<tool id="pick_otus_through_otu_table" name="pick_otus_through_otu_table" version="1.2.0">
 <description>A workflow script for picking OTUs through building OTU tables</description>
 <requirements>
  <requirement type="binary">pick_otus_through_otu_table.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_outputdir='$log.extra_files_path'
  --galaxy_datasets='^log_\S+\.txt$:'$log,'^\S+_otus.txt$:'$seqs_otus,'^\S+_rep_set.fasta$:'$seqs_rep_set,'^\S+_rep_set_tax_assignments.txt$:'$seqs_rep_set_tax_assignments,'^\S+_otu_table.txt$:'$seqs_otu_table,'^\S+_rep_set_aligned.fasta$:'$seqs_rep_set_aligned,'^\S+_rep_set_aligned_pfiltered.fasta$:'$seqs_rep_set_aligned_pfiltered,'^\S+_rep_set.tre$:'$seqs_rep_set_tre
  pick_otus_through_otu_table.py
  --input_fp=$input_fp
  #if $parameter.source == 'hist':
   --parameter_fp=$parameter.parameter_fp
  #else:
   --parameter_fp=$parameter_generated
  #end if
  #if $denoise.choice == 'yes':
   --sff_fp=$denoise.sff_fp
   --mapping_fp=$denoise.mapping_fp
  #end if
  --output_dir='$log.extra_files_path'
  --force
  $parallel
 </command>
 <inputs>
  <param name="input_fp" type="data" format="fasta" label="input_fp"
   help="the input fasta file [REQUIRED]"/>
  <conditional name="parameter">
   <param name="source" type="select" label="Grouping Design from" help="">
    <option value="hist">Your History</option>
    <option value="build">Build a grouping design</option>
   </param>
   <when value="hist">
    <param name="parameter_fp" type="data" format="qiimeparams" label="parameter_fp"
     help="path to the parameter file [REQUIRED]"/>
   </when> <!-- hist -->
   <when value="build">
   </when> <!-- build -->
  </conditional> <!-- parameter -->
  <conditional name="denoise">
   <param name="choice" type="select" label="Denoise (requires sff flowgram and a mapping faile)" help="">
    <option value="no">No</option>
    <option value="yes">Yes</option>
   </param>
   <when value="yes">
    <param name="sff_fp" type="data" format="ssf" label="sff_fp"
     help="the sff flowgram file [REQUIRED for denoising]"/>
    <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp"
     help="the mapping filepath [REQUIRED for denoising]"/>
   </when> <!-- hist -->
   <when value="no"/>
  </conditional> <!-- denoise -->
  <param name="parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="parallel"
   help="Run in parallel where available [default: False]"/>
 </inputs>
  <!-- Construct a parameter file
  -->
 <configfiles>
  <configfile name="parameter_generated">
##OTU picker parameters
pick_otus:otu_picking_method	uclust
pick_otus:clustering_algorithm	furthest
pick_otus:max_cdhit_memory	400
pick_otus:refseqs_fp
pick_otus:blast_db
pick_otus:similarity	0.97
pick_otus:max_e_value	1e-10
pick_otus:prefix_prefilter_length
pick_otus:trie_prefilter
pick_otus:prefix_length
pick_otus:suffix_length
pick_otus:optimal_uclust
pick_otus:exact_uclust
pick_otus:user_sort
pick_otus:suppress_presort_by_abundance_uclust
pick_otus:suppress_new_clusters
pick_otus:suppress_uclust_stable_sort
pick_otus:max_accepts
pick_otus:max_rejects
pick_otus:word_length
pick_otus:stepwords
##Representative set picker parameters
pick_rep_set:rep_set_picking_method	first
pick_rep_set:sort_by	otu
##Multiple sequence alignment parameters
align_seqs:template_fp
align_seqs:alignment_method	pynast
align_seqs:pairwise_alignment_method	uclust
align_seqs:blast_db
align_seqs:min_length	150
align_seqs:min_percent_id	75.0
##Alignment filtering (prior to tree-building) parameters
filter_alignment:lane_mask_fp
filter_alignment:allowed_gap_frac	0.999999
filter_alignment:remove_outliers	False
filter_alignment:threshold	3.0
##Taxonomy assignment parameters
assign_taxonomy:id_to_taxonomy_fp
assign_taxonomy:reference_seqs_fp
assign_taxonomy:assignment_method	rdp
assign_taxonomy:blast_db
assign_taxonomy:confidence	0.8
#assign_taxonomy:e_value	0.001
##Phylogenetic tree building parameters
make_phylogeny:tree_method	fasttree
make_phylogeny:root_method	tree_method_default
##align_seqs:template_fp
##filter_alignment:lane_mask_fp	
  </configfile>
 </configfiles>
 <outputs>
 <!--
This script will produce a set of cluster centroids (as a FASTA file) 
and a cluster mapping file (from denoise.py if sff.txt and mapping file were provided), 
an OTU mapping file (pick_otus.py), 
a representative set of sequences (FASTA file from pick_rep_set.py), 
a sequence alignment file (FASTA file from align_seqs.py), 
taxonomy assignment file (from assign_taxonomy.py), 
a filtered sequence alignment (from filter_alignment.py), 
a phylogenetic tree (Newick file from make_phylogeny.py) and an OTU table (from make_otu_table.py).

wf_da2/log_20110305084135.txt
wf_da2/uclust_picked_otus/seqs_otus.txt
wf_da/uclust_picked_otus/rep_set/seqs_rep_set.fasta
wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.txt
wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table//seqs_otu_table.txt
wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned.fasta
wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned_pfiltered.fasta
wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre


wf_da2/log_20110305084135.txt
wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre
wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set_phylogeny.log
wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned.fasta
wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned_pfiltered.fasta
wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_failures.fasta
wf_da2/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_log.txt
wf_da2/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt
wf_da2/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.log
wf_da2/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.txt
wf_da2/uclust_picked_otus/rep_set/seqs_rep_set.fasta
wf_da2/uclust_picked_otus/rep_set/seqs_rep_set.log
wf_da2/uclust_picked_otus/seqs_clusters.uc
wf_da2/uclust_picked_otus/seqs_otus.log
wf_da2/uclust_picked_otus/seqs_otus.txt

wf_da2/log_20110305084135.txt
wf_da2/uclust_picked_otus/seqs_otus.txt
wf_da/uclust_picked_otus/rep_set/seqs_rep_set.fasta
wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.txt
wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt
wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned.fasta
wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/seqs_rep_set_aligned_pfiltered.fasta
wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre
-->
   <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
   <data format="qiimeotu" name="seqs_otus" label="${tool.name} on ${on_string}: seqs_otus" />
   <data format="fasta" name="seqs_rep_set" label="${tool.name} on ${on_string}: seqs_rep_set.fasta" />
   <data format="seq.taxonomy" name="seqs_rep_set_tax_assignments" label="${tool.name} on ${on_string}: seqs_rep_set_tax_assignments" />
   <data format="qiimeotutable" name="seqs_otu_table" label="${tool.name} on ${on_string}: seqs_otu_table" />
   <data format="align" name="seqs_rep_set_aligned" label="${tool.name} on ${on_string}: seqs_rep_set_aligned.fasta" />
   <data format="align" name="seqs_rep_set_aligned_pfiltered" label="${tool.name} on ${on_string}: seqs_rep_set_aligned_pfiltered.fasta" />
   <data format="tre" name="seqs_rep_set_tre" label="${tool.name} on ${on_string}: seqs_rep_set.tre" />

  
 </outputs>
 <tests>
 </tests>
 <help>

        The steps performed by this function are:
          0) Optionally denoise the sequences (if sff_input_fp=True);
          1) Pick OTUs;
          2) Pick a representative set;
          3) Align the representative set; 
          4) Assign taxonomy;
          5) Filter the alignment prior to tree building - remove positions
             which are all gaps, and specified as 0 in the lanemask
          6) Build a phylogenetic tree;
          7) Build an OTU table.


pick_otus_through_otu_table.py -i split_library_output/seqs.fna -p custom_parameters.txt -o wf_da --print_only

python /usr/local/bin/pick_otus.py -i split_library_output/seqs.fna -o wf_da/uclust_picked_otus --max_e_value 1e-10 --clustering_algorithm furthest --similarity 0.97 --otu_picking_method uclust --max_cdhit_memory 400

python /usr/local/bin/pick_rep_set.py -i wf_da/uclust_picked_otus/seqs_otus.txt -f split_library_output/seqs.fna -l wf_da/uclust_picked_otus/rep_set//seqs_rep_set.log -o wf_da/uclust_picked_otus/rep_set//seqs_rep_set.fasta --rep_set_picking_method first --sort_by otu

python /usr/local/bin/assign_taxonomy.py -o wf_da/uclust_picked_otus/rep_set//rdp_assigned_taxonomy -i wf_da/uclust_picked_otus/rep_set//seqs_rep_set.fasta --confidence 0.8 --assignment_method rdp

python /usr/local/bin/make_otu_table.py -i wf_da/uclust_picked_otus/seqs_otus.txt -t wf_da/uclust_picked_otus/rep_set//rdp_assigned_taxonomy/seqs_rep_set_tax_assignments.txt -o wf_da/uclust_picked_otus/rep_set//rdp_assigned_taxonomy/otu_table//seqs_otu_table.txt 

python /usr/local/bin/align_seqs.py -i wf_da/uclust_picked_otus/rep_set//seqs_rep_set.fasta -o wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs --alignment_method pynast --pairwise_alignment_method uclust --min_percent_id 75.0 --min_length 150

python /usr/local/bin/filter_alignment.py -o wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs -i wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs/seqs_rep_set_aligned.fasta --allowed_gap_frac 0.999999 --threshold 3.0

python /usr/local/bin/make_phylogeny.py -i wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs/seqs_rep_set_aligned_pfiltered.fasta -o wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre -l wf_da/uclust_picked_otus/rep_set//pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set_phylogeny.log --root_method tree_method_default --tree_method fasttree

  
 </help>
</tool>