputFileName --sep "characterWhichSeparatesCSVFile"
+# USAGE: python FSD_Galaxy_1.4_commandLine_FINAL.py --inputFile1 filename --inputName1 filename --inputFile2 filename2 --inputName2 filename2 --inputFile3 filename3 --inputName3 filename3 --inputFile4 filename4 --inputName4 filename4 --sep "characterWhichSeparatesCSVFile" --output_csv outptufile_name_csv --output_pdf outptufile_name_pdf
 
 import numpy
 import matplotlib.pyplot as plt
@@ -55,7 +54,6 @@
 
     firstFile = args.inputFile1
     name1 = args.inputName1
-    #firstFile = args.inputName1
     
     secondFile = args.inputFile2
     name2 = args.inputName2
@@ -75,8 +73,8 @@
     plt.rc('figure', figsize=(11.69, 8.27))  # A4 format
     plt.rcParams['patch.edgecolor'] = "black"
     plt.rcParams['axes.facecolor'] = "E0E0E0"  # grey background color
-    plt.rcParams['xtick.labelsize'] = 12
-    plt.rcParams['ytick.labelsize'] = 12
+    plt.rcParams['xtick.labelsize'] = 14
+    plt.rcParams['ytick.labelsize'] = 14
 
     list_to_plot = []
     label = []
@@ -86,8 +84,6 @@
        fig = plt.figure()
        plt.subplots_adjust(bottom=0.25)
        if firstFile != str(None):
-           print(firstFile)
-           
            file1 = readFileReferenceFree(firstFile)
            integers = numpy.array(file1[:, 0]).astype(int)  ## keep original family sizes
 
@@ -217,8 +213,8 @@
        plt.xticks(numpy.array(ticks), ticks1)
 
        plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(0.9, 1))
-       plt.title("Family Size Distribution", fontsize=14)
-       plt.xlabel("No. of Family Members", fontsize=14)
+     #  plt.title("Family Size Distribution", fontsize=14)
+       plt.xlabel("Family size", fontsize=14)
        plt.ylabel("Absolute Frequency", fontsize=14)
        plt.margins(0.01, None)
        plt.grid(b=True, which="major", color="#424242", linestyle=":")
@@ -325,8 +321,8 @@
             last = counts[0][2][len(counts[0][0]) - 1]  # large families
 
             plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True)
-            plt.title(name1, fontsize=14)
-            plt.xlabel("No. of Family Members", fontsize=14)
+         #   plt.title(name1, fontsize=14)
+            plt.xlabel("Family size", fontsize=14)
             plt.ylabel("Absolute Frequency", fontsize=14)
             plt.margins(0.01, None)
             plt.grid(b=True, which="major", color="#424242", linestyle=":")

--- a/fsd.xml	Wed May 09 09:41:38 2018 -0400
+++ b/fsd.xml	Tue May 15 13:49:34 2018 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!-- galaxy version 16.04 -->
-<tool id="fsd" name="Duplex Sequencing Analysis:" version="0.0.10">
+<tool id="fsd" name="Duplex Sequencing Analysis:" version="0.0.11">
     <description>Family size distribution (FSD) of tags</description>
     <requirements>
         <requirement type="package" version="2.7">python</requirement>
@@ -8,13 +8,13 @@
     </requirements>
     
     <command>
-        python2 $__tool_directory__/fsd.py --inputFile1 "$file1" --inputName1 "$file1.name" --inputFile2 "$file2" --inputName2 "$file2.name" --inputFile3 "$file3" --inputName3 "$file3.name" --inputFile4 "$file4" --inputName4 "$file4.name" --sep $separator --output_csv $output_csv --output_pdf $output_pdf
+        python2 $__tool_directory__/fsd.py --inputFile1 "$file1" --inputName1 "$file1.name" --inputFile2 "$file2" --inputName2 "$file2.name" --inputFile3 "$file3" --inputName3 "$file3.name" --inputFile4 "$file4" --inputName4 "$file4.name" --sep $separator --output_pdf $output_pdf --output_csv $output_csv 
     </command>
     <inputs>
         <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/>
         <param name="file2" type="data" format="tabular" label="Dataset 2: input tags" optional="true"  />
         <param name="file3" type="data" format="tabular" label="Dataset 3: input tags" optional="true" />
-        <param name="file4" type="data" format="tabular" label="Dataset 4: input tags" optional="true"  help="Input in tabular format with the family size, tags and the direction of the strand ('ab' or 'ba') for each family. Name of the files can have max. 34 charcters, blanks are not allowed!"/>
+        <param name="file4" type="data" format="tabular" label="Dataset 4: input tags" optional="true"  help="Input in tabular format with the family size, tags and the direction of the strand ('ab' or 'ba') for each family. Name of the files can have max. 34 charcters!"/>
         <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/>
     </inputs>
     <outputs>
@@ -43,7 +43,7 @@
         
     This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands. 
     
-    **!!! Name of the files can have max. 34 charcters, blanks are not allowed !!!**
+    **!!! Name of the files can have max. 34 charcters !!!**
     
     +-----+----------------------------+----+
     | 1   | AAAAAAAAAAAATGTTGGAATCTT   | ba |