Mercurial > repos > jjohnson > qiime
diff pick_otus.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
author | Jim Johnson <jj@umn.edu> |
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date | Sun, 17 Jul 2011 10:30:11 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pick_otus.xml Sun Jul 17 10:30:11 2011 -0500 @@ -0,0 +1,169 @@ +<tool id="pick_otus" name="pick_otus" version="1.2.1"> + <description>OTU picking</description> + <requirements> + <requirement type="binary">pick_otus.py</requirement> + </requirements> + <command interpreter="python"> + qiime_wrapper.py + --galaxy_outputdir='$log.extra_files_path' + #if $pick.otu_picking_method == 'uclust' and $pick.refseqs_fp.__str__ != 'None': + --galaxy_datasets='^\S+_otus\.txt$:'$otus,'^\S+_otus\.log$:'$log,'^\S+_failures\.txt$:'$failures + #else: + --galaxy_datasets='^\S+_otus\.txt$:'$otus,'^\S+_otus\.log$:'$log + #end if + pick_otus.py + --input_seqs_filepath=$input_seqs_filepath + #if $pick.otu_picking_method == 'uclust': + #if $pick.refseqs_fp.__str__ != 'None': + --refseqs_fp=$pick.refseqs_fp + --otu_picking_method='uclust_ref' + $pick.suppress_new_clusters + #else: + --otu_picking_method=$pick.otu_picking_method + #end if + --similarity=$pick.similarity + $pick.enable_rev_strand_match + $pick.optimal_uclust + $pick.exact_uclust + $pick.user_sort + $pick.suppress_presort_by_abundance_uclust + --max_accepts=$pick.max_accepts + --max_rejects=$pick.max_rejects + --stepwords=$pick.stepwords + --word_length=$pick.word_length + --uclust_otu_id_prefix=$pick.uclust_otu_id_prefix + $pick.uclust_stable_sort + $pick.save_uc_files + #elif $pick.otu_picking_method == 'mothur': + --otu_picking_method=$pick.otu_picking_method + --clustering_algorithm=$pick.clustering_algorithm + --similarity=$pick.similarity + #elif $pick.otu_picking_method == 'trie': + --otu_picking_method=$pick.otu_picking_method + $pick.trie_reverse_seqs + #elif $pick.otu_picking_method == 'prefix_suffix': + --otu_picking_method=$pick.otu_picking_method + --prefix_length=$pick.prefix_length + --suffix_length=$pick.suffix_length + #elif pick.otu_picking_method == 'blast': + --otu_picking_method=$pick.otu_picking_method + #if $refseqs_fp.__str__ != 'None': + --refseqs_fp=$pick.refseqs_fp + #end if + --blast_db=$pick.blast_db + --similarity=$pick.similarity + --max_e_value=$pick.max_e_value + --min_aligned_percent=$pick.min_aligned_percent + #elif $pick.otu_picking_method == 'cdhit': + --otu_picking_method=$pick.otu_picking_method + --similarity=$pick.similarity + --max_cdhit_memory=$pick.max_cdhit_memory + --prefix_prefilter_length=$pick.prefix_prefilter_length + $pick.trie_prefilter + #end if + --output_dir='$log.extra_files_path' + </command> + <inputs> + <param name="input_seqs_filepath" type="data" format="fasta" label="input_seqs_filepath" + help="Input sequences [REQUIRED]"/> + <conditional name="pick"> + <param name="otu_picking_method" type="select" label="otu_picking_method" + help="Method for picking OTUs. Valid choices are: mothur, trie, uclust_ref, prefix_suffix, blast, cdhit, uclust. The mothur method requires an input file of aligned sequences [default: uclust]"> + <option value="uclust" selected="true">uclust</option> + <option value="mothur">mothur</option> + <option value="trie">trie</option> + <option value="prefix_suffix">prefix_suffix</option> + <option value="blast">blast</option> + <option value="cdhit">cdhit</option> + </param> + <when value="mothur"> + <param name="clustering_algorithm" type="select" label="clustering_algorithm" + help="Clustering algorithm for mothur otu picking method. Valid choices are: furthest, nearest, average. [default: furthest]"> + <option value="furthest" selected="true">furthest</option> + <option value="nearest">nearest</option> + <option value="average">average</option> + </param> + <param name="similarity" type="float" value="0.97" label="similarity" + help="Sequence similarity threshold (for cdhit, uclust, or uclust_ref) [default: 0.97]"/> + </when> <!-- mothur --> + <when value="trie"> + <param name="trie_reverse_seqs" type="boolean" truevalue="--trie_reverse_seqs" falsevalue="" checked="false" label="trie_reverse_seqs" + help="Reverse seqs before picking OTUs with the Trie OTU picker for suffix (rather than prefix) collapsing [default: False]"/> + </when> <!-- trie --> + <when value="uclust"> + <param name="refseqs_fp" type="data" format="fasta" label="refseqs_fp" optional="true" + help="Reference sequences to search against"/> + <param name="suppress_new_clusters" type="boolean" truevalue="--suppress_new_clusters" falsevalue="" checked="false" label="suppress_new_clusters" + help="Suppress creation of new clusters using seqs that don't match reference when using -m uclust_ref [default: False]"/> + <param name="suppress_presort_by_abundance_uclust" type="boolean" truevalue="--suppress_presort_by_abundance_uclust" falsevalue="" checked="false" label="suppress_presort_by_abundance_uclust" + help="Suppress presorting of sequences by abundance when picking OTUs with uclust or uclust_ref [default: False]"/> + <param name="similarity" type="float" value="0.97" label="similarity" + help="Sequence similarity threshold (for cdhit, uclust, or uclust_ref) [default: 0.97]"/> + <param name="enable_rev_strand_match" type="boolean" truevalue="--enable_rev_strand_match" falsevalue="" checked="false" label="enable_rev_strand_match" + help="Enable reverse strand matching for uclust otu picking, will double the amount of memory used. [default: False]"/> + <param name="optimal_uclust" type="boolean" truevalue="--optimal_uclust" falsevalue="" checked="false" label="optimal_uclust" + help="Pass the --optimal flag to uclust for uclust otu picking. [default: False]"/> + <param name="exact_uclust" type="boolean" truevalue="--exact_uclust" falsevalue="" checked="false" label="exact_uclust" + help="Pass the --exact flag to uclust for uclust otu picking. [default: False]"/> + <param name="user_sort" type="boolean" truevalue="--user_sort" falsevalue="" checked="false" label="user_sort" + help="Pass the --user_sort flag to uclust for uclust otu picking. [default: False]"/> + <param name="max_accepts" type="integer" value="20" label="max_accepts" + help="max_accepts value to uclust and uclust_ref [default: 20]"/> + <param name="max_rejects" type="integer" value="500" label="max_rejects" + help="max_rejects value to uclust and uclust_ref [default: 500]"/> + + <param name="stepwords" type="integer" value="20" label="stepwords" + help="stepwords value to uclust and uclust_ref [default: 20]"/> + <param name="word_length" type="integer" value="12" label="word_length" + help="w value to uclust and uclust_ref [default: 12]"/> + + <param name="uclust_otu_id_prefix" type="text" label="uclust_otu_id_prefix" + help="OTU identifier prefix (string) for the de novo uclust OTU picker [default: %default, OTU ids are ascending integers]"/> + <param name="uclust_stable_sort" type="boolean" truevalue="--uclust_stable_sort" falsevalue="" checked="false" label="uclust_stable_sort" + help="pass --stable_sort to uclust (uclust versions uclustq1.2.15 and later only) [default: False]"/> + <param name="save_uc_files" type="boolean" truevalue="" falsevalue="--save_uc_files" checked="false" label="save_uc_files" + help="Enable preservation of intermediate uclust (.uc) files that are used to generate clusters via uclust. [default: True]"/> + </when> <!-- uclust --> + <when value="prefix_suffix"> + <param name="prefix_length" type="integer" value="50" label="prefix_length" + help="Prefix length when using the prefix_suffix otu picker; WARNING: CURRENTLY DIFFERENT FROM prefix_prefilter_length (-n)! [default: 50]"/> + <param name="suffix_length" type="integer" value="50" label="suffix_length" + help="Suffix length when using the prefix_suffix otu picker [default: 50]"/> + + </when> <!-- prefix_suffix --> + <when value="blast"> + <param name="refseqs_fp" type="data" format="fasta" label="refseqs_fp" optional="true" + help="Reference sequences to search against"/> + <param name="blast_db" type="text" label="blast_db" + help="Pre-existing database to blast against when using -m blast [default: ('NO', 'DEFAULT')]"/> + <param name="min_aligned_percent" type="float" value="0.5" label="min_aligned_percent" + help="Minimum percent of query sequence that can be aligned to consider a hit (BLAST OTU picker only) [default: 0.5]"/> + <param name="max_e_value" type="float" value="1e-10" label="max_e_value" + help="Max E-value when clustering with BLAST [default: 1e-10]"/> + </when> <!-- blast --> + <when value="cdhit"> + <param name="max_cdhit_memory" type="integer" value="400" label="max_cdhit_memory" + help="Maximum available memory to cd-hit-est (via the program's -M option) for cdhit OTU picking method (units of Mbyte) [default: 400]"/> + <param name="similarity" type="float" value="0.97" label="similarity" + help="Sequence similarity threshold (for cdhit, uclust, or uclust_ref) [default: 0.97]"/> + <param name="prefix_prefilter_length" type="integer" value="-1" label="prefix_prefilter_length" + help="Prefilter data so seqs with identical first prefix_prefilter_length are automatically grouped into a single OTU. This is useful for large sequence collections where OTU picking doesn't scale well [default: %default; 100 is a good value]"/> + <param name="trie_prefilter" type="boolean" truevalue="--trie_prefilter" falsevalue="" checked="false" label="trie_prefilter" + help="prefilter data so seqs which are identical prefixes of a longer seq are automatically grouped into a single OTU; useful for large sequence collections where OTU picking doesn't scale well [default: False]"/> + </when> <!-- cdhit --> + </conditional> <!-- pick --> + </inputs> + <outputs> + <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> + <data format="qiimeotu" name="otus" label="${tool.name} on ${on_string}: otus" /> + <data format="txt" name="failures" label="${tool.name} on ${on_string}: failures.txt" > + <filter>(pick['otu_picking_method'] == 'uclust' and pick['refseqs_fp'])</filter> + </data> + </outputs> + <tests> + </tests> + <help> + + </help> +</tool> +