Mercurial > repos > jjohnson > qiime
diff pick_otus_through_otu_table.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Sun, 17 Jul 2011 10:30:11 -0500 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pick_otus_through_otu_table.xml Sun Jul 17 10:30:11 2011 -0500 @@ -0,0 +1,203 @@ +<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> +