# HG changeset patch
# User fangly
# Date 1318916894 14400
# Node ID 68576b1d2d8bb66e7dd9e6bc9cae5aaf7b4ed62e
# Parent  5ba7c9ac056a6fc96aeb0237bdca6b1291a34f90
Uploaded

diff -r 5ba7c9ac056a -r 68576b1d2d8b grinder.xml
--- a/grinder.xml	Tue Oct 04 02:01:58 2011 -0400
+++ b/grinder.xml	Tue Oct 18 01:48:14 2011 -0400
@@ -1,13 +1,4 @@
-<tool id="grinder" name="Grinder" version="0.3.8" force_history_refresh="True">
-
-  <!--
-    Author: florent.angly@gmail.com
-    TODO:
-    • See bfast tool (tools/sr_mapping/bfast_wrapper.xml) for how to use datatables easily
-    • Basic tests
-    • Link to full manual
-    • Better sync with Grinder parameters, defaults and help
-  -->
+<tool id="grinder" name="Grinder" version="0.3.9">
 
   <description>genomic, metagenomic and amplicon read simulator</description>
 
@@ -17,12 +8,8 @@
 
   <version_string>grinder --version</version_string>
 
-  <command>
-    #set $tool_dir = os.path.join( os.path.abspath($__root_dir__), 'tools', 'ngs_simulation' )
-    #set $script1  = os.path.join( $tool_dir, 'stderr_wrapper.py' )
-    #set $script2  = os.path.join( $tool_dir, 'grinder_multiple_outputs.py' )
-
-    $script1
+  <command interpreter="python">
+    stderr_wrapper.py
       grinder
       #if $reference_file.specify == "builtin":
         -reference_file   ${ filter( lambda x: str( x[0] ) == str( $reference_file.value ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }
@@ -101,7 +88,7 @@
       #if str($qual_levels):
         -qual_levels      $qual_levels
       #end if
-      #if str($fastq_output):
+      #if str($fastq_output) == '1':
         -fastq_output     $fastq_output
       #end if
       #if str($profile_file) != "None":
@@ -110,16 +97,6 @@
       <!-- When Galaxy bug #661 is resolved, then we can use the same method to check for all optional argument  -->
       <!-- i.e. either   if str($param) != "None":   or   if str($param):                                        -->
       <!-- URL: https://bitbucket.org/galaxy/galaxy-central/issue/661/optional-arguments-problems#comment-655611 -->
-
-      #set $output_dir = $__new_file_path__
-      -output_dir         $output_dir
-
-      #set $base_name  = $output.id
-      -base_name          $base_name
-    ;
-
-    $script2 $output_dir $base_name
-
   </command>
 
   <inputs>
@@ -199,7 +176,7 @@
    1/ uniform distribution: uniform,
    2/ powerlaw distribution with parameter 0.1: powerlaw 0.1." />
 
-    <param name="num_libraries" type="text" value="1" optional="true" label="Number of libraries" help="Number of independent libraries to create. Specify how diverse and similar they should be using the options diversity, shared percent; and permuted percent. Assign them different MID tags with the multiplex mids option." />
+    <param name="num_libraries" type="text" value="1" optional="true" label="Number of libraries" help="Number of independent libraries to create. Specify how diverse and similar they should be using the options diversity, shared percent; and permuted percent. Assign them different MID tags with the multiplex mids option. Note that in Galaxy, the maximum number of libraries is 10." />
 
     <param name="multiplex_ids" type="data" format="fasta" optional="true" label="Specify MID tags file" help="Specify an optional FASTA file that contains sequence identifiers (a.k.a MIDs or barcodes) to add to the sequences (one per library)."/>
 
@@ -248,7 +225,164 @@
   -->
 
   <outputs>
-    <data format="text" name="output" />
+
+    <!-- single library output -->
+    <data format="tabular" name="ranks" from_work_dir="grinder-ranks.txt"   label="${tool.name} ranks from ${on_string}">
+      <filter>int(str(num_libraries)) == 1</filter>
+    </data>
+    <data format="fasta"   name="fasta" from_work_dir="grinder-reads.fa"    label="${tool.name} reads from ${on_string}">
+      <filter>int(str(num_libraries)) == 1 and fastq_output == 0</filter>
+    </data>
+    <data format="qual"    name="qual"  from_work_dir="grinder-reads.qual"  label="${tool.name} quals from ${on_string}">
+      <filter>int(str(num_libraries)) == 1 and str(qual_levels) and fastq_output == 0</filter>
+    </data>
+    <data format="fastq"   name="fastq" from_work_dir="grinder-reads.fastq" label="${tool.name} reads from ${on_string}">
+      <filter>int(str(num_libraries)) == 1 and fastq_output == 1</filter>
+    </data>
+
+    <!-- When Galaxy bug #670 is resolved, then we won't have to harcode the number of output datasets  -->
+    <!-- URL: https://bitbucket.org/galaxy/galaxy-central/issue/670/better-support-for-multiple-outputs -->
+
+    <!-- multiple libraries: library 1 -->
+    <data format="tabular" name="ranks1" from_work_dir="grinder-1-ranks.txt"   label="${tool.name} lib 1 ranks from ${on_string}">
+      <filter>int(str(num_libraries)) >= 2</filter>
+    </data>
+    <data format="fasta"   name="fasta1" from_work_dir="grinder-1-reads.fa"    label="${tool.name} lib 1 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 2 and fastq_output == 0</filter>
+    </data>
+    <data format="qual"    name="qual1"  from_work_dir="grinder-1-reads.qual"  label="${tool.name} lib 1 quals from ${on_string}">
+      <filter>int(str(num_libraries)) >= 2 and str(qual_levels) and fastq_output == 0</filter>
+    </data>
+    <data format="fastq"   name="fastq1" from_work_dir="grinder-1-reads.fastq" label="${tool.name} lib 1 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 2 and fastq_output == 1</filter>
+    </data>
+
+    <!-- multiple libraries: library 2 -->
+    <data format="tabular" name="ranks2" from_work_dir="grinder-2-ranks.txt"   label="${tool.name} lib 2 ranks from ${on_string}">
+      <filter>int(str(num_libraries)) >= 2</filter>
+    </data>
+    <data format="fasta"   name="fasta2" from_work_dir="grinder-2-reads.fa"    label="${tool.name} lib 2 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 2 and fastq_output == 0</filter>
+    </data>
+    <data format="qual"    name="qual2"  from_work_dir="grinder-2-reads.qual"  label="${tool.name} lib 2 quals from ${on_string}">
+      <filter>int(str(num_libraries)) >= 2 and str(qual_levels) and fastq_output == 0</filter>
+    </data>
+    <data format="fastq"   name="fastq2" from_work_dir="grinder-2-reads.fastq" label="${tool.name} lib 2 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 2 and fastq_output == 1</filter>
+    </data>
+
+    <!-- multiple libraries: library 3 -->
+    <data format="tabular" name="ranks3" from_work_dir="grinder-3-ranks.txt"   label="${tool.name} lib 3 ranks from ${on_string}">
+      <filter>int(str(num_libraries)) >= 3</filter>
+    </data>
+    <data format="fasta"   name="fasta3" from_work_dir="grinder-3-reads.fa"    label="${tool.name} lib 3 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 3 and fastq_output == 0</filter>
+    </data>
+    <data format="qual"    name="qual3"  from_work_dir="grinder-3-reads.qual"  label="${tool.name} lib 3 quals from ${on_string}">
+      <filter>int(str(num_libraries)) >= 3 and str(qual_levels) and fastq_output == 0</filter>
+    </data>
+    <data format="fastq"   name="fastq3" from_work_dir="grinder-3-reads.fastq" label="${tool.name} lib 3 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 3 and fastq_output == 1</filter>
+    </data>
+
+    <!-- multiple libraries: library 4 -->
+    <data format="tabular" name="ranks4" from_work_dir="grinder-4-ranks.txt"   label="${tool.name} lib 4 ranks from ${on_string}">
+      <filter>int(str(num_libraries)) >= 4</filter>
+    </data>
+    <data format="fasta"   name="fasta4" from_work_dir="grinder-4-reads.fa"    label="${tool.name} lib 4 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 4 and fastq_output == 0</filter>
+    </data>
+    <data format="qual"    name="qual4"  from_work_dir="grinder-4-reads.qual"  label="${tool.name} lib 4 quals from ${on_string}">
+      <filter>int(str(num_libraries)) >= 4 and str(qual_levels) and fastq_output == 0</filter>
+    </data>
+    <data format="fastq"   name="fastq4" from_work_dir="grinder-4-reads.fastq" label="${tool.name} lib 4 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 4 and fastq_output == 1</filter>
+    </data>
+
+    <!-- multiple libraries: library 5 -->
+    <data format="tabular" name="ranks5" from_work_dir="grinder-5-ranks.txt"   label="${tool.name} lib 5 ranks from ${on_string}">
+      <filter>int(str(num_libraries)) >= 5</filter>
+    </data>
+    <data format="fasta"   name="fasta5" from_work_dir="grinder-5-reads.fa"    label="${tool.name} lib 5 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 5 and fastq_output == 0</filter>
+    </data>
+    <data format="qual"    name="qual5"  from_work_dir="grinder-5-reads.qual"  label="${tool.name} lib 5 quals from ${on_string}">
+      <filter>int(str(num_libraries)) >= 5 and str(qual_levels) and fastq_output == 0</filter>
+    </data>
+    <data format="fastq"   name="fastq5" from_work_dir="grinder-5-reads.fastq" label="${tool.name} lib 5 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 5 and fastq_output == 1</filter>
+    </data>
+
+    <!-- multiple libraries: library 6 -->
+    <data format="tabular" name="ranks6" from_work_dir="grinder-6-ranks.txt"   label="${tool.name} lib 6 ranks from ${on_string}">
+      <filter>int(str(num_libraries)) >= 6</filter>
+    </data>
+    <data format="fasta"   name="fasta6" from_work_dir="grinder-6-reads.fa"    label="${tool.name} lib 6 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 6 and fastq_output == 0</filter>
+    </data>
+    <data format="qual"    name="qual6"  from_work_dir="grinder-6-reads.qual"  label="${tool.name} lib 6 quals from ${on_string}">
+      <filter>int(str(num_libraries)) >= 6 and str(qual_levels) and fastq_output == 0</filter>
+    </data>
+    <data format="fastq"   name="fastq6" from_work_dir="grinder-6-reads.fastq" label="${tool.name} lib 6 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 6 and fastq_output == 1</filter>
+    </data>
+
+    <!-- multiple libraries: library 7 -->
+    <data format="tabular" name="ranks7" from_work_dir="grinder-7-ranks.txt"   label="${tool.name} lib 7 ranks from ${on_string}">
+      <filter>int(str(num_libraries)) >= 7</filter>
+    </data>
+    <data format="fasta"   name="fasta7" from_work_dir="grinder-7-reads.fa"    label="${tool.name} lib 7 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 7 and fastq_output == 0</filter>
+    </data>
+    <data format="qual"    name="qual7"  from_work_dir="grinder-7-reads.qual"  label="${tool.name} lib 7 quals from ${on_string}">
+      <filter>int(str(num_libraries)) >= 7 and str(qual_levels) and fastq_output == 0</filter>
+    </data>
+    <data format="fastq"   name="fastq7" from_work_dir="grinder-7-reads.fastq" label="${tool.name} lib 7 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 7 and fastq_output == 1</filter>
+    </data>
+
+    <!-- multiple libraries: library 8 -->
+    <data format="tabular" name="ranks8" from_work_dir="grinder-8-ranks.txt"   label="${tool.name} lib 8 ranks from ${on_string}">
+      <filter>int(str(num_libraries)) >= 8</filter>
+    </data>
+    <data format="fasta"   name="fasta8" from_work_dir="grinder-8-reads.fa"    label="${tool.name} lib 8 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 8 and fastq_output == 0</filter>
+    </data>
+    <data format="qual"    name="qual8"  from_work_dir="grinder-8-reads.qual"  label="${tool.name} lib 8 quals from ${on_string}">
+      <filter>int(str(num_libraries)) >= 8 and str(qual_levels) and fastq_output == 0</filter>
+    </data>
+    <data format="fastq"   name="fastq8" from_work_dir="grinder-8-reads.fastq" label="${tool.name} lib 8 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 8 and fastq_output == 1</filter>
+    </data>
+
+    <!-- multiple libraries: library 9 -->
+    <data format="tabular" name="ranks9" from_work_dir="grinder-9-ranks.txt"   label="${tool.name} lib 9 ranks from ${on_string}">
+      <filter>int(str(num_libraries)) >= 9</filter>
+    </data>
+    <data format="fasta"   name="fasta9" from_work_dir="grinder-9-reads.fa"    label="${tool.name} lib 9 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 9 and fastq_output == 0</filter>
+    </data>
+    <data format="qual"    name="qual9"  from_work_dir="grinder-9-reads.qual"  label="${tool.name} lib 9 quals from ${on_string}">
+      <filter>int(str(num_libraries)) >= 9 and str(qual_levels) and fastq_output == 0</filter>
+    </data>
+    <data format="fastq"   name="fastq9" from_work_dir="grinder-9-reads.fastq" label="${tool.name} lib 9 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 9 and fastq_output == 1</filter>
+    </data>
+
+    <!-- multiple libraries: library 10 -->
+    <data format="tabular" name="ranks10" from_work_dir="grinder-10-ranks.txt"   label="${tool.name} lib 10 ranks from ${on_string}">
+      <filter>int(str(num_libraries)) >= 10</filter>
+    </data>
+    <data format="fasta"   name="fasta10" from_work_dir="grinder-10-reads.fa"    label="${tool.name} lib 10 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 10 and fastq_output == 0</filter>
+    </data>
+    <data format="qual"    name="qual10"  from_work_dir="grinder-10-reads.qual"  label="${tool.name} lib 10 quals from ${on_string}">
+      <filter>int(str(num_libraries)) >= 10 and str(qual_levels) and fastq_output == 0</filter>
+    </data>
+    <data format="fastq"   name="fastq10" from_work_dir="grinder-10-reads.fastq" label="${tool.name} lib 10 reads from ${on_string}">
+      <filter>int(str(num_libraries)) >= 10 and fastq_output == 1</filter>
+    </data>
+
   </outputs>
 
   <tests>
@@ -270,7 +404,6 @@
       <output name="qual" file="" />
     </test>
     -->
-
   </tests>
 
   <help>
diff -r 5ba7c9ac056a -r 68576b1d2d8b grinder_multiple_outputs.py
--- a/grinder_multiple_outputs.py	Tue Oct 04 02:01:58 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Move files create by Grinder to a location where it is going to be recognized by
-Galaxy as multiple output files with the right format. See
-http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple Output Files
-Example: python grinder_move_outputs output_dir output_id
-Author: Florent Angly
-"""
-
-import sys, os, re
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-def stop_err( msg ):
-    sys.stderr.write( "%s\n" % msg )
-    sys.exit()
-
-def __main__():
-    # Get output dir and ID
-    args = sys.argv
-    output_dir = args[1]
-    output_id  = args[2]
-
-    # Move Grinder files to the proper output
-    # Grinder filenames look like this
-    #   grinder-ranks.txt
-    #   grinder-reads.fa
-    #   grinder-reads.qual
-    #   grinder-1-ranks.txt
-    #   grinder-1-reads.fa
-    #   grinder-1-reads.qual
-    #   grinder-2-ranks.txt
-    #   grinder-2-reads.fa
-    #   grinder-2-reads.qual
-
-    p = re.compile(output_id)
-    q = re.compile('-(\d+)-')
-    r = re.compile('-(\w+)$')
-    
-
-    for fname in os.listdir(output_dir):
-
-        # Skip files that do not start with the output_id
-        source = os.path.join( output_dir, fname )
-        basename, extension = os.path.splitext(fname)
-        if not p.match(fname):
-           continue
-
-        # Assign the dataset format
-        if extension == '.txt': 
-           format = 'text'
-        elif extension == '.fq':
-           format = 'fastqsanger'
-        elif extension == '.fastq':
-           format = 'fastqsanger'
-        elif extension == '.fa':
-           format = 'fasta'
-        elif extension == '.fna':
-           format = 'fasta'
-        elif extension == '.faa':
-           format = 'fasta'
-        elif extension == '.fasta':
-           format = 'fasta'
-        elif extension == '.qual':
-           format = 'qual'
-        else:
-           stop_err( 'Error: File %s had the unknown extension %s' % ( fname, extension ) )
-        
-        # Assign the dataset name
-        name = ''
-        match = q.search(basename)
-        if match != None:
-          lib_num = match.group(1)
-          name = 'lib%s-' % lib_num
-
-        match = r.search(basename)
-        if match == None:
-          stop_err( 'Error: File with basename %s did not have a recognized name' % (basename) )
-        
-        lib_type = match.group(1)
-        if format == 'qual':
-          lib_type = 'qual'
-
-        name = name + lib_type        
-
-        # Move the dataset to the proper place
-        #db_ref = ''
-        #destination = os.path.join( output_dir, 'primary_%s_%s_visible_%s_%s' % (output_id, name, format, db_ref) )
-        destination = os.path.join( output_dir, 'primary_%s_%s_visible_%s' % (output_id, name, format) )
-
-        print "moving %s to %s" % (source, destination)
-
-        try:
-          os.rename(source, destination)
-        except Exception, e:
-          stop_err( 'Error: ' + str( e ) )
-
-if __name__ == "__main__": __main__()