# HG changeset patch # User azuzolo # Date 1339014761 14400 # Node ID 3b1401bf4cb1c2052449d4d75661e10582cd314f # Parent 2e14fb0fd7926815f048d77b189e78adc50217db Deleted selected files diff -r 2e14fb0fd792 -r 3b1401bf4cb1 README --- a/README Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ -This was a first attempt at providing galaxy tool_wrappers for the Qiime metagenomics package: -You must first istall Qiime: http://qiime.sourceforge.net/install/install.html - - - -Initial tool wrappers were generated by a script searching the qiime scripts (version 1.2.1) for usage info, -and then were hand edited afterwards. - -NOTE: A few of the tool configs worked on the galaxy-central code in April 2011. -I haven't taken time to check them with more recent galaxy releases. - - -I executed the qiime scripts via qiime_wrapper.py -This was to accommmodate moving multiple outputs to history items: http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files - - -The datatypes file: metagenomics.py has Mothur datatypes with a start at qiime types added at the end. - - - - -The most common used qiime scripts are: -- check_id_map.py -- split_libraries.py -- pick_otus_through_otu_table.py -- beta_diversity_through_3d_plots.py -- alpha_rarefaction.py -- jackknifed_beta_diversity.py -- filter_by_metadata.py -- filter_otu_table.py -- merge_otu_tables.py -- merge_mapping_files.py - - -Tool_config development status: -The tool configs with a * indicate that the tool at least displayed in galaxy at least once upon time. -( Since these were intially auto generated, some may not make sense in a galaxy framework. ) - - add_taxa.xml - adjust_seq_orientation.xml -* align_seqs.xml -* alpha_diversity.xml metrics - select input/output repeat conditional tree -* alpha_rarefaction.xml -* assign_taxonomy.xmlA assignment_method-select -* beta_diversity.xml -* beta_diversity_through_3d_plots.xml html-plots - beta_significance.xml - blast_wrapper.xml -* check_id_map.xml - collate_alpha.xml -* compare_3d_plots.xml - consensus_tree.xml - convert_otu_table_to_unifrac_sample_mapping.xml - convert_unifrac_sample_mapping_to_otu_table.xml -* denoise.xml -* dissimilarity_mtx_stats.xml - exclude_seqs_by_blast.xml - extract_seqs_by_sample_id.xml -* filter_alignment.xml - filter_by_metadata.xml - filter_fasta.xml - filter_otu_table.xml -* filter_otus_by_sample.xml - fix_arb_fasta.xml - identify_chimeric_seqs.xml -* jackknifed_beta_diversity.xml -* make_2d_plots.xml -* make_3d_plots.xml - make_bootstrapped_tree.xml - make_distance_histograms.xml - make_fastq.xml - make_library_id_lists.xml -* make_otu_heatmap_html.xml -* make_otu_network.xml - make_otu_table.xml - make_per_library_sff.xml - make_phylogeny.xml - make_pie_charts.xml - make_prefs_file.xml - make_qiime_py_file.xml -* make_qiime_rst_file.xml -* make_rarefaction_plots.xml -* make_sra_submission.xml -* merge_denoiser_output.xml - merge_mapping_files.xml - merge_otu_maps.xml - merge_otu_tables.xml - multiple_rarefactions.xml - multiple_rarefactions_even_depth.xml - otu_category_significance.xml -* parallel_align_seqs_pynast.xml - parallel_alpha_diversity.xml -* parallel_assign_taxonomy_blast.xml -* parallel_assign_taxonomy_rdp.xml - parallel_beta_diversity.xml -* parallel_blast.xml - parallel_identify_chimeric_seqs.xml - parallel_multiple_rarefactions.xml -* parallel_pick_otus_blast.xml -* parallel_pick_otus_uclust_ref.xml - per_library_stats.xml -* pick_otus.xml -* pick_otus_through_otu_table.xml - pick_rep_set.xml -* plot_rank_abundance_graph.xml - poller.xml - poller_example.xml - pool_by_metadata.xml - principal_coordinates.xml - print_qiime_config.xml -* process_sff.xml -* process_sra_submission.xml -* quality_scores_plot.xml - shared_phylotypes.xml - single_rarefaction.xml - sort_denoiser_output.xml -* split_libraries.xml -* split_libraries_illumina.xml - sra_spreadsheet_to_map_files.xml - start_parallel_jobs.xml - summarize_otu_by_cat.xml - summarize_taxa.xml -* supervised_learning.xml -* transform_coordinate_matrices.xml -* tree_compare.xml - trflp_file_to_otu_table.xml - trim_sff_primers.xml -* truncate_fasta_qual_files.xml - upgma_cluster.xml diff -r 2e14fb0fd792 -r 3b1401bf4cb1 add_taxa.xml --- a/add_taxa.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ - - Add taxa to OTU table - - add_taxa.py - - - qiime_wrapper.py - add_taxa.py - --otu_file=$otu_file - --taxonomy_file=$taxonomy_file - --output_file=$output_file - --id_map_file=$id_map_file - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 adjust_seq_orientation.xml --- a/adjust_seq_orientation.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ - - Get the reverse complement of all sequences - - adjust_seq_orientation.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - adjust_seq_orientation.py - --input_fasta_fp=$input_fasta_fp - --output_fp=$output_fp - $retain_seq_id - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 align_seqs.xml --- a/align_seqs.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ - - Align sequences using a variety of alignment methods - - align_seqs.py - - - qiime_wrapper.py - --galaxy_outputdir='$log.extra_files_path' - --galaxy_datasets='^\S+_aligned\.\S+$:'$aligned_fasta,'^\S+_log\.txt$:'$log,'^\S+_failures\.fasta$:'$failures - align_seqs.py - --input_fasta_fp=$input_fasta_fp - --alignment_method=$alignment_method - #if $alignment_method.__str__ == 'pynast': - #if $alignment.template_fp != None and $alignment.template_fp.__str__ != 'None' and $alignment.template_fp.__str__ != '': - --template_fp=$alignment.template_fp - #end if - --pairwise_alignment_method=$pairwise_alignment_method - --min_length=$min_length - --min_percent_id=$min_percent_id - #if $blast_db != None and $blast_db.__str__ != 'None' and $blast_db.__str__ != '': - --blast_db=$blast_db - #end if - #elif $alignment_method.__str__ == 'infernal': - --template_fp=$alignment.template_fp - #end if - - --output_dir='$log.extra_files_path' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. class:: warningmark -Note: MUSCLE alignment is still not verified. Use at your own risk. - -For more information, see align_seqs_ in the Qiime documentation. - -Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _align_seqs: http://qiime.org/scripts/align_seqs.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 align_seqs_py.xml --- a/align_seqs_py.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ - - Align sequences using a variety of alignment methods - - align_seqs.py - - - qiime_wrapper.py - --galaxy_outputdir='$log.extra_files_path' - --galaxy_datasets='^\S+_aligned\.\S+$:'$aligned_fasta,'^\S+_log\.txt$:'$log,'^\S+_failures\.fasta$:'$failures - align_seqs.py - --input_fasta_fp=$input_fasta_fp - --alignment_method=$align.alignment_method - #if $align.alignment_method == 'pynast': - --template_fp=$align.alignment.template_fp - --pairwise_alignment_method=$align.pairwise_alignment_method - --min_length=$align.min_length - --min_percent_id=$align.min_percent_id - --blast_db=$align.blast_db - #elif $align.alignment_method == 'infernal': - --template_fp=$align.alignment.template_fp - #elif $align.alignment_method == 'clustalw': - #elif $align.alignment_method == 'muscle': - #elif $align.alignment_method == 'mafft': - #end if - - --output_dir='$log.extra_files_path' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 alpha_diversity.xml --- a/alpha_diversity.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,86 +0,0 @@ - - Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics - - alpha_diversity.py - - - qiime_wrapper.py - #if $run_type.input_type.__str__ == "multi": - --galaxy_logfile=$output_path - --galaxy_outputdir=$output_path.extra_files_path - #end if - alpha_diversity.py - #if $run_type.input_type.__str__ == "multi": - --input_path=$input_path.extra_files_path - --output_path=$output_path.extra_files_path - #else: - --output_path=$output_path - --input_path=$input_path - #end if - --metrics=$metrics - #if $metrics.__str__ == 'PD_whole_tree': - --tree_path=$tree_path - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This tool calculates alpha diversity, or within-sample diversity, using an otu table. Metrics may be selected in any combination. Input can be the log file from multiple_rarefactions (batch alpha diversity), or a single rarefied OTU table (single_rarefaction/single file alpha diversity). When the phylogenetic metric PD_whole_tree is selected, a .tre file must be supplied for the tool to run. The output file is a log file listing all the alpha rarefaction files produced. - -For more information, see alpha_diversity_ in the Qiime documentation. - -Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _alpha_diversity: http://qiime.org/scripts/alpha_diversity.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 alpha_rarefaction.xml --- a/alpha_rarefaction.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,108 +0,0 @@ - - A workflow script for performing alpha rarefaction - - alpha_rarefaction.py - - - qiime_wrapper.py - --galaxy_summary_html='$output_html' - --galaxy_outputdir='$output_html.extra_files_path' - --galaxy_summary_template='$output_template' - ## --galaxy_datasets='^rarefaction_plots.html$:'$output_html - alpha_rarefaction.py - --otu_table_fp=$otu_table_fp - --mapping_fp=$mapping_fp - --output_dir=$output_html.extra_files_path - #if $parameter.source == 'hist': - --parameter_fp=$parameter_fp - #else: - --parameter_fp=$parameter_generated - #end if - --num_steps=$num_steps - $force - $print_only - $parallel - #if $tree_fp != None and $tree_fp.__str__ != 'None': - --tree_fp=$tree_fp - #end if - - - - - - - - - - - - - - - - - - - - - - - - -alpha_diversity:metrics chao1,observed_species,PD_whole_tree -multiple_rarefactions_even_depth:num-reps 20 -parallel:jobs_to_start 2 -parallel:retain_temp_files False -parallel:seconds_to_sleep 60 -collate_alpha:example_path -make_rarefaction_plots:imagetype png -make_rarefaction_plots:resolution 75 -make_rarefaction_plots:background_color white -make_rarefaction_plots:prefs_path - - - - -rarefaction_plots.html - - -]]> - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 assign_taxonomy.xml --- a/assign_taxonomy.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ - - Assign taxonomy to each sequence - - assign_taxonomy.py - - - qiime_wrapper.py - --galaxy_outputdir='$outputfile.extra_files_path' - --galaxy_datasets='^\S+\.txt$:'$outputfile - assign_taxonomy.py - --input_fasta_fp=$input_fasta_fp - #if $id_to_taxonomy_fp != None and $id_to_taxonomy_fp.__str__ != 'None' and $id_to_taxonomy_fp.__str__ != '': - --id_to_taxonomy_fp=$id_to_taxonomy_fp - #end if - #if $reference_seqs_fp != None and $reference_seqs_fp.__str__ != 'None' and $reference_seqs_fp.__str__ != '': - --reference_seqs_fp=$reference_seqs_fp - #end if - #if $training_data_properties_fp != None and $training_data_properties_fp.__str__ != 'None' and $training_data_properties_fp.__str__ != '': - --training_data_properties_fp.$training_data_properties_fp - #end if - --confidence=$confidence - --assignment_method=rdp - --output_dir='$outputfile.extra_files_path' - - - - - - - - - - - - - - - Only uses RDP. For blast, use MBAC blast tools. - -For more information, see assign_taxonomy_ in the Qiime documentation. - -Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _assign_taxonomy: http://qiime.org/scripts/assign_taxonomy.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 beta_diversity.xml --- a/beta_diversity.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,351 +0,0 @@ - - Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables - - beta_diversity.py - - - qiime_wrapper.py - --galaxy_outputdir=$__new_file_path__ - #set datasets = [] - #set $path = "" - #if $binary_chisq.__str__ != "None": - #set datasets = $datasets + ["'binary_chisq_.*$:'" + $binary_chisq.__str__] - #if path == "": - #set $path=$binary_chisq.extra_files_path - #end if - #end if - #if $binary_chord.__str__ != "None": - #set datasets = $datasets + ["'binary_chord_.*$:'" + $binary_chord.__str__] - #if path == "": - #set $path=$binary_chord.extra_files_path - #end if - #end if - #if $binary_euclidean.__str__ != "None": - #set datasets = $datasets + ["'binary_euclidean_.*$:'" + $binary_euclidean.__str__] - #if path == "": - #set $path=$binary_euclidean.extra_files_path - #end if - #end if - #if $binary_hamming.__str__ != "None": - #set datasets = $datasets + ["'binary_hamming_.*$:'" + $binary_hamming.__str__] - #if path == "": - #set $path=$binary_hamming.extra_files_path - #end if - #end if - #if $binary_jaccard.__str__ != "None": - #set datasets = $datasets + ["'binary_jaccard_.*$:'" + $binary_jaccard.__str__] - #if path == "": - #set $path=$binary_jaccard.extra_files_path - #end if - #end if - #if $binary_lennon.__str__ != "None": - #set datasets = $datasets + ["'binary_lennon_.*$:'" + $binary_lennon.__str__] - #if path == "": - #set $path=$binary_lennon.extra_files_path - #end if - #end if - #if $binary_ochiai.__str__ != "None": - #set datasets = $datasets + ["'binary_ochiai_.*$:'" + $binary_ochiai.__str__] - #if path == "": - #set $path=$binary_ochiai.extra_files_path - #end if - #end if - #if $binary_pearson.__str__ != "None": - #set datasets = $datasets + ["'binary_pearson_.*$:'" + $binary_pearson.__str__] - #if path == "": - #set $path=$binary_pearson.extra_files_path - #end if - #end if - #if $binary_sorensen_dice.__str__ != "None": - #set datasets = $datasets + ["'binary_sorensen_dice_.*$:'" + $binary_sorensen_dice.__str__] - #if path == "": - #set $path=$binary_sorensen.extra_files_path - #end if - #end if - #if $bray_curtis.__str__ != "None": - #set datasets = $datasets + ["'bray_curtis_.*$:'" + $bray_curtis.__str__] - #if path == "": - #set $path=$bray_curtis.extra_files_path - #end if - #end if - #if $canberra.__str__ != "None": - #set datasets = $datasets + ["'canberra_.*$:'" + $canberra.__str__] - #if path == "": - #set $path=$canberra.extra_files_path - #end if - #end if - #if $chisq.__str__ != "None": - #set datasets = $datasets + ["'chisq_.*$:'" + $chisq.__str__] - #if path == "": - #set $path=$binary_euclidean.extra_files_path - #end if - #end if - #if $chord.__str__ != "None": - #set datasets = $datasets + ["'chord_.*$:'" + $chord.__str__] - #if path == "": - #set $path=$chord.extra_files_path - #end if - #end if - #if $euclidean.__str__ != "None": - #set datasets = $datasets + ["'euclidean_.*$:'" + $euclidean.__str__] - #if path == "": - #set $path=$euclidean.extra_files_path - #end if - #end if - #if $gower.__str__ != "None": - #set datasets = $datasets + ["'gower_.*$:'" + $gower.__str__] - #if path == "": - #set $path=$gower.extra_files_path - #end if - #end if - #if $hellinger.__str__ != "None": - #set datasets = $datasets + ["'hellinger_.*$:'" + $hellinger.__str__] - #if path == "": - #set $path=$hellinger.extra_files_path - #end if - #end if - #if $kulczynski.__str__ != "None": - #set datasets = $datasets + ["'kulczynski_.*$:'" + $kulczynski.__str__] - #if path == "": - #set $path=$kulczynski.extra_files_path - #end if - #end if - #if $manhattan.__str__ != "None": - #set datasets = $datasets + ["'manhattan_.*$:'" + $manhattan.__str__] - #if path == "": - #set $path=$manhattan.extra_files_path - #end if - #end if - #if $morisita_horn.__str__ != "None": - #set datasets = $datasets + ["'morisita_horn_.*$:'" + $morisita_horn.__str__] - #if path == "": - #set $path=$morisita_horn.extra_files_path - #end if - #end if - #if $pearson.__str__ != "None": - #set datasets = $datasets + ["'pearson_.*$:'" + $pearson.__str__] - #if path == "": - #set $path=$pearson.extra_files_path - #end if - #end if - #if $soergel.__str__ != "None": - #set datasets = $datasets + ["'soergel_.*$:'" + $soergel.__str__] - #if path == "": - #set $path=$soergel.extra_files_path - #end if - #end if - #if $spearman_approx.__str__ != "None": - #set datasets = $datasets + ["'spearman_approx_.*$:'" + $spearman_approx.__str__] - #if path == "": - #set $path=$spearman_approx.extra_files_path - #end if - #end if - #if $specprof.__str__ != "None": - #set datasets = $datasets + ["'specprof_.*$:'" + $specprof.__str__] - #if path == "": - #set $path=$specprof.extra_files_path - #end if - #end if - #if $unifrac.__str__ != "None": - #set datasets = $datasets + ["'unifrac_.*$:'" + $unifrac.__str__] - #if path == "": - #set $path=$unifrac.extra_files_path - #end if - #end if - #if $unifrac_g.__str__ != "None": - #set datasets = $datasets + ["'unifrac_g_.*$:'" + $unifrac_g.__str__] - #if path == "": - #set $path=$unifrac_g.extra_files_path - #end if - #end if - #if $unifrac_g_full_tree.__str__ != "None": - #set datasets = $datasets + ["'unifrac_g_full_tree_.*$:'" + $unifrac_g_full_tree.__str__] - #if path == "": - #set $path=$unifrac_g_full_tree.extra_files_path - #end if - #end if - #if $unweighted_unifrac.__str__ != "None": - #set datasets = $datasets + ["'unweighted_unifrac_.*$:'" + $unweighted_unifrac.__str__] - #if path == "": - #set $path=$unweighted_unifrac.extra_files_path - #end if - #end if - #if $unweighted_unifrac_full_tree.__str__ != "None": - #set datasets = $datasets + ["'unweighted_unifrac_full_tree_.*$:'" + $unweighted_unifrac_full_tree.__str__] - #if path == "": - #set $path=$unweighted_unifrac_full_tree.extra_files_path - #end if - #end if - #if $weighted_normalized_unifrac.__str__ != "None": - #set datasets = $datasets + ["'weighted_normalized_unifrac_.*$:'" + $weighted_normalized_unifrac.__str__] - #if path == "": - #set $path=$weighted_normalized_unifrac.extra_files_path - #end if - #end if - #if $weighted_unifrac.__str__ != "None": - #set datasets = $datasets + ["'weighted_unifrac_.*$:'" + $weighted_unifrac.__str__] - #if path == "": - #set $path=$weighted_unifrac.extra_files_path - #end if - #end if - --galaxy_datasets=#echo ','.join($datasets) - --galaxy_new_files_path='$path' - beta_diversity.py - --input_path=$input_path - #if $rows.__str__ != '': - --rows=$rows - #end if - --output_dir=$__new_file_path__ - --metrics=$metrics - #if $tree_path.__str__ != "None" and len($tree_path.__str__) > 0: - --tree_path=$tree_path - #end if - $full_tree - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'binary_chisq' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'binary_chord' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'binary_euclidean' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'binary_hamming' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'binary_jaccard' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'binary_lennon' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'binary_ochiai' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'binary_pearson' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'binary_sorensen_dice' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'bray_curtis' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'canberra' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'chisq' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'chord' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'euclidean' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'gower' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'hellinger' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'kulczynski' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'manhattan' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'morisita_horn' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'pearson' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'soergel' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'spearman_approx' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'specprof' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'unifrac' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'unifrac_g' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'unifrac_g_full_tree' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'unweighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'unweighted_unifrac_full_tree' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'weighted_normalized_unifrac' in (metrics if isinstance(metrics,list) else [metrics]) - - - 'weighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics]) - - - - - For more information, see beta_diversity_ in the Qiime documentation. - -Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _beta_diversity: http://qiime.org/scripts/beta_diversity.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 beta_diversity_through_3d_plots.xml --- a/beta_diversity_through_3d_plots.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,131 +0,0 @@ - - A workflow script for computing beta diversity distance matrices and the corresponding 3D plots - - beta_diversity_through_3d_plots.py - - - qiime_wrapper.py - --galaxy_outputdir='$log.extra_files_path' - --galaxy_datasets='^log_\S+\.txt$:'$log,'^prefs\.txt$:'$prefs - beta_diversity_through_3d_plots.py - --otu_table_fp=$otu_table_fp - --mapping_fp=$mapping_fp - --output_dir='$log.extra_files_path' - --force - #if $parameter.source == 'hist': - --parameter_fp=$parameter_fp - #else: - --parameter_fp=$parameter_generated - #end if - --tree_fp=$tree_fp - #if int($seqs_per_sample) > 0: - --seqs_per_sample=$seqs_per_sample - #end if - $parallel - - - - - - - - - - - - - - - - - - - - - - - -beta_diversity:metrics -alpha_diversity:metrics chao1,observed_species,PD_whole_tree -multiple_rarefactions_even_depth:num-reps 20 -parallel:jobs_to_start 2 -parallel:retain_temp_files False -parallel:seconds_to_sleep 60 -collate_alpha:example_path -make_rarefaction_plots:imagetype png -make_rarefaction_plots:resolution 75 -make_rarefaction_plots:background_color white -make_rarefaction_plots:prefs_path - - - - - -rarefaction_plots.html - - -]]> - - - - - - - - {weighted_unifrac}_{dataset_4477.dat} - - - - - - - - -$ beta_diversity_through_3d_plots.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -m Fasting_Map.txt -o wf_bdiv_even146_test/ -p custom_parameters.tt -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre -e 146 --print_only - -single_rarefaction.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -o wf_bdiv_even146_test//seqs_otu_table_even146.txt -d 146 -make_prefs_file.py -m Fasting_Map.txt -o wf_bdiv_even146_test//prefs.txt --monte_carlo_dists 10 --background_color black --mapping_headers_to_use Treatment,DOB -beta_diversity.py -i wf_bdiv_even146_test//seqs_otu_table_even146.txt -o wf_bdiv_even146_test/ --metrics weighted_unifrac -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre -principal_coordinates.py -i wf_bdiv_even146_test//weighted_unifrac_seqs_otu_table_even146.txt -o wf_bdiv_even146_test//weighted_unifrac_pc.txt -make_3d_plots.py -p wf_bdiv_even146_test//prefs.txt -i wf_bdiv_even146_test//weighted_unifrac_pc.txt -o wf_bdiv_even146_test//weighted_unifrac_3d_continuous/ -m Fasting_Map.txt --ellipsoid_smoothness 1 -make_3d_plots.py -b "SampleID,BarcodeSequence,LinkerPrimerSequence,Treatment,DOB,Description" -i wf_bdiv_even146_test//weighted_unifrac_pc.txt -o wf_bdiv_even146_test//weighted_unifrac_3d_discrete/ -m Fasting_Map.txt --ellipsoid_smoothness 1 -beta_diversity.py -i wf_bdiv_even146_test//seqs_otu_table_even146.txt -o wf_bdiv_even146_test/ --metrics unweighted_unifrac -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre -principal_coordinates.py -i wf_bdiv_even146_test//unweighted_unifrac_seqs_otu_table_even146.txt -o wf_bdiv_even146_test//unweighted_unifrac_pc.txt -make_3d_plots.py -p wf_bdiv_even146_test//prefs.txt -i wf_bdiv_even146_test//unweighted_unifrac_pc.txt -o wf_bdiv_even146_test//unweighted_unifrac_3d_continuous/ -m Fasting_Map.txt --ellipsoid_smoothness 1 -make_3d_plots.py -b "SampleID,BarcodeSequence,LinkerPrimerSequence,Treatment,DOB,Description" -i wf_bdiv_even146_test//unweighted_unifrac_pc.txt -o wf_bdiv_even146_test//unweighted_unifrac_3d_discrete/ -m Fasting_Map.txt --ellipsoid_smoothness 1 - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 beta_significance.xml --- a/beta_significance.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ - - This script runs any of a set of common tests to determine if a sample is statistically significantly different from another sample - - beta_significance.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - beta_significance.py - --input_path=$input_path - --output_path=$output_path - --significance_test=$significance_test - --tree_path=$tree_path - --num_iters=$num_iters - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 blast_wrapper.xml --- a/blast_wrapper.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ - - Blast Interface - - blast_wrapper.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - blast_wrapper.py - --input_fasta_fp=$input_fasta_fp - --refseqs_fp=$refseqs_fp - --num_seqs_per_blast_run=$num_seqs_per_blast_run - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 categorized_dist_scatterplot.xml --- a/categorized_dist_scatterplot.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ - - makes a figure representing average distances between samples, broken down by categories. I call it a 'categorized distance scatterplot' - - categorized_dist_scatterplot.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - categorized_dist_scatterplot.py - --map=$map - --distance_matrix=$distance_matrix - --primary_state=$primary_state - --axis_category=$axis_category - --output_path=$output_path - --colorby=$colorby - --secondary_state=$secondary_state - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 check_id_map.xml --- a/check_id_map.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ - - Checks user's metadata mapping file for required data, valid format - - check_id_map.py - - - qiime_wrapper.py - --galaxy_outputdir='$log.extra_files_path' - --galaxy_datasets='^\S+_corrected\.txt$:'$corrected_mapping,'^\S+\.log:'$log - check_id_map.py - --map=$map - --output_dir='$log.extra_files_path' - --char_replace=$char_replace - $not_barcoded - $variable_len_barcodes - $disable_primer_check - $verbose - #if $added_demultiplex_field != None and $added_demultiplex_field.__str__ != "": - --added_demultiplex_field=$added_demultiplex_field - #end if - - - - - - - - - - - - - - - - - For more information, see check_id_map_ in the Qiime documentation. - -Updated and validated 01/19/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _check_id_map: http://qiime.org/scripts/check_id_map.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 collate_alpha.xml --- a/collate_alpha.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - Collate alpha diversity results - - collate_alpha.py - - - qiime_wrapper.py - --galaxy_outputdir=$output1.extra_files_path - --galaxy_new_files_path='$__new_file_path__' - --galaxy_logfile=$output1 - --galaxy_new_datasets='^\S+\.txt$:txt' - --galaxy_datasetid=$output1.id - collate_alpha.py - --input_path=$input_path.extra_files_path - --output_path='$__new_file_path__' - - - - - - - - - - - This tool concatenates all the files generated by alpha_diversity in order to generate rarefaction curves. The input is therefore the log file generated by alpha_diversity, and the output is a log file listing all the output files, as well as the files themselves. Galaxy must be manually refreshed after running this tool to view all output files. - -For more information, see collate_alpha_ in the Qiime documentation. - -Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _collate_alpha: http://qiime.org/scripts/collate_alpha.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 compare_3d_plots.xml --- a/compare_3d_plots.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ - - Plot several PCoA files on the same 3D plot - - compare_3d_plots.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - compare_3d_plots.py - --coord_fnames=$coord_fnames - --map_fname=$map_fname - --colorby=$colorby - --custom_axes=$custom_axes - --prefs_path=$prefs_path - --background_color=$background_color - --edges_file=$edges_file - $serial - --output_dir=$__new_file_path__ - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 consensus_tree.xml --- a/consensus_tree.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ - - This script outputs a majority consensus tree given a collection of input trees. - - consensus_tree.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - consensus_tree.py - --input_dir=$input_dir - --output_fname=$output_fname - $strict - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 convert_otu_table_to_unifrac_sample_mapping.xml --- a/convert_otu_table_to_unifrac_sample_mapping.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - - Convert a QIIME OTU table to a UniFrac sample mapping file - - convert_otu_table_to_unifrac_sample_mapping.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - convert_otu_table_to_unifrac_sample_mapping.py - --otu_table_fp=$otu_table_fp - --output_fp=$output_fp - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 convert_unifrac_sample_mapping_to_otu_table.xml --- a/convert_unifrac_sample_mapping_to_otu_table.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - - Convert a UniFrac sample mapping file to an OTU table - - convert_unifrac_sample_mapping_to_otu_table.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - convert_unifrac_sample_mapping_to_otu_table.py - --sample_mapping_fp=$sample_mapping_fp - --output_fp=$output_fp - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 denoise.xml --- a/denoise.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ - - Denoise a flowgram file - - denoise.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - denoise.py - --input_file=$input_file - --fasta_file=$fasta_file - --output_dir=$__new_file_path__ - --method=$method - $keep_intermediates - --cut-off=$cut_off - --precision=$precision - --num_cpus=$num_cpus - $force_overwrite - --map_fname=$map_fname - --primer=$primer - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 dissimilarity_mtx_stats.xml --- a/dissimilarity_mtx_stats.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - - Calculate mean, median and standard deviation from a set of distance matrices - - dissimilarity_mtx_stats.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - dissimilarity_mtx_stats.py - --input_dir=$input_dir - --output_dir=$__new_file_path__ - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 exclude_seqs_by_blast.xml --- a/exclude_seqs_by_blast.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ - - Exclude contaminated sequences using BLAST - - exclude_seqs_by_blast.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - exclude_seqs_by_blast.py - --querydb=$querydb - --subjectdb=$subjectdb - --outputfilename=$outputfilename - --e_value=$e_value - --percent_aligned=$percent_aligned - $no_clean - --blastmatroot=$blastmatroot - --working_dir=$working_dir - --max_hits=$max_hits - --word_size=$word_size - $no_format_db - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 extract_seqs_by_sample_id.xml --- a/extract_seqs_by_sample_id.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ - - Extract sequences based on the SampleID - - extract_seqs_by_sample_id.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - extract_seqs_by_sample_id.py - --input_fasta_fp=$input_fasta_fp - --sample_ids=$sample_ids - --output_fasta_fp=$output_fasta_fp - $negate - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 filter_alignment.xml --- a/filter_alignment.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ - - Filter sequence alignment by removing highly variable regions - - filter_alignment.py - - - qiime_wrapper.py - ## --galaxy_tmpdir='$__new_file_path__' - --galaxy_outputdir='$pfiltered_fasta.extra_files_path' - --galaxy_datasets='^\S+_pfiltered\.\S+$:'$pfiltered_fasta - filter_alignment.py - --input_fasta_file=$input_fasta_file - --output_dir='$pfiltered_fasta.extra_files_path' - --lane_mask_fp=$lane_mask_fp - $suppress_lane_mask_filter - --allowed_gap_frac=$allowed_gap_frac - $remove_outliers - --threshold=$threshold - #if $entropy_threshold != 0.0: - --entropy_threshold=$entropy_threshold - #end if - - - - - - - - - - - - - - - - For more information, see filter_alignment_ in the Qiime documentation. - -Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _filter_alignment: http://qiime.org/scripts/filter_alignment.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 filter_by_metadata.xml --- a/filter_by_metadata.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ - - Filter OTU table by removal of specified metadata - - filter_by_metadata.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - filter_by_metadata.py - --otu_table_fp=$otu_table_fp - --map=$map - --states=$states - --otu_outfile=$otu_outfile - --map_outfile=$map_outfile - --num_seqs_per_otu=$num_seqs_per_otu - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 filter_fasta.xml --- a/filter_fasta.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ - - This script can be applied to remove sequences from a fasta file based on input criteria. - - filter_fasta.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - filter_fasta.py - --input_fasta_fp=$input_fasta_fp - --output_fasta_fp=$output_fasta_fp - --otu_map=$otu_map - --seq_id_fp=$seq_id_fp - --subject_fasta_fp=$subject_fasta_fp - --seq_id_prefix=$seq_id_prefix - $negate - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 filter_otu_table.xml --- a/filter_otu_table.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ - - Filters OTU table by minimum OTU count and number of samples or by taxonomy - - filter_otu_table.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - filter_otu_table.py - --otu_table_fp=$otu_table_fp - --min_count=$min_count - --min_samples=$min_samples - --include_taxonomy=$include_taxonomy - --exclude_taxonomy=$exclude_taxonomy - --dir_path=$dir_path - --seqs_per_sample=$seqs_per_sample - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 filter_otus_by_sample.xml --- a/filter_otus_by_sample.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ - - Filter OTU mapping file and sequences by SampleIDs - - filter_otus_by_sample.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - filter_otus_by_sample.py - --otu_map_fp=$otu_map_fp - --input_fasta_fp=$input_fasta_fp - --samples_to_extract=$samples_to_extract - --output_dir=$__new_file_path__ - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 fix_arb_fasta.xml --- a/fix_arb_fasta.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ - - Reformat ARB FASTA files - - fix_arb_fasta.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - fix_arb_fasta.py - --input_fasta_fp=$input_fasta_fp - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 identify_chimeric_seqs.xml --- a/identify_chimeric_seqs.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ - - Identify chimeric sequences in input FASTA file - - identify_chimeric_seqs.py - - - qiime_wrapper.py - identify_chimeric_seqs.py - --input_fasta_fp=$input_fasta_fp - #if $pick.chimera_detection_method == 'ChimeraSlayer': - --chimera_detection_method=$pick.chimera_detection_method - --aligned_reference_seqs_fp=$pick.aligned_reference_seqs_fp - #if $pick.min_div_ratio.__str__ != '0.0': - --min_div_ratio=$pick.min_div_ratio - #end if - #elif $pick.chimera_detection_method == 'blast_fragments': - --chimera_detection_method=$pick.chimera_detection_method - --id_to_taxonomy_fp=$pick.id_to_taxonomy_fp - #if $pick.blast_db != None and $pick.blast_db.__str__ != "": - --blast_db=$pick.blast_db - #else: - --reference_seqs_fp=$pick.reference_seqs_fp - #end if - --num_fragments=$pick.num_fragments - --taxonomy_depth=$pick.taxonomy_depth - --max_e_value=$pick.max_e_value - #end if - --output_fp=$output_fp - - - - - - - - - - - - - - - - - - - - - - - - - - - - For more information, see identify_chimeric_seqs_ in the Qiime documentation. - -Updated and validated 01/19/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _identify_chimeric_seqs: http://qiime.org/scripts/identify_chimeric_seqs.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 jackknifed_beta_diversity.xml --- a/jackknifed_beta_diversity.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,101 +0,0 @@ - - A workflow script for performing jackknifed UPGMA clustering and build jackknifed 2d and 3D PCoA plots. - - jackknifed_beta_diversity.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - jackknifed_beta_diversity.py - --otu_table_fp=$otu_table_fp - --output_dir=$__new_file_path__ - $force - #if $parameter.source == 'hist': - --parameter_fp=$parameter_fp - #else: - --parameter_fp=$parameter_generated - #end if - --seqs_per_sample=$seqs_per_sample - --mapping_fp=$mapping_fp - --tree_fp=$tree_fp - --master_tree=$master_tree - $print_only - $parallel - - - - - - - - - - - - - - - - - - - - - - - - - - - - -alpha_diversity:metrics chao1,observed_species,PD_whole_tree -multiple_rarefactions_even_depth:num-reps 20 -parallel:jobs_to_start 2 -parallel:retain_temp_files False -parallel:seconds_to_sleep 60 -collate_alpha:example_path -make_rarefaction_plots:imagetype png -make_rarefaction_plots:resolution 75 -make_rarefaction_plots:background_color white -make_rarefaction_plots:prefs_path - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 lib/.DS_Store Binary file lib/.DS_Store has changed diff -r 2e14fb0fd792 -r 3b1401bf4cb1 lib/._.DS_Store Binary file lib/._.DS_Store has changed diff -r 2e14fb0fd792 -r 3b1401bf4cb1 lib/._galaxy Binary file lib/._galaxy has changed diff -r 2e14fb0fd792 -r 3b1401bf4cb1 lib/galaxy/.DS_Store Binary file lib/galaxy/.DS_Store has changed diff -r 2e14fb0fd792 -r 3b1401bf4cb1 lib/galaxy/._.DS_Store Binary file lib/galaxy/._.DS_Store has changed diff -r 2e14fb0fd792 -r 3b1401bf4cb1 lib/galaxy/._datatypes Binary file lib/galaxy/._datatypes has changed diff -r 2e14fb0fd792 -r 3b1401bf4cb1 lib/galaxy/datatypes/._metagenomics.py Binary file lib/galaxy/datatypes/._metagenomics.py has changed diff -r 2e14fb0fd792 -r 3b1401bf4cb1 lib/galaxy/datatypes/metagenomics.py --- a/lib/galaxy/datatypes/metagenomics.py Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1121 +0,0 @@ -""" -metagenomics datatypes -James E Johnson - University of Minnesota -for Mothur -""" - -import data -import logging, os, sys, time, tempfile, shutil, string, glob, re -import galaxy.model -from galaxy.datatypes import metadata -from galaxy.datatypes import tabular -from galaxy.datatypes import sequence -from galaxy.datatypes.metadata import MetadataElement -from galaxy.datatypes.tabular import Tabular -from galaxy.datatypes.sequence import Fasta -from galaxy import util -from galaxy.datatypes.images import Html -from sniff import * - -log = logging.getLogger(__name__) - - -## Mothur Classes - -class Otu( Tabular ): - file_ext = 'otu' - - def sniff( self, filename ): - """ - Determines whether the file is a otu (operational taxonomic unit) format - """ - try: - fh = open( filename ) - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break #EOF - if line: - if line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) < 2: - return False - try: - check = int(linePieces[1]) - if check + 2 != len(linePieces): - return False - except ValueError: - return False - count += 1 - if count == 5: - return True - fh.close() - if count < 5 and count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class OtuList( Otu ): - file_ext = 'list' - -class Sabund( Otu ): - file_ext = 'sabund' - - def sniff( self, filename ): - """ - Determines whether the file is a otu (operational taxonomic unit) format - labelcount[value(1..n)] - - """ - try: - fh = open( filename ) - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break #EOF - if line: - if line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) < 2: - return False - try: - check = int(linePieces[1]) - if check + 2 != len(linePieces): - return False - for i in range( 2, len(linePieces)): - ival = int(linePieces[i]) - except ValueError: - return False - count += 1 - if count >= 5: - return True - fh.close() - if count < 5 and count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class Rabund( Sabund ): - file_ext = 'rabund' - -class GroupAbund( Otu ): - file_ext = 'grpabund' - def init_meta( self, dataset, copy_from=None ): - Otu.init_meta( self, dataset, copy_from=copy_from ) - def set_meta( self, dataset, overwrite = True, skip=1, max_data_lines = 100000, **kwd ): - # See if file starts with header line - if dataset.has_data(): - try: - fh = open( dataset.file_name ) - line = fh.readline() - line = line.strip() - linePieces = line.split('\t') - if linePieces[0] == 'label' and linePieces[1] == 'Group': - skip=1 - else: - skip=0 - finally: - fh.close() - Otu.set_meta( self, dataset, overwrite, skip, max_data_lines, **kwd) - def sniff( self, filename, vals_are_int=False): - """ - Determines whether the file is a otu (operational taxonomic unit) Shared format - labelgroupcount[value(1..n)] - The first line is column headings as of Mothur v 1.20 - """ - log.info( "sniff GroupAbund vals_are_int %s" % vals_are_int) - try: - fh = open( filename ) - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break #EOF - if line: - if line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) < 3: - return False - if count > 0 or linePieces[0] != 'label': - try: - check = int(linePieces[2]) - if check + 3 != len(linePieces): - return False - for i in range( 3, len(linePieces)): - if vals_are_int: - ival = int(linePieces[i]) - else: - fval = float(linePieces[i]) - except ValueError: - return False - count += 1 - if count >= 5: - return True - fh.close() - if count < 5 and count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class SharedRabund( GroupAbund ): - file_ext = 'shared' - - - def sniff( self, filename ): - """ - Determines whether the file is a otu (operational taxonomic unit) Shared format - labelgroupcount[value(1..n)] - The first line is column headings as of Mothur v 1.20 - """ - # return GroupAbund.sniff(self,filename,True) - isme = GroupAbund.sniff(self,filename,True) - log.info( "is SharedRabund %s" % isme) - return isme - - -class RelAbund( GroupAbund ): - file_ext = 'relabund' - - def sniff( self, filename ): - """ - Determines whether the file is a otu (operational taxonomic unit) Relative Abundance format - labelgroupcount[value(1..n)] - The first line is column headings as of Mothur v 1.20 - """ - # return GroupAbund.sniff(self,filename,False) - isme = GroupAbund.sniff(self,filename,False) - log.info( "is RelAbund %s" % isme) - return isme - -class SecondaryStructureMap(Tabular): - file_ext = 'map' - def __init__(self, **kwd): - """Initialize secondary structure map datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['Map'] - - def sniff( self, filename ): - """ - Determines whether the file is a secondary structure map format - A single column with an integer value which indicates the row that this row maps to. - check you make sure is structMap[10] = 380 then structMap[380] = 10. - """ - try: - fh = open( filename ) - line_num = 0 - rowidxmap = {} - while True: - line = fh.readline() - line_num += 1 - line = line.strip() - if not line: - break #EOF - if line: - try: - pointer = int(line) - if pointer > 0: - if pointer > line_num: - rowidxmap[line_num] = pointer - elif pointer < line_num & rowidxmap[pointer] != line_num: - return False - except ValueError: - return False - fh.close() - if count < 5 and count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class SequenceAlignment( Fasta ): - file_ext = 'align' - def __init__(self, **kwd): - Fasta.__init__( self, **kwd ) - """Initialize AlignCheck datatype""" - - def sniff( self, filename ): - """ - Determines whether the file is in Mothur align fasta format - Each sequence line must be the same length - """ - - try: - fh = open( filename ) - len = -1 - while True: - line = fh.readline() - if not line: - break #EOF - line = line.strip() - if line: #first non-empty line - if line.startswith( '>' ): - #The next line.strip() must not be '', nor startwith '>' - line = fh.readline().strip() - if line == '' or line.startswith( '>' ): - break - if len < 0: - len = len(line) - elif len != len(line): - return False - else: - break #we found a non-empty line, but its not a fasta header - if len > 0: - return True - except: - pass - finally: - fh.close() - return False - -class AlignCheck( Tabular ): - file_ext = 'align.check' - def __init__(self, **kwd): - """Initialize AlignCheck datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] - self.column_types = ['str','int','int','int','int','int','int','int'] - self.comment_lines = 1 - - def set_meta( self, dataset, overwrite = True, **kwd ): - # Tabular.set_meta( self, dataset, overwrite = overwrite, first_line_is_header = True, skip = 1 ) - data_lines = 0 - if dataset.has_data(): - dataset_fh = open( dataset.file_name ) - while True: - line = dataset_fh.readline() - if not line: break - data_lines += 1 - dataset_fh.close() - dataset.metadata.comment_lines = 1 - dataset.metadata.data_lines = data_lines - 1 if data_lines > 0 else 0 - dataset.metadata.column_names = self.column_names - dataset.metadata.column_types = self.column_types - -class AlignReport(Tabular): - """ -QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template -AY457915 501 82283 1525 kmer 89.07 needleman 5 501 1 499 499 2 0 0 97.6 - """ - file_ext = 'align.report' - def __init__(self, **kwd): - """Initialize AlignCheck datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['QueryName','QueryLength','TemplateName','TemplateLength','SearchMethod','SearchScore', - 'AlignmentMethod','QueryStart','QueryEnd','TemplateStart','TemplateEnd', - 'PairwiseAlignmentLength','GapsInQuery','GapsInTemplate','LongestInsert','SimBtwnQuery&Template' - ] - -class BellerophonChimera( Tabular ): - file_ext = 'bellerophon.chimera' - def __init__(self, **kwd): - """Initialize AlignCheck datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['Name','Score','Left','Right'] - -class SecondaryStructureMatch(Tabular): - """ - name pound dash plus equal loop tilde total - 9_1_12 42 68 8 28 275 420 872 - 9_1_14 36 68 6 26 266 422 851 - 9_1_15 44 68 8 28 276 418 873 - 9_1_16 34 72 6 30 267 430 860 - 9_1_18 46 80 2 36 261 - """ - def __init__(self, **kwd): - """Initialize SecondaryStructureMatch datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] - -class DistanceMatrix(data.Text): - file_ext = 'dist' - """Add metadata elements""" - MetadataElement( name="sequence_count", default=0, desc="Number of sequences", readonly=False, optional=True, no_value=0 ) - - -class LowerTriangleDistanceMatrix(DistanceMatrix): - file_ext = 'lower.dist' - def __init__(self, **kwd): - """Initialize secondary structure map datatype""" - DistanceMatrix.__init__( self, **kwd ) - - def sniff( self, filename ): - """ - Determines whether the file is a lower-triangle distance matrix (phylip) format - The first line has the number of sequences in the matrix. - The remaining lines have the sequence name followed by a list of distances from all preceeding sequences - 5 - U68589 - U68590 0.3371 - U68591 0.3609 0.3782 - U68592 0.4155 0.3197 0.4148 - U68593 0.2872 0.1690 0.3361 0.2842 - """ - try: - fh = open( filename ) - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break #EOF - if line: - if line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) != 3: - return False - try: - check = float(linePieces[2]) - except ValueError: - return False - count += 1 - if count == 5: - return True - fh.close() - if count < 5 and count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class SquareDistanceMatrix(DistanceMatrix,Tabular): - file_ext = 'square.dist' - sequence_count = -1 - - def __init__(self, **kwd): - """Initialize secondary structure map datatype""" - Tabular.__init__( self, **kwd ) - def init_meta( self, dataset, copy_from=None ): - data.Text.init_meta( self, dataset, copy_from=copy_from ) - def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): - dataset.metadata.sequences = 0 - - def sniff( self, filename ): - """ - Determines whether the file is a square distance matrix (Column-formatted distance matrix) format - The first line has the number of sequences in the matrix. - The following lines have the sequence name in the first column plus a column for the distance to each sequence - in the row order in which they appear in the matrix. - 3 - U68589 0.0000 0.3371 0.3610 - U68590 0.3371 0.0000 0.3783 - U68590 0.3371 0.0000 0.3783 - """ - try: - fh = open( filename ) - count = 0 - line = fh.readline() - line = line.strip() - sequence_count = int(line) - col_cnt = seq_cnt + 1 - while True: - line = fh.readline() - line = line.strip() - if not line: - break #EOF - if line: - if line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) != col_cnt : - return False - try: - for i in range(1, col_cnt): - check = float(linePieces[i]) - except ValueError: - return False - count += 1 - if count == 5: - return True - fh.close() - if count < 5 and count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class PairwiseDistanceMatrix(DistanceMatrix,Tabular): - file_ext = 'pair.dist' - def __init__(self, **kwd): - """Initialize secondary structure map datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['Sequence','Sequence','Distance'] - self.column_types = ['str','str','float'] - self.comment_lines = 1 - - def sniff( self, filename ): - """ - Determines whether the file is a pairwise distance matrix (Column-formatted distance matrix) format - The first and second columns have the sequence names and the third column is the distance between those sequences. - """ - try: - fh = open( filename ) - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break #EOF - if line: - if line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) != 3: - return False - try: - check = float(linePieces[2]) - except ValueError: - return False - count += 1 - if count == 5: - return True - fh.close() - if count < 5 and count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class AlignCheck(Tabular): - file_ext = 'align.check' - def __init__(self, **kwd): - """Initialize secondary structure map datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] - self.columns = 8 - -class Names(Tabular): - file_ext = 'names' - def __init__(self, **kwd): - """Name file shows the relationship between a representative sequence(col 1) and the sequences(comma-separated) it represents(col 2)""" - Tabular.__init__( self, **kwd ) - self.column_names = ['name','representatives'] - self.columns = 2 - -class Summary(Tabular): - file_ext = 'summary' - def __init__(self, **kwd): - """summarizes the quality of sequences in an unaligned or aligned fasta-formatted sequence file""" - Tabular.__init__( self, **kwd ) - self.column_names = ['seqname','start','end','nbases','ambigs','polymer'] - self.columns = 6 - -class Group(Tabular): - file_ext = 'groups' - def __init__(self, **kwd): - """Name file shows the relationship between a representative sequence(col 1) and the sequences it represents(col 2)""" - Tabular.__init__( self, **kwd ) - self.column_names = ['name','group'] - self.columns = 2 - -class Design(Tabular): - file_ext = 'design' - def __init__(self, **kwd): - """Name file shows the relationship between a group(col 1) and a grouping (col 2), providing a way to merge groups.""" - Tabular.__init__( self, **kwd ) - self.column_names = ['group','grouping'] - self.columns = 2 - -class AccNos(Tabular): - file_ext = 'accnos' - def __init__(self, **kwd): - """A list of names""" - Tabular.__init__( self, **kwd ) - self.column_names = ['name'] - self.columns = 1 - -class Oligos( data.Text ): - file_ext = 'oligos' - - def sniff( self, filename ): - """ - Determines whether the file is a otu (operational taxonomic unit) format - """ - try: - fh = open( filename ) - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break #EOF - else: - if line[0] != '#': - linePieces = line.split('\t') - if len(linePieces) == 2 and re.match('forward|reverse',linePieces[0]): - count += 1 - continue - elif len(linePieces) == 3 and re.match('barcode',linePieces[0]): - count += 1 - continue - else: - return False - if count > 20: - return True - if count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class Frequency(Tabular): - file_ext = 'freq' - def __init__(self, **kwd): - """A list of names""" - Tabular.__init__( self, **kwd ) - self.column_names = ['position','frequency'] - self.column_types = ['int','float'] - - def sniff( self, filename ): - """ - Determines whether the file is a frequency tabular format for chimera analysis - #1.14.0 - 0 0.000 - 1 0.000 - ... - 155 0.975 - """ - try: - fh = open( filename ) - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break #EOF - else: - if line[0] != '#': - try: - linePieces = line.split('\t') - i = int(linePieces[0]) - f = float(linePieces[1]) - count += 1 - continue - except: - return False - if count > 20: - return True - if count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class Quantile(Tabular): - file_ext = 'quan' - MetadataElement( name="filtered", default=False, no_value=False, optional=True , desc="Quantiles calculated using a mask", readonly=True) - MetadataElement( name="masked", default=False, no_value=False, optional=True , desc="Quantiles calculated using a frequency filter", readonly=True) - def __init__(self, **kwd): - """Quantiles for chimera analysis""" - Tabular.__init__( self, **kwd ) - self.column_names = ['num','ten','twentyfive','fifty','seventyfive','ninetyfive','ninetynine'] - self.column_types = ['int','float','float','float','float','float','float'] - def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): - log.info( "Mothur Quantile set_meta %s" % kwd) - def sniff( self, filename ): - """ - Determines whether the file is a quantiles tabular format for chimera analysis - 1 0 0 0 0 0 0 - 2 0.309198 0.309198 0.37161 0.37161 0.37161 0.37161 - 3 0.510982 0.563213 0.693529 0.858939 1.07442 1.20608 - ... - """ - try: - fh = open( filename ) - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break #EOF - else: - if line[0] != '#': - try: - linePieces = line.split('\t') - i = int(linePieces[0]) - f = float(linePieces[1]) - f = float(linePieces[2]) - f = float(linePieces[3]) - f = float(linePieces[4]) - f = float(linePieces[5]) - f = float(linePieces[6]) - count += 1 - continue - except: - return False - if count > 10: - return True - if count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class FilteredQuantile(Quantile): - file_ext = 'filtered.quan' - def __init__(self, **kwd): - """Quantiles for chimera analysis""" - Quantile.__init__( self, **kwd ) - self.filtered = True - -class MaskedQuantile(Quantile): - file_ext = 'masked.quan' - def __init__(self, **kwd): - """Quantiles for chimera analysis""" - Quantile.__init__( self, **kwd ) - self.masked = True - self.filtered = False - -class FilteredMaskedQuantile(Quantile): - file_ext = 'filtered.masked.quan' - def __init__(self, **kwd): - """Quantiles for chimera analysis""" - Quantile.__init__( self, **kwd ) - self.masked = True - self.filtered = True - -class LaneMask(data.Text): - file_ext = 'filter' - - def sniff( self, filename ): - """ - Determines whether the file is a lane mask filter: 1 line consisting of zeros and ones. - """ - try: - fh = open( filename ) - while True: - buff = fh.read(1000) - if not buff: - break #EOF - else: - if not re.match('^[01]+$',line): - return False - return True - except: - pass - finally: - close(fh) - return False - -class SequenceTaxonomy(Tabular): - file_ext = 'seq.taxonomy' - """ - A table with 2 columns: - - SequenceName - - Taxonomy (semicolon-separated taxonomy in descending order) - Example: - X56533.1 Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma; - X97975.1 Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida; - AF052717.1 Eukaryota;Parabasalidea; - """ - def __init__(self, **kwd): - Tabular.__init__( self, **kwd ) - self.column_names = ['name','taxonomy'] - - def sniff( self, filename ): - """ - Determines whether the file is a SequenceTaxonomy - """ - try: - pat = '^([^ \t\n\r\f\v;]+([(]\d+[)])?[;])+$' - fh = open( filename ) - count = 0 - while True: - line = fh.readline() - if not line: - break #EOF - line = line.strip() - if line: - fields = line.split('\t') - if len(fields) != 2: - return False - if not re.match(pat,fields[1]): - return False - count += 1 - if count > 10: - break - if count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class RDPSequenceTaxonomy(SequenceTaxonomy): - file_ext = 'rdp.taxonomy' - """ - A table with 2 columns: - - SequenceName - - Taxonomy (semicolon-separated taxonomy in descending order, RDP requires exactly 6 levels deep) - Example: - AB001518.1 Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;unclassified_Sphingobacteriales; - AB001724.1 Bacteria;Cyanobacteria;Cyanobacteria;Family_II;GpIIa; - AB001774.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; - """ - def sniff( self, filename ): - """ - Determines whether the file is a SequenceTaxonomy - """ - try: - pat = '^([^ \t\n\r\f\v;]+([(]\d+[)])?[;]){6}$' - fh = open( filename ) - count = 0 - while True: - line = fh.readline() - if not line: - break #EOF - line = line.strip() - if line: - fields = line.split('\t') - if len(fields) != 2: - return False - if not re.match(pat,fields[1]): - return False - count += 1 - if count > 10: - break - if count > 0: - return True - except: - pass - finally: - fh.close() - return False - -class ConsensusTaxonomy(Tabular): - file_ext = 'cons.taxonomy' - def __init__(self, **kwd): - """A list of names""" - Tabular.__init__( self, **kwd ) - self.column_names = ['OTU','count','taxonomy'] - -class TaxonomySummary(Tabular): - file_ext = 'tax.summary' - def __init__(self, **kwd): - """A Summary of taxon classification""" - Tabular.__init__( self, **kwd ) - self.column_names = ['taxlevel','rankID','taxon','daughterlevels','total'] - -class Phylip(data.Text): - file_ext = 'phy' - - def sniff( self, filename ): - """ - Determines whether the file is in Phylip format (Interleaved or Sequential) - The first line of the input file contains the number of species and the - number of characters, in free format, separated by blanks (not by - commas). The information for each species follows, starting with a - ten-character species name (which can include punctuation marks and blanks), - and continuing with the characters for that species. - http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles - Interleaved Example: - 6 39 - Archaeopt CGATGCTTAC CGCCGATGCT - HesperorniCGTTACTCGT TGTCGTTACT - BaluchitheTAATGTTAAT TGTTAATGTT - B. virginiTAATGTTCGT TGTTAATGTT - BrontosaurCAAAACCCAT CATCAAAACC - B.subtilisGGCAGCCAAT CACGGCAGCC - - TACCGCCGAT GCTTACCGC - CGTTGTCGTT ACTCGTTGT - AATTGTTAAT GTTAATTGT - CGTTGTTAAT GTTCGTTGT - CATCATCAAA ACCCATCAT - AATCACGGCA GCCAATCAC - """ - try: - fh = open( filename ) - # counts line - line = fh.readline().strip() - linePieces = line.split() - count = int(linePieces[0]) - seq_len = int(linePieces[1]) - # data lines - """ - TODO check data lines - while True: - line = fh.readline() - # name is the first 10 characters - name = line[0:10] - seq = line[10:].strip() - # nucleic base or amino acid 1-char designators (spaces allowed) - bases = ''.join(seq.split()) - # float per base (each separated by space) - """ - return True - except: - pass - finally: - close(fh) - return False - - -class Axes(Tabular): - file_ext = 'axes' - - def __init__(self, **kwd): - """Initialize axes datatype""" - Tabular.__init__( self, **kwd ) - def sniff( self, filename ): - """ - Determines whether the file is an axes format - The first line may have column headings. - The following lines have the name in the first column plus float columns for each axis. - ==> 98_sq_phylip_amazon.fn.unique.pca.axes <== - group axis1 axis2 - forest 0.000000 0.145743 - pasture 0.145743 0.000000 - - ==> 98_sq_phylip_amazon.nmds.axes <== - axis1 axis2 - U68589 0.262608 -0.077498 - U68590 0.027118 0.195197 - U68591 0.329854 0.014395 - """ - try: - fh = open( filename ) - count = 0 - line = fh.readline() - line = line.strip() - col_cnt = None - while True: - line = fh.readline() - line = line.strip() - if not line: - break #EOF - if line: - fields = line.split('\t') - if col_cnt == None: # ignore values in first line as they may be column headings - col_cnt = len(fields) - else: - if len(fields) != col_cnt : - return False - try: - for i in range(1, col_cnt): - check = float(fields[i]) - except ValueError: - return False - count += 1 - if count > 10: - return True - if count > 0: - return True - except: - pass - finally: - fh.close() - return False - -## Qiime Classes - -class QiimeMetadataMapping(Tabular): - MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] ) - file_ext = 'qiimemapping' - - def __init__(self, **kwd): - """ - http://qiime.sourceforge.net/documentation/file_formats.html#mapping-file-overview - Information about the samples necessary to perform the data analysis. - # self.column_names = ['#SampleID','BarcodeSequence','LinkerPrimerSequence','Description'] - """ - Tabular.__init__( self, **kwd ) - - def sniff( self, filename ): - """ - Determines whether the file is a qiime mapping file - Just checking for an appropriate header line for now, could be improved - """ - try: - pat = '#SampleID(\t[a-zA-Z][a-zA-Z0-9_]*)*\tDescription' - fh = open( filename ) - while True: - line = dataset_fh.readline() - if re.match(pat,line): - return True - except: - pass - finally: - close(fh) - return False - - def set_column_names(self, dataset): - if dataset.has_data(): - dataset_fh = open( dataset.file_name ) - line = dataset_fh.readline() - if line.startswith('#SampleID'): - dataset.metadata.column_names = line.strip().split('\t'); - dataset_fh.close() - - def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = None, **kwd ): - Tabular.set_meta(self, dataset, overwrite, skip, max_data_lines) - self.set_column_names(dataset) - -class QiimeOTU(Tabular): - """ - Associates OTUs with sequence IDs - Example: - 0 FLP3FBN01C2MYD FLP3FBN01B2ALM - 1 FLP3FBN01DF6NE FLP3FBN01CKW1J FLP3FBN01CHVM4 - 2 FLP3FBN01AXQ2Z - """ - file_ext = 'qiimeotu' - -class QiimeOTUTable(Tabular): - """ - #Full OTU Counts - #OTU ID PC.354 PC.355 PC.356 Consensus Lineage - 0 0 1 0 Root;Bacteria;Firmicutes;"Clostridia";Clostridiales - 1 1 3 1 Root;Bacteria - 2 0 2 2 Root;Bacteria;Bacteroidetes - """ - MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] ) - file_ext = 'qiimeotutable' - def init_meta( self, dataset, copy_from=None ): - tabular.Tabular.init_meta( self, dataset, copy_from=copy_from ) - def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): - self.set_column_names(dataset) - def set_column_names(self, dataset): - if dataset.has_data(): - dataset_fh = open( dataset.file_name ) - line = dataset_fh.readline() - line = dataset_fh.readline() - if line.startswith('#OTU ID'): - dataset.metadata.column_names = line.strip().split('\t'); - dataset_fh.close() - dataset.metadata.comment_lines = 2 - -class QiimeDistanceMatrix(Tabular): - """ - PC.354 PC.355 PC.356 - PC.354 0.0 3.177 1.955 - PC.355 3.177 0.0 3.444 - PC.356 1.955 3.444 0.0 - """ - file_ext = 'qiimedistmat' - def init_meta( self, dataset, copy_from=None ): - tabular.Tabular.init_meta( self, dataset, copy_from=copy_from ) - def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): - self.set_column_names(dataset) - def set_column_names(self, dataset): - if dataset.has_data(): - dataset_fh = open( dataset.file_name ) - line = dataset_fh.readline() - # first line contains the names - dataset.metadata.column_names = line.strip().split('\t'); - dataset_fh.close() - dataset.metadata.comment_lines = 1 - -class QiimePCA(Tabular): - """ - Principal Coordinate Analysis Data - The principal coordinate (PC) axes (columns) for each sample (rows). - Pairs of PCs can then be graphed to view the relationships between samples. - The bottom of the output file contains the eigenvalues and % variation explained for each PC. - Example: - pc vector number 1 2 3 - PC.354 -0.309063936588 0.0398252112257 0.0744672231759 - PC.355 -0.106593922619 0.141125998277 0.0780204374172 - PC.356 -0.219869362955 0.00917241121781 0.0357281314115 - - - eigvals 0.480220500471 0.163567082874 0.125594470811 - % variation explained 51.6955484555 17.6079322939 - """ - file_ext = 'qiimepca' - -class QiimeParams(Tabular): - """ -###pick_otus_through_otu_table.py parameters### - -# OTU picker parameters -pick_otus:otu_picking_method uclust -pick_otus:clustering_algorithm furthest - -# Representative set picker parameters -pick_rep_set:rep_set_picking_method first -pick_rep_set:sort_by otu - """ - file_ext = 'qiimeparams' - -class QiimePrefs(data.Text): - """ - A text file, containing coloring preferences to be used by make_distance_histograms.py, make_2d_plots.py and make_3d_plots.py. - Example: -{ -'background_color':'black', - -'sample_coloring': - { - 'Treatment': - { - 'column':'Treatment', - 'colors':(('red',(0,100,100)),('blue',(240,100,100))) - }, - 'DOB': - { - 'column':'DOB', - 'colors':(('red',(0,100,100)),('blue',(240,100,100))) - } - }, -'MONTE_CARLO_GROUP_DISTANCES': - { - 'Treatment': 10, - 'DOB': 10 - } -} - """ - file_ext = 'qiimeprefs' - -class QiimeTaxaSummary(Tabular): - """ - Taxon PC.354 PC.355 PC.356 - Root;Bacteria;Actinobacteria 0.0 0.177 0.955 - Root;Bacteria;Firmicutes 0.177 0.0 0.444 - Root;Bacteria;Proteobacteria 0.955 0.444 0.0 - """ - MetadataElement( name="column_names", default=[], desc="Column Names", readonly=False, visible=True, no_value=[] ) - file_ext = 'qiimetaxsummary' - - def set_column_names(self, dataset): - if dataset.has_data(): - dataset_fh = open( dataset.file_name ) - line = dataset_fh.readline() - if line.startswith('Taxon'): - dataset.metadata.column_names = line.strip().split('\t'); - dataset_fh.close() - - def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = None, **kwd ): - Tabular.set_meta(self, dataset, overwrite, skip, max_data_lines) - self.set_column_names(dataset) - -if __name__ == '__main__': - import doctest, sys - doctest.testmod(sys.modules[__name__]) - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_2d_plots.xml --- a/make_2d_plots.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ - - Make 2D PCoA Plots - - make_2d_plots.py - - - qiime_wrapper.py - --galaxy_outputdir=$plot.extra_files_path - ##--galaxy_tmpdir='$__new_file_path__' - ##--galaxy_datasets='^\S+_2D_PCoA_plots\.html$:'$plot - --galaxy_datasets='^\S+\.html$:'$plot - ##--galaxy_datasetid=$output1.id - ##--galaxy_new_files_path='$__new_file_path__' - ##--galaxy_tmpdir='$__new_file_path__' - make_2d_plots.py - --coord_fname=$coord_fname - --map_fname=$map_fname - #if $colorby != None and $colorby.__str__ != 'None': - --colorby=$colorby - #end if - #if $prefs_path != None and $prefs_path.__str__ != 'None' and len($prefs_path.__str__) > 0: - --prefs_path=$prefs_path - #end if - --background_color=$background_color - --ellipsoid_opacity=$ellipsoid_opacity - --ellipsoid_method=$ellipsoid_method - #if $master_pcoa != None and $master_pcoa.__str__ != 'None' and len($master_pcoa.__str__) > 0: - --master_pcoa=$master_pcoa - #end if - --output_dir=$plot.extra_files_path - - - - - - - - - - - - - - - - - - - - For more information, see make_2d_plots_ in the Qiime documentation. - -Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _make_2d_plots: http://qiime.org/scripts/make_2d_plots.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_3d_plots.xml --- a/make_3d_plots.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,89 +0,0 @@ - - Make 3D PCoA plots - - make_3d_plots.py - - - qiime_wrapper.py - --galaxy_summary_html='$output_html' - --galaxy_outputdir='$output_html.extra_files_path' - --galaxy_summary_template='$output_template' - make_3d_plots.py - --coord_fname=$coord_fname - --map_fname=$map_fname - --colorby=$colorby - --custom_axes=$custom_axes - --prefs_path=$prefs_path - --background_color=$background_color - --output_dir=$__new_file_path__ - --ellipsoid_smoothness=$ellipsoid_smoothness - --ellipsoid_opacity=$ellipsoid_opacity - --ellipsoid_method=$ellipsoid_method - --taxa_fname=$taxa_fname - --n_taxa_keep=$n_taxa_keep - --biplot_output_file=$biplot_output_file - --master_pcoa=$master_pcoa - --output_format=$output_format - --interpolation_points=$interpolation_points - --polyhedron_points=$polyhedron_points - --polyhedron_offset=$polyhedron_offset - - - - - - - - - - - - - - - - - - - - - - - - - - - -weighted_unifrac_pc.txt_3D.html - - -]]> - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_bootstrapped_tree.xml --- a/make_bootstrapped_tree.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ - - Make bootstrapped tree - - make_bootstrapped_tree.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - make_bootstrapped_tree.py - --master_tree=$master_tree - --support=$support - --output_file=$output_file - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_distance_histograms.xml --- a/make_distance_histograms.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ - - Make distance histograms - - make_distance_histograms.py - - - qiime_wrapper.py - --galaxy_outputdir=$plot.extra_files_path - --galaxy_datasets='^\S+\.html$:'$plot - make_distance_histograms.py - --distance_matrix_file=$distance_matrix_file - --map_fname=$map_fname - #if $prefs_path != None and $prefs_path.__str__ != 'None' and len($prefs_path.__str__) > 0: - --prefs_path=$prefs_path - #end if - --dir_path=$plot.extra_files_path - --background_color=$background_color - $monte_carlo - #if $fields != None and $fields.__str__ != ' ' and $fields.__str__ !='': - --fields=$fields - #end if - --monte_carlo_iters=$monte_carlo_iters - - - - - - - - - - - - - - - - - - - For more information, see make_distance_histograms_ in the Qiime documentation. - -Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _make_distance_histograms: http://qiime.org/scripts/make_distance_histograms.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_fastq.xml --- a/make_fastq.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ - - Make fastq file for ERA submission from paired fasta and qual files - - make_fastq.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - make_fastq.py - --input_fasta_fp=$input_fasta_fp - --qual=$qual - --result_fp=$result_fp - $split - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_library_id_lists.xml --- a/make_library_id_lists.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ - - Make library id lists - - make_library_id_lists.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - make_library_id_lists.py - --input_fasta=$input_fasta - --screened_rep_seqs=$screened_rep_seqs - --otus=$otus - --outdir=$outdir - --field=$field - $debug - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_otu_heatmap_html.xml --- a/make_otu_heatmap_html.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ - - Make heatmap of OTU table - - make_otu_heatmap_html.py - - - qiime_wrapper.py - --galaxy_outputdir='$otu_heatmp.extra_files_path' - --galaxy_datasets='^\S+\.html$:'$otu_heatmp - make_otu_heatmap_html.py - --otu_table_fp=$otu_table_fp - --output_dir='$otu_heatmp.extra_files_path' - --num_otu_hits=$num_otu_hits - #if $tree != None and $tree.__str__ != 'None': - --tree=$tree - #end if - #if $map_fname != None and $map_fname.__str__ != 'None' > 0: - --map_fname=$map_fname - #end if - #if $sample_tree != None and $sample_tree.__str__ != 'None': - --sample_tree=$sample_tree - #end if - $log_transform - --log_eps=$log_eps - - - - - - - - - - - - - - - - - For more information, see make_otu_heatmap_html_ in the Qiime documentation. - -Updated and validated 02/10/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _make_otu_heatmap_html: http://qiime.org/scripts/make_otu_heatmap_html.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_otu_network.xml --- a/make_otu_network.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - Make an OTU network and calculate statistics - - make_otu_network.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - make_otu_network.py - --mapping_file=$mapping_file - --input_file=$input_file - --colorby=$colorby - --prefs_path=$prefs_path - --background_color=$background_color - --output_dir=$__new_file_path__ - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_otu_table.xml --- a/make_otu_table.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ - - Make OTU table - - make_otu_table.py - - - qiime_wrapper.py - make_otu_table.py - --otu_map_fp=$otu_map_fp - --output_fp=$output_fp - #if $taxonomy.__str__ != 'None': - --taxonomy=$taxonomy - #end if - #if $exclude_otus_fp.__str__ != 'None': - --exclude_otus_fp=$exclude_otus_fp - #end if - - - - - - - - - - - - For more information, see make_otu_table_ in the Qiime documentation. - -Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _make_otu_table: http://qiime.org/scripts/make_otu_table - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_per_library_sff.xml --- a/make_per_library_sff.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ - - Make per-library sff files from id lists - - make_per_library_sff.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - make_per_library_sff.py - --input_sff=$input_sff - --libdir=$libdir - --sfffile_path=$sfffile_path - $use_sfftools - $debug - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_phylogeny.pl --- a/make_phylogeny.pl Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ -#!/usr/bin/perl -# (c) 2011 Amanda Zuzolo c.o. George Mason University - -# 08/22/2011 Created - -### give start time; define input and output ### -my $start = time(); - -my $inputfasta = @ARGV[0]; -my $tree_method = @ARGV[1]; -my $root_method = @ARGV[2]; -my $result_file = @ARGV[3]; - -## change directory; concat filenames to temp ## -chdir "\/tmp"; - -my $tempfasta = "temp_fasta_$userid$start.fasta"; -#my $tempoutput = "tempout_$userid$start.txt"; -#my $outputdir = "$userid$start"; -system("cat $inputfasta > $tempfasta"); - -##### make system call to run qiime script ##### - -system("make_phylogeny.py -i $tempfasta -t $tree_method -r $root_method"); - -## cat qiime tre file to output; delete temps ## - -system("cat temp_fasta_$userid$start.tre > $result_file"); -system("rm $tempfasta"); -system("rm temp_fasta_$userid$start.tre"); - -print $result_file; diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_phylogeny.xml --- a/make_phylogeny.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ - - Make Phylogeny - - make_phylogeny.py - - - qiime_wrapper.py - --galaxy_inputdir='$__new_file_path__' - --galaxy_ext_change='$input_fp' - --galaxy_new_ext='fasta' - make_phylogeny.py - --input_fp='$__new_file_path__'/temporary.fasta - --tree_method=$tree_method - --result_fp=$result_fp - --log_fp=$log_fp - --root_method=$root_method - - - - - - - - - - - - - - - - - - - - - - For more information, see make_phylogeny_ in the Qiime documentation. - -Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _make_phylogeny: http://qiime.org/scripts/make_phylogeny.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_pie_charts.xml --- a/make_pie_charts.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ - - Make pie charts based on taxonomy assignment - - make_pie_charts.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - make_pie_charts.py - --input_files=$input_files - --labels=$labels - $sample_flag - --num=$num - --dir-prefix=$dir_prefix - --colorby=$colorby - --prefs_path=$prefs_path - --background_color=$background_color - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_prefs_file.xml --- a/make_prefs_file.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ - - Generate preferences file - - make_prefs_file.py - - - qiime_wrapper.py - make_prefs_file.py - --map_fname=$map_fname - --output_fp=$output_fp - #if $mapping_headers_to_use != None and $mapping_headers_to_use.__str__ != '': - --mapping_headers_to_use=$mapping_headers_to_use - #end if - --background_color=$background_color - --monte_carlo_dists=$monte_carlo_dists - #if $input_taxa_file != None and $input_taxa_file.__str__ != '' and $input_taxa_file.__str__ != 'None': - --input_taxa_file=$input_taxa_file - #end if - --ball_scale=$ball_scale - --arrow_line_color=$arrow_line_color - --arrow_head_color=$arrow_head_color - - - - - - - - - - - - - - - - - For more information, see make_prefs_file_ in the Qiime documentation. - -Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _make_prefs_file: http://qiime.org/scripts/make_prefs_file.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_qiime_py_file.xml --- a/make_qiime_py_file.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - Create python file - - make_qiime_py_file.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - make_qiime_py_file.py - --output_fp=$output_fp - $script - $test - --author_name=$author_name - --author_email=$author_email - --copyright=$copyright - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_qiime_rst_file.xml --- a/make_qiime_rst_file.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - - Make Sphinx RST file - - make_qiime_rst_file.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - make_qiime_rst_file.py - --input_script=$input_script - --output_dir=$__new_file_path__ - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 make_rarefaction_plots.xml --- a/make_rarefaction_plots.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ - - Generate Rarefaction Plots - - make_rarefaction_plots.py - - - qiime_wrapper.py - --galaxy_datasets='^\S+\.html$:'$plot - --galaxy_outputdir=$plot.extra_files_path - make_rarefaction_plots.py - --input_dir=$input_dir.extra_files_path - --map_fname=$map_fname - #if $colorby != None and $colorby.__str__ != 'None' and len($colorby.__str__) > 0: - --colorby=$colorby - #end if - #if $prefs_path != None and $prefs_path.__str__ != 'None': - --prefs_path=$prefs_path - #end if - #if $ymax != None and $ymax.__str__ != '': - --ymax=$ymax - #end if - --background_color=$background_color - --imagetype=$imagetype - --resolution=$resolution - --output_dir=$plot.extra_files_path - - - - - - - - - - - - - - - - - - - - - - - - This tool takes the log file output from collate_alpha to create an html file of rarefaction plots wherein you can plot by sample and/or by category. - -For more information, see make_rarefaction_plots_ in the Qiime documentation. - -Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _make_rarefaction_plots: http://qiime.org/scripts/make_rarefaction_plots.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 mbac_align_seqs.xml --- a/mbac_align_seqs.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,127 +0,0 @@ - - Align sequences using a variety of alignment methods - - align_seqs.py - - - qiime_wrapper.py - --galaxy_outputdir='$log.extra_files_path' - --galaxy_datasets='^\S+_aligned\.\S+$:'$aligned_fasta,'^\S+_log\.txt$:'$log,'^\S+_failures\.fasta$:'$failures - align_seqs.py - --input_fasta_fp=$input_fasta_fp - --alignment_method=$align.alignment_method - #if $align.alignment_method == 'pynast': - --template_fp=$align.alignment.template_fp - --pairwise_alignment_method=$align.pairwise_alignment_method - --min_length=$align.min_length - --min_percent_id=$align.min_percent_id - --blast_db=$align.blast_db - #elif $align.alignment_method == 'infernal': - --template_fp=$align.alignment.template_fp - #elif $align.alignment_method == 'clustalw': - #echo '' - #elif $align.alignment_method == 'muscle': - #echo '' - #elif $align.alignment_method == 'mafft': - #echo '' - #end if - - --output_dir='$log.extra_files_path' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - align['alignment_method'] == 'pynast' - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 mbac_alpha_diversity.xml --- a/mbac_alpha_diversity.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ - - Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics - - alpha_diversity.py - - - qiime_wrapper.py - alpha_diversity.py - --input_path=$input_path - --output_path=$output_path - --metrics=$metrics - #if $tree_path.__str__ != 'None' and len($tree_path.__str__) != 0: - --tree_path=$tree_path - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 mbac_pick_otus.xml --- a/mbac_pick_otus.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,161 +0,0 @@ - - OTU picking [VALIDATED 8/18/2011] - - pick_otus.py - - - qiime_wrapper.py - --galaxy_outputdir='$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=$pick.max_rejects - --uclust_otu_id_prefix=$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' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - (pick['otu_picking_method'] == 'uclust' and pick['refseqs_fp']) - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 mbac_split_libraries.xml --- a/mbac_split_libraries.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,132 +0,0 @@ - - Split libraries according to barcodes specified in mapping file [VALIDATED 8/18/2011] - - split_libraries.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - --galaxy_datasets='^seqs.fna$:'$sequences,'histograms.txt:'$histograms,'split_library_log.txt:'$log - split_libraries.py - --map=$map - #set fnas = [] - #for i in $inputs: - #set fnas = $fnas + [$i.fasta.__str__] - #end for - --fasta=#echo ','.join($fnas) - #set quals = [] - #for i in $inputs: - #if $i.qual != None and $i.qual.__str__ != 'None': - #set quals = $quals + [$i.qual.__str__] - #end if - #end for - #if len($quals) > 0: - --qual=#echo ','.join($quals) - #end if - #if len($min_seq_length.__str__) > 0 and $min_seq_length > 0: - --min-seq-length=$min_seq_length - #end if - #if len($max_seq_length.__str__) > 0: - --max-seq-length=$max_seq_length - #end if - $trim_seq_length - #if len($min_qual_score.__str__) > 0: - --min-qual-score=$min_qual_score - #end if - $keep_primer - $keep_barcode - #if len($max_ambig.__str__) > 0: - --max-ambig=$max_ambig - #end if - #if len($max_homopolymer.__str__) > 0: - --max-homopolymer=$max_homopolymer - #end if - #if len($max_primer_mismatch.__str__) > 0: - --max-primer-mismatch=$max_primer_mismatch - #end if - --barcode-type=$barcode_type - ## --dir-prefix=$dir_prefix - #if $max_barcode_errors >= 0.: - --max-barcode-errors=$max_barcode_errors - #end if - #if len($start_numbering_at.__str__) > 0: - --start-numbering-at=$start_numbering_at - #end if - $remove_unassigned - $disable_bc_correction - #if len($qual_score_window.__str__) > 0: - --qual_score_window=$qual_score_window - #end if - $disable_primers - --reverse_primers=$reverse_primers - $record_qual_scores - $discard_bad_windows - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 merge_denoiser_output.xml --- a/merge_denoiser_output.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ - - Merge the output of denoising step back into QIIME - - merge_denoiser_output.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - merge_denoiser_output.py - --map_file=$map_file - --otu_picker_map_file=$otu_picker_map_file - --fasta_fp=$fasta_fp - --denoised_fasta_fp=$denoised_fasta_fp - --output_dir=$__new_file_path__ - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 merge_mapping_files.xml --- a/merge_mapping_files.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ - - Merge mapping files - - merge_mapping_files.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - merge_mapping_files.py - --mapping_fps=$mapping_fps - --output_fp=$output_fp - --no_data_value=$no_data_value - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 merge_otu_maps.xml --- a/merge_otu_maps.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ - - Merge OTU mapping files - - merge_otu_maps.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - merge_otu_maps.py - --otu_map_fps=$otu_map_fps - --output_fp=$output_fp - --failures_fp=$failures_fp - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 merge_otu_tables.xml --- a/merge_otu_tables.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - - - - merge_otu_tables.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - merge_otu_tables.py - --input_fps=$input_fps - --output_fp=$output_fp - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 multiple_rarefactions.xml --- a/multiple_rarefactions.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ - - Perform multiple subsamplings/rarefactions on an otu table - - multiple_rarefactions.py - - - qiime_wrapper.py - --galaxy_logfile=$output1 - --galaxy_outputdir=$output1.extra_files_path - multiple_rarefactions.py - --input_path=$input_path - --output_path=$output1.extra_files_path - --min=$min - --max=$max - --step=$step - --num-reps=$num_reps - $lineages_included - $keep_empty_otus - - - - - - - - - - - - - - - - This tool rarefies OTU tables for use in jackknife, bootstrap, and rarefaction analyses. Samples with fewer sequences than the rarefaction depth requested for a given output otu table are omitted from those otu tables. The input is an OTU table (e.g., the output from make_otu_table). The output file is a log file listing all the rarefied otu tables produced. - -For more information, see multiple_rarefactions_ in the Qiime documentation. - -Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _multiple_rarefactions: http://qiime.org/scripts/multiple_rarefactions.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 multiple_rarefactions_even_depth.xml --- a/multiple_rarefactions_even_depth.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - Perform multiple rarefactions on a single otu table, at one depth of sequences/sample - - multiple_rarefactions_even_depth.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - multiple_rarefactions_even_depth.py - --input_path=$input_path - --output_path=$output_path - --depth=$depth - --num-reps=$num_reps - $lineages_included - $keep_empty_otus - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 otu_category_significance.xml --- a/otu_category_significance.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ - - OTU significance and co-occurence analysis - - otu_category_significance.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - otu_category_significance.py - --otu_table_fp=$otu_table_fp - --category_mapping_fp=$category_mapping_fp - --category=$category - --test=$test - --output_fp=$output_fp - --filter=$filter - --threshold=$threshold - --otu_include_fp=$otu_include_fp - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 parallel_align_seqs_pynast.xml --- a/parallel_align_seqs_pynast.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ - - Parallel sequence alignment using PyNAST - - parallel_align_seqs_pynast.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - parallel_align_seqs_pynast.py - --input_fasta_fp=$input_fasta_fp - --output_dir=$__new_file_path__ - --template_fp=$template_fp - --pairwise_alignment_method=$pairwise_alignment_method - --blast_db=$blast_db - --min_length=$min_length - --min_percent_id=$min_percent_id - --align_seqs_fp=$align_seqs_fp - --jobs_to_start=$jobs_to_start - --poller_fp=$poller_fp - $retain_temp_files - $suppress_submit_jobs - $poll_directly - --cluster_jobs_fp=$cluster_jobs_fp - $suppress_polling - --job_prefix=$job_prefix - --python_exe_fp=$python_exe_fp - --seconds_to_sleep=$seconds_to_sleep - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 parallel_alpha_diversity.xml --- a/parallel_alpha_diversity.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ - - Parallel alpha diversity - - parallel_alpha_diversity.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - parallel_alpha_diversity.py - --input_path=$input_path - --output_path=$output_path - --metrics=$metrics - --tree_path=$tree_path - --alpha_diversity_fp=$alpha_diversity_fp - --poller_fp=$poller_fp - $retain_temp_files - $suppress_submit_jobs - $poll_directly - --cluster_jobs_fp=$cluster_jobs_fp - $suppress_polling - --job_prefix=$job_prefix - --python_exe_fp=$python_exe_fp - --seconds_to_sleep=$seconds_to_sleep - --jobs_to_start=$jobs_to_start - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 parallel_assign_taxonomy_blast.xml --- a/parallel_assign_taxonomy_blast.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ - - Parallel taxonomy assignment using BLAST - - parallel_assign_taxonomy_blast.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - parallel_assign_taxonomy_blast.py - --input_fasta_fp=$input_fasta_fp - --id_to_taxonomy_fp=$id_to_taxonomy_fp - --output_dir=$__new_file_path__ - --reference_seqs_fp=$reference_seqs_fp - --blast_db=$blast_db - --e_value=$e_value - --blastmat_dir=$blastmat_dir - --assign_taxonomy_fp=$assign_taxonomy_fp - --jobs_to_start=$jobs_to_start - --poller_fp=$poller_fp - $retain_temp_files - $suppress_submit_jobs - $poll_directly - --cluster_jobs_fp=$cluster_jobs_fp - $suppress_polling - --job_prefix=$job_prefix - --python_exe_fp=$python_exe_fp - --seconds_to_sleep=$seconds_to_sleep - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 parallel_assign_taxonomy_rdp.xml --- a/parallel_assign_taxonomy_rdp.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ - - Parallel taxonomy assignment using RDP - - parallel_assign_taxonomy_rdp.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - parallel_assign_taxonomy_rdp.py - --input_fasta_fp=$input_fasta_fp - --output_dir=$__new_file_path__ - --rdp_classifier_fp=$rdp_classifier_fp - --confidence=$confidence - --assign_taxonomy_fp=$assign_taxonomy_fp - --jobs_to_start=$jobs_to_start - --poller_fp=$poller_fp - $retain_temp_files - $suppress_submit_jobs - $poll_directly - --cluster_jobs_fp=$cluster_jobs_fp - $suppress_polling - --job_prefix=$job_prefix - --python_exe_fp=$python_exe_fp - --seconds_to_sleep=$seconds_to_sleep - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 parallel_beta_diversity.xml --- a/parallel_beta_diversity.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,68 +0,0 @@ - - Parallel beta diversity - - parallel_beta_diversity.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - parallel_beta_diversity.py - --input_path=$input_path - --output_path=$output_path - --metrics=$metrics - --tree_path=$tree_path - --beta_diversity_fp=$beta_diversity_fp - --poller_fp=$poller_fp - $retain_temp_files - $suppress_submit_jobs - $poll_directly - --cluster_jobs_fp=$cluster_jobs_fp - $suppress_polling - --job_prefix=$job_prefix - --python_exe_fp=$python_exe_fp - --seconds_to_sleep=$seconds_to_sleep - --jobs_to_start=$jobs_to_start - $full_tree - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 parallel_blast.xml --- a/parallel_blast.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,80 +0,0 @@ - - Parallel BLAST - - parallel_blast.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - parallel_blast.py - --infile_path=$infile_path - --refseqs_path=$refseqs_path - --output_dir=$__new_file_path__ - $disable_low_complexity_filter - --e_value=$e_value - --num_hits=$num_hits - --word_size=$word_size - $suppress_format_blastdb - --blastmat_dir=$blastmat_dir - --blastall_fp=$blastall_fp - --jobs_to_start=$jobs_to_start - --poller_fp=$poller_fp - $retain_temp_files - $suppress_submit_jobs - $poll_directly - --cluster_jobs_fp=$cluster_jobs_fp - $suppress_polling - --job_prefix=$job_prefix - --python_exe_fp=$python_exe_fp - --seconds_to_sleep=$seconds_to_sleep - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 parallel_identify_chimeric_seqs.xml --- a/parallel_identify_chimeric_seqs.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,89 +0,0 @@ - - Parallel chimera detection - - parallel_identify_chimeric_seqs.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - parallel_identify_chimeric_seqs.py - --input_fasta_fp=$input_fasta_fp - --aligned_reference_seqs_fp=$aligned_reference_seqs_fp - --id_to_taxonomy_fp=$id_to_taxonomy_fp - --reference_seqs_fp=$reference_seqs_fp - --blast_db=$blast_db - --chimera_detection_method=$chimera_detection_method - --num_fragments=$num_fragments - --taxonomy_depth=$taxonomy_depth - --max_e_value=$max_e_value - --min_div_ratio=$min_div_ratio - --output_fp=$output_fp - --identify_chimeric_seqs_fp=$identify_chimeric_seqs_fp - --jobs_to_start=$jobs_to_start - --poller_fp=$poller_fp - $retain_temp_files - $suppress_submit_jobs - $poll_directly - --cluster_jobs_fp=$cluster_jobs_fp - $suppress_polling - --job_prefix=$job_prefix - --python_exe_fp=$python_exe_fp - --seconds_to_sleep=$seconds_to_sleep - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 parallel_multiple_rarefactions.xml --- a/parallel_multiple_rarefactions.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ - - Parallel multiple file rarefaction - - parallel_multiple_rarefactions.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - parallel_multiple_rarefactions.py - --input_path=$input_path - --output_path=$output_path - --min=$min - --max=$max - --step=$step - --num-reps=$num_reps - $lineages_included - --single_rarefaction_fp=$single_rarefaction_fp - --poller_fp=$poller_fp - $retain_temp_files - $suppress_submit_jobs - $poll_directly - --cluster_jobs_fp=$cluster_jobs_fp - $suppress_polling - --job_prefix=$job_prefix - --python_exe_fp=$python_exe_fp - --seconds_to_sleep=$seconds_to_sleep - --jobs_to_start=$jobs_to_start - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 parallel_pick_otus_blast.xml --- a/parallel_pick_otus_blast.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ - - Parallel pick otus using BLAST - - parallel_pick_otus_blast.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - parallel_pick_otus_blast.py - --input_fasta_fp=$input_fasta_fp - --output_dir=$__new_file_path__ - --max_e_value=$max_e_value - --similarity=$similarity - --refseqs_fp=$refseqs_fp - --blast_db=$blast_db - --min_aligned_percent=$min_aligned_percent - --pick_otus_fp=$pick_otus_fp - --jobs_to_start=$jobs_to_start - --poller_fp=$poller_fp - $retain_temp_files - $suppress_submit_jobs - $poll_directly - --cluster_jobs_fp=$cluster_jobs_fp - $suppress_polling - --job_prefix=$job_prefix - --python_exe_fp=$python_exe_fp - --seconds_to_sleep=$seconds_to_sleep - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 parallel_pick_otus_uclust_ref.xml --- a/parallel_pick_otus_uclust_ref.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,95 +0,0 @@ - - Parallel pick otus using uclust_ref - - parallel_pick_otus_uclust_ref.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - parallel_pick_otus_uclust_ref.py - --input_fasta_fp=$input_fasta_fp - --output_dir=$__new_file_path__ - --refseqs_fp=$refseqs_fp - --similarity=$similarity - $enable_rev_strand_match - $optimal_uclust - $exact_uclust - --max_accepts=$max_accepts - --max_rejects=$max_rejects - --stepwords=$stepwords - --word_length=$word_length - $uclust_stable_sort - $suppress_uclust_stable_sort - $save_uc_files - --pick_otus_fp=$pick_otus_fp - --jobs_to_start=$jobs_to_start - --poller_fp=$poller_fp - $retain_temp_files - $suppress_submit_jobs - $poll_directly - --cluster_jobs_fp=$cluster_jobs_fp - $suppress_polling - --job_prefix=$job_prefix - --python_exe_fp=$python_exe_fp - --seconds_to_sleep=$seconds_to_sleep - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 per_library_stats.xml --- a/per_library_stats.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ - - Calculate per library statistics - - per_library_stats.py - - - qiime_wrapper.py - per_library_stats.py - --otu_table_fp=$otu_table_fp - #if $mapfile != None and $mapfile.__str__ != 'None' and $mapfile.__str__ != '': - --mapfile=$mapfile - #end if - --outputfile=$outputfile - - - - - - - - - - - .. class:: warningmark Warning: log data from standard output currently not available. - -For more information, see per_library_stats_ in the Qiime documentation. - -Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _per_library_stats: http://qiime.org/scripts/per_library_stats.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 pick_otus.xml --- a/pick_otus.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,171 +0,0 @@ - - OTU picking - - pick_otus.py - - - qiime_wrapper.py - --galaxy_outputdir='$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.__str__ == '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 - #if $pick.uclust_otu_id_prefix != None and $pick.uclust_otu_id_prefix.__str__ != 'None' and $pick.uclust_otu_id_prefix.__str__ != '': - --uclust_otu_id_prefix=$pick.uclust_otu_id_prefix - #end if - $pick.uclust_stable_sort - $pick.save_uc_files - #elif $pick.otu_picking_method.__str__ == 'mothur': - --otu_picking_method=$pick.otu_picking_method - --clustering_algorithm=$pick.clustering_algorithm - --similarity=$pick.similarity - #elif $pick.otu_picking_method.__str__ == 'trie': - --otu_picking_method=$pick.otu_picking_method - $pick.trie_reverse_seqs - #elif $pick.otu_picking_method.__str__ == 'prefix_suffix': - --otu_picking_method=$pick.otu_picking_method - --prefix_length=$pick.prefix_length - --suffix_length=$pick.suffix_length - #elif pick.otu_picking_method.__str__ == 'blast': - --otu_picking_method=$pick.otu_picking_method - #if $refseqs_fp.__str__ != 'None': - --refseqs_fp=$pick.refseqs_fp - #end if - #if $pick.blast_db != None and $pick.blast_db.__str__ != 'None' and $pick.blast_db.__str__ != '': - --blast_db=$pick.blast_db - #end if - --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 - #if $pick.prefix_prefilter_length != 0: - --prefix_prefilter_length=$pick.prefix_prefilter_length - #end if - $pick.trie_prefilter - #end if - --output_dir='$log.extra_files_path' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - (pick['otu_picking_method'] == 'uclust' and pick['refseqs_fp']) - - - - - For more information, see pick_otus_ in the Qiime documentation. - -Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _pick_otus: http://qiime.org/scripts/pick_otus.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 pick_otus_through_otu_table.xml --- a/pick_otus_through_otu_table.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,203 +0,0 @@ - - A workflow script for picking OTUs through building OTU tables - - pick_otus_through_otu_table.py - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -##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 - - - - - - - - - - - - - - - - - - - - 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 - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 pick_reference_otus_through_otu_table.xml --- a/pick_reference_otus_through_otu_table.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ - - Reference OTU picking/Shotgun UniFrac workflow. - - pick_reference_otus_through_otu_table.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - pick_reference_otus_through_otu_table.py - --input_fp=$input_fp - --reference_fp=$reference_fp - --output_dir=$__new_file_path__ - #if $parameter.source == 'hist': - --parameter_fp=$parameter_fp - #else: - --parameter_fp=$parameter_generated - #end if - --taxonomy_fp=$taxonomy_fp - $force - $print_only - $parallel - - - - - - - - - - - - - - - - - - - - - - - - - -alpha_diversity:metrics chao1,observed_species,PD_whole_tree -multiple_rarefactions_even_depth:num-reps 20 -parallel:jobs_to_start 2 -parallel:retain_temp_files False -parallel:seconds_to_sleep 60 -collate_alpha:example_path -make_rarefaction_plots:imagetype png -make_rarefaction_plots:resolution 75 -make_rarefaction_plots:background_color white -make_rarefaction_plots:prefs_path - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 pick_rep_set.xml --- a/pick_rep_set.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ - - Pick representative set of sequences - - pick_rep_set.py - - - qiime_wrapper.py - pick_rep_set.py - --input_file=$input_file - #if $reference_seqs_fp.__str__ != 'None' or $reference_seqs_fp != None and $reference_seqs_fp.__str__ == '': - --reference_seqs_fp=$reference_seqs_fp - #else: - --fasta_file=$fasta_file - #end if - --rep_set_picking_method=$rep_set_picking_method - --sort_by=$sort_by - --log_fp=$log_fp - --result_fp=$result_fp - - - - - - - - - - - - - - - - - - - - - - - For more information, see pick_rep_set_ in the Qiime documentation. - -Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - -.. _pick_rep_set: http://qiime.org/scripts/pick_rep_set.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 plot_rank_abundance_graph.xml --- a/plot_rank_abundance_graph.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ - - plot rank-abundance curve - - plot_rank_abundance_graph.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - plot_rank_abundance_graph.py - --otu_table_fp=$otu_table_fp - --sample_name=$sample_name - --output_dir=$__new_file_path__ - $absolute_counts - $no_legend - $x_linear_scale - $y_linear_scale - --file_type=$file_type - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 plot_taxa_summary.xml --- a/plot_taxa_summary.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,99 +0,0 @@ - - Make taxaonomy summary charts based on taxonomy assignment - - plot_taxa_summary.py - - - qiime_wrapper.py - --galaxy_outputdir='$taxonomy_summary_chart.extra_files_path' - --galaxy_datasets='^\S+_charts\.html$:'$taxonomy_summary_chart - plot_taxa_summary.py - #set $counts = [] - #for i in $inputs: - #set $counts = $counts + [$i.counts_fname.__str__] - #end for - --counts_fname=#echo ','.join($counts) - #if $labels != None and $labels.__str__ != 'None' and $labels.__str__ != '': - --labels=$labels - #end if - --num_categories=$num_categories - #if $colorby != None and $colorby.__str__ != 'None' and $colorby.__str__ != '': - --colorby=$colorby - #end if - #if $prefs_path != None and $prefs_path.__str__ != 'None': - --prefs_path=$prefs_path - #end if - --background_color=$background_color - --dpi=$dpi - --x_width=$x_width - --y_height=$y_height - --bar_width=$bar_width - --type_of_file=$type_of_file - --chart_type=$chart_type - --resize_nth_label=$resize_nth_label - $include_html_legend - $include_html_counts - --label_type=$label_type - --dir_path='$taxonomy_summary_chart.extra_files_path' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - For more information, see plot_taxa_summary_ in the Qiime documentation. - -Updated and validated 01/20/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _plot_taxa_summary: http://qiime.org/scripts/plot_taxa_summary.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 poller.xml --- a/poller.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ - - Poller for parallel QIIME scripts. - - poller.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - poller.py - --check_run_complete_file=$check_run_complete_file - --check_run_complete_f=$check_run_complete_f - --process_run_results_f=$process_run_results_f - --process_run_results_file=$process_run_results_file - --clean_up_f=$clean_up_f - --clean_up_file=$clean_up_file - --time_to_sleep=$time_to_sleep - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 poller_example.xml --- a/poller_example.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ - - Create python file - - poller_example.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - poller_example.py - --polled_dir=$polled_dir - --poller_fp=$poller_fp - --python_exe_fp=$python_exe_fp - $suppress_custom_functions - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 pool_by_metadata.xml --- a/pool_by_metadata.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ - - pool samples in OTU table and mapping file based on sample metadata from mapping file - - pool_by_metadata.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - pool_by_metadata.py - --otu_table_fp=$otu_table_fp - --map=$map - --states=$states - --otu_outfile=$otu_outfile - --map_outfile=$map_outfile - --pooled_sample_name=$pooled_sample_name - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 principal_coordinates.xml --- a/principal_coordinates.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ - - Principal Coordinates Analysis (PCoA) - - principal_coordinates.py - - - qiime_wrapper.py - principal_coordinates.py - --input_path=$input_path - --output_path=$output_path - - - - - - - - - - - - - - - - - - - - - For more information, see principle_coordinates_ in the Qiime documentation. - -Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _principle_coordinates: http://qiime.org/scripts/principal_coordinates.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 print_qiime_config.xml --- a/print_qiime_config.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ - - Print out the qiime config settings. - - print_qiime_config.py - - - print_qiime_config.py - $test - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 process_sff.xml --- a/process_sff.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ - - Convert sff to FASTA and QUAL files - - process_sff.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - process_sff.py - --input_dir=$input_dir - $make_flowgram - $convert_to_FLX - $use_sfftools - --output_dir=$__new_file_path__ - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 qiime_wrapper.py --- a/qiime_wrapper.py Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,312 +0,0 @@ -#!/usr/bin/env python -import logging, os, string, sys, tempfile, glob, shutil, types, urllib, optparse, re -import shlex, subprocess - -""" -sys.argv -this --galaxy_datasets= --quime_script - -alpha_rarefaction - output html - wf_arare/alpha_rarefaction_plots/rarefaction_plots.html - wf_arare/alpha_rarefaction_plots/html_plots/ - wf_arare/alpha_div - wf_arare/alpha_div/alpha_rarefaction_101_0.txt - - --galaxy_summary_html=$output_html - --galaxy_summary_template=$output_template - --galaxy_summary_links='label:link,label:link' - --galaxy_outputdir=$output_html.extra_files_path - - -""" - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - -def __main__(): - debug = False - tmp_dir = None - inputdir = None - outputdir = None - dataset_patterns = None - datasetid = None - new_dataset_patterns = None - new_files_path = None - summary_html=None - summary_template=None - summary_links=None - ## adds "log file" printing capabilities for primary output in dynamic file output - logfile = None - ## added support for correcting file extensions - newext = None - extchange = None - ## check if there are files to generate - cmd_args = [] - for arg in sys.argv[1:]: - if arg.startswith('--galaxy_'): - (opt,val) = arg.split('=') if arg.find('=') > 0 else (arg,None) - ''' - if opt == '--galaxy_tmpdir': - try: - if not os.path.exists(val): - os.makedirs(val) - tmp_dir = val - except Exception, ex: - stop_err(ex) - ''' - if opt == '--galaxy_outputdir': - try: - if not os.path.exists(val): - os.makedirs(val) - outputdir = val - except Exception, ex: - stop_err(ex) - if opt == '--galaxy_datasets': - dataset_patterns = val.split(',') - if opt == '--galaxy_datasetid': - datasetid = val - if opt == '--galaxy_new_datasets': - new_dataset_patterns = val.split(',') - if opt == '--galaxy_new_files_path': - if not os.path.exists(val): - os.makedirs(val) - new_files_path = val - if opt == '--galaxy_summary_html': - summary_html=val - if opt == '--galaxy_summary_template': - summary_template=val - if opt == '--galaxy_summary_links': - summary_links=val - if opt == '--galaxy_debug': - debug = True - if opt == '--galaxy_logfile': - logfile = val - if opt == '--galaxy_ext_change': - extchange = val - if opt == '--galaxy_new_ext': - newext = val - if opt == '--galaxy_inputdir': - inputdir = val - else: - cmd_args.append(arg) - if debug: print >> sys.stdout, '\n : '.join(cmd_args) - try: - stderr = '' - # allow for changing of file extension for files which require it - if extchange != None and inputdir != None and newext != None: - #newfile = os.path.join(inputdir,"temporary."+newext) - try: - os.link(extchange,inputdir+"/temporary."+newext) - except: - shutil.copy2(extchange,inputdir+"/temporary."+newext) - cmdline = ' '.join(cmd_args) - if debug: print >> sys.stdout, cmdline - ''' - if tmp_dir == None or not os.path.isdir(tmp_dir): - tmp_dir = tempfile.mkdtemp() - if outputdir == None or not os.path.isdir(outputdir): - outputdir = tmp_dir - ''' - tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name - tmp_stderr = open( tmp_stderr_name, 'wb' ) - tmp_stdout_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.out' ).name - tmp_stdout = open( tmp_stdout_name, 'wb' ) - proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp_stderr_name, 'rb' ) - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - if debug: print >> sys.stderr, stderr - except OverflowError: - pass - tmp_stderr.close() - if returncode != 0: - if debug: print >> sys.stderr, "returncode = %d" % returncode - raise Exception, stderr - #raise Exception, sys.stderr - # collect results - if dataset_patterns != None: - for root, dirs, files in os.walk(outputdir): - for fname in files: - fpath = os.path.join(root,fname) - if dataset_patterns != None: - for output in dataset_patterns: - (pattern,path) = output.split(':') - if debug: print >> sys.stdout, '%s -> %s' % (pattern,path) - if path == None or path == 'None': - continue - if debug: print >> sys.stdout, 'outdir %s match: %s' % (fname,re.match(pattern,fname)) - if re.match(pattern,fname): - found = True - # flist.remove(fname) - try: - shutil.copy2(fpath, path) - if new_files_path != None: - os.link(fpath, os.path.join(new_files_path,fname)) - except Exception, ex: - stop_err('%s' % ex) - # move result to outdir - # Need to flatten the dir hierachy in order for galaxy to serve the href links - if summary_html != None: - """ - for root, dirs, files in os.walk(outputdir): - if root != outputdir: - for fname in files: - fpath = os.path.join(root,fname) - """ - ## move everything up one level - dlist = os.listdir(outputdir) - for dname in dlist: - dpath = os.path.join(outputdir,dname) - if os.path.isdir(dpath): - flist = os.listdir(dpath) - for fname in flist: - fpath = os.path.join(dpath,fname) - shutil.move(fpath,outputdir) - if summary_template != None: - shutil.copy(summary_template,summary_html) - """ - flist = os.listdir(outputdir) - if debug: print >> sys.stdout, 'outputdir: %s' % outputdir - if debug: print >> sys.stdout, 'files: %s' % ','.join(flist) - if dataset_patterns != None: - for output in dataset_patterns: - (pattern,path) = output.split(':') - if debug: print >> sys.stdout, '%s -> %s' % (pattern,path) - if path == None or path == 'None': - continue - for fname in flist: - if debug: print >> sys.stdout, 'outdir %s match: %s' % (fname,re.match(pattern,fname)) - if re.match(pattern,fname): - found = True - flist.remove(fname) - fpath = os.path.join(outputdir,fname) - try: - shutil.copy2(fpath, path) - except Exception, ex: - stop_err('%s' % ex) - """ - # Handle the dynamically generated galaxy datasets - # http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput - # --new_datasets = specifies files to be found in the new_file_path - # The list items are separated by commas - # Each item conatins: a regex pattern for matching filenames and a galaxy datatype (separated by :) - # The regex match.groups()[0] is used as the id name of the dataset, and must result in unique name for each output - # The --galaxy_output flag is used for instances where data needs to be copied to the extra_files_path for later - # directory use - if new_dataset_patterns != None and new_files_path != None and datasetid != None: - for output in new_dataset_patterns: - if ':' in output: pattern,ext = output.split(':',1) - flist = os.listdir(new_files_path) - for fname in flist: - m = re.match(pattern,fname) - if m: - fpath = os.path.join(new_files_path,fname) - if len(m.groups()) > 0: - root = m.groups()[0] - else: - # remove the ext from the name if it exists, galaxy will add back later - # remove underscores since galaxy uses that as a field separator for dynamic datasets - root = re.sub('\.?'+ext+'$','',fname).replace('_','').replace('.','') - # filename pattern required by galaxy - fn = "%s_%s_%s_%s_%s" % ( 'primary', datasetid, root, 'visible', ext ) - if debug: print >> sys.stdout, '> %s' % fpath - if debug: print >> sys.stdout, '< %s' % os.path.join(new_files_path,fn) - try: - os.link(fpath, os.path.join(new_files_path,fn)) - # needed for files with variable output and a directory structure - if outputdir != None: - os.link(fpath, os.path.join(outputdir,fname)) - # clean out files from tmp directory, may be unnecessary - #os.remove(fpath) - except: - shutil.copy2(fpath, os.path.join(new_files_path,fn)) - # needed for files with variable output and a directory structure - if outputdir != None: - os.link(fpath, os.path.join(outputdir,fname)) - - print "bob" + logfile - ''' - if logfile != None: - print "bleep" - if outputdir != None: - print "beep" - logwrite = open(logfile, 'w+') - logwrite.write('Tool started. Files created by tool: \n') - flist = os.listdir(outputdir) - for fname in flist: - if 'DS_Store' not in fname: - logwrite.write(fname+'\n') - logwrite.write('Tool Finished.') - logwrite.close() - if new_files_path != None: - print "boop" - logwrite = open(logfile, 'w+') - if len(logfile.readline() > 0): - logwrite.write('Tool started. Files created by tool: \n') - flist = os.listdir(new_files_path) - for fname in flist: - if 'DS_Store' not in fname: - logwrite.write(fname+'\n') - logwrite.write('Tool Finished.') - logwrite.close() - ''' - except Exception, e: - msg = str(e) + stderr - #msg = str(e) + str(sys.stderr) - #stop_err( 'Error running ' + msg) - finally: - # Only remove temporary directories and files from temporary directory - # Enclose in try block, so we don't report error on stale nfs handles - try: - if logfile != None: - if outputdir != None: - logwrite = open(logfile, 'r+') - logwrite.write('Tool started. Files created by tool: \n') - flist = os.listdir(outputdir) - for fname in flist: - if 'DS_Store' not in fname and 'primary' not in fname: - logwrite.write(fname+'\n') - logwrite.write('Tool Finished.') - logwrite.close() - if new_files_path != None: - logwrite = open(logfile, 'r+') - logwrite.write('Tool started. Files created by tool: \n') - flist = os.listdir(new_files_path) - for fname in flist: - if 'DS_Store' not in fname and 'primary' not in fname: - logwrite.write(fname+'\n') - logwrite.write('Tool Finished.') - logwrite.close() - if tmp_dir != None and os.path.exists(tmp_dir) and os.path.isfile(tmp_dir): - #shutil.rmtree(tmp_dir) - pass - if outputdir != None and 'files' not in outputdir: - flist = os.listdir(outputdir) - for fname in flist: - if 'DS_Store' not in fname and 'primary' not in fname: - os.remove(os.path.join(outputdir,fname)) - if inputdir != None and 'files' not in inputdir: - flist = os.listdir(inputdir) - for fname in flist: - if 'DS_Store' not in fname and 'primary' not in fname: - os.remove(os.path.join(inputdir,fname)) - if new_files_path != None and 'files' not in new_files_path: - flist = os.listdir(new_files_path) - for fname in flist: - if 'DS_Store' not in fname and 'primary' not in fname: - os.remove(os.path.join(new_files_path,fname)) - - except: - pass - -if __name__ == "__main__": __main__() - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 quality_scores_plot.xml --- a/quality_scores_plot.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ - - Generates histograms of sequence quality scores and number of nucleotides recorded at a particular index - - quality_scores_plot.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - quality_scores_plot.py - --qual_fp=$qual_fp - --output_dir=$__new_file_path__ - --score_min=$score_min - --verbose - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 shared_phylotypes.xml --- a/shared_phylotypes.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ - - Compute shared OTUs between all pairs of samples - - shared_phylotypes.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - shared_phylotypes.py - --otu_table_fp=$otu_table_fp - --output_fp=$output_fp - --reference_sample=$reference_sample - $force_overwrite - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 single_rarefaction.xml --- a/single_rarefaction.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ - - Perform rarefaction on an otu table - - single_rarefaction.py - - - qiime_wrapper.py - single_rarefaction.py - --input_path=$input_path - --output_path=$output_path - --depth=$depth - $suppress_lineages_included - $keep_empty_otus - - - - - - - - - - - - - For more information, see single_rarefaction_ in the Qiime documentation. - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _single_rarefaction: http://qiime.org/scripts/single_rarefaction.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 sort_denoiser_output.xml --- a/sort_denoiser_output.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - - Sort denoiser output by cluster size. - - sort_denoiser_output.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - sort_denoiser_output.py - --input_fasta_fp=$input_fasta_fp - --output_file=$output_file - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 sort_otu_table.xml --- a/sort_otu_table.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ - - Script for sorting the sample IDs in an OTU table based on a specified value in a mapping file. - - sort_otu_table.py - - - qiime_wrapper.py - sort_otu_table.py - --input_otu_table=$input_otu_table - --mapping_fp=$mapping_fp - --sort_field=$sort_field - --output_fp=$output_fp - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 split_libraries.xml --- a/split_libraries.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,148 +0,0 @@ - - Split libraries according to barcodes specified in mapping file - - split_libraries.py - - - qiime_wrapper.py - --galaxy_datasets='^seqs\.fna$:'$sequences,'histograms\.txt:'$histograms,'split_library_log\.txt:'$log - --galaxy_outputdir='$log.extra_files_path' - split_libraries.py - --dir-prefix='$log.extra_files_path' - --map=$map - #set fnas = [] - #for i in $inputs: - #set fnas = $fnas + [$i.fasta.__str__] - #end for - --fasta=#echo ','.join($fnas) - #set quals = [] - #for i in $inputs: - #if $i.qual != None and $i.qual.__str__ != 'None': - #set quals = $quals + [$i.qual.__str__] - #end if - #end for - #if len($quals) > 0: - --qual=#echo ','.join($quals) - #end if - #if len($min_seq_length.__str__) > 0 and $min_seq_length > 0: - --min-seq-length=$min_seq_length - #end if - #if len($max_seq_length.__str__) > 0: - --max-seq-length=$max_seq_length - #end if - $trim_seq_length - #if len($min_qual_score.__str__) > 0: - --min-qual-score=$min_qual_score - #end if - $keep_primer - $keep_barcode - #if len($max_ambig.__str__) > 0: - --max-ambig=$max_ambig - #end if - #if len($max_homopolymer.__str__) > 0: - --max-homopolymer=$max_homopolymer - #end if - #if len($max_primer_mismatch.__str__) > 0: - --max-primer-mismatch=$max_primer_mismatch - #end if - --barcode-type=$barcode_type - #if $max_barcode_errors >= 0.: - --max-barcode-errors=$max_barcode_errors - #end if - #if len($start_numbering_at.__str__) > 0: - --start-numbering-at=$start_numbering_at - #end if - $retain_unassigned_reads - $disable_bc_correction - #if len($qual_score_window.__str__) > 0: - --qual_score_window=$qual_score_window - #end if - $disable_primers - --reverse_primers=$reverse_primers - #if $reverse_primer_mismatches != None and $reverse_primer_mismatches.__str__ != "" and $reverse_primers.__str__!='disable': - --reverse_primer_mismatches=$reverse_primer_mismatches - #end if - $record_qual_scores - $discard_bad_windows - #if $median_length_filtering != None and $median_length_filtering.__str__ != "": - --median_length_filtering=$median_length_filtering - #end if - #if $added_demultiplex_field != None and $added_demultiplex_field.__str__ != "": - --added_demultiplex_field=$added_demultiplex_field - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - For more information, see split_libraries_ in the Qiime documentation. - -Updated and validated 01/19/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _split_libraries: http://qiime.org/scripts/split_libraries.html - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 split_libraries_illumina.xml --- a/split_libraries_illumina.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ - - Script for processing raw Illumina Genome Analyzer II data. - - split_libraries_illumina.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - split_libraries_illumina.py - --mapping_fp=$mapping_fp - --five_prime_read_fp=$five_prime_read_fp - --three_prime_read_fp=$three_prime_read_fp - --output_dir=$__new_file_path__ - $store_unassigned - --quality_threshold=$quality_threshold - --max_bad_run_length=$max_bad_run_length - --min_per_read_length=$min_per_read_length - --sequence_max_n=$sequence_max_n - --start_seq_id=$start_seq_id - $rev_comp_barcode - $barcode_in_header - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 start_parallel_jobs.xml --- a/start_parallel_jobs.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ - - Starts multiple jobs in parallel on multicore or multiprocessor systems. - - start_parallel_jobs.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - start_parallel_jobs.py - $make_jobs - $submit_jobs - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 submit_to_mgrast.xml --- a/submit_to_mgrast.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ - - This script submits a FASTA file to MG-RAST - - submit_to_mgrast.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - submit_to_mgrast.py - --input_fasta_fp=$input_fasta_fp - --web_key_auth=$web_key_auth - --project_id=$project_id - --output_dir=$__new_file_path__ - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 summarize_otu_by_cat.xml --- a/summarize_otu_by_cat.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - Create a summarized OTU table for a specific metadata category - - summarize_otu_by_cat.py - - - qiime_wrapper.py - summarize_otu_by_cat.py - --mapping_fp=$mapping_fp - --otu_table_fp=$otu_table_fp - --mapping_category=$mapping_category - --output_fp=$output_fp - $normalize_flag - - - - - - - - - - - - - For more information, see summarize_otu_by_cat_ in the Qiime documentation. - -Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _summarize_otu_by_cat: http://qiime.org/scripts/summarize_otu_by_cat.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 summarize_taxa.xml --- a/summarize_taxa.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ - -Summarize Taxa - - summarize_taxa.py - - - qiime_wrapper.py - #set $levelnums = str($level).split(",") - #set $filestr = "" - #if $len($level.__str__) > 1: - #for $i in $levelnums: - #set $filestr = $filestr + '^\\\\S+_L'+$i+'\\\\.txt$:txt,' - #end for - --galaxy_new_datasets=$filestr - --galaxy_datasetid=$output1.id - --galaxy_new_files_path='$__new_file_path__' - --galaxy_logfile=$output1.__str__ - #else: - --galaxy_datasets='^\S+_L'$level'\.txt$:'$output1 - --galaxy_outputdir='$output1.extra_files_path' - #end if - summarize_taxa.py - --otu_table_fp=$otu_table_fp - --level=$level - #if $mapping != None and $mapping.__str__ != 'None': - --mapping=$mapping - #end if - #if $len($level.__str__) > 1: - --output_dir=$__new_file_path__ - #else: - --output_dir='$output1.extra_files_path' - #end if - $absolute_abundance - #if $lower_percentage > 0.0 and $lower_percentage.__str__ != '': - --lower_percentage=$lower_percentage - #end if - #if $upper_percentage > 0.0 and $upper_percentage.__str__ != '': - --upper_percentage=$upper_percentage - #end if - $transposed_output - #if $delimiter.__str__ != ';': - --delimiter=$delimiter - #end if - - - - - - - - - - - - - - - - - - - - - - - - - -.. class:: warningmark - -Please reload your browser to see all results in your history. - -For more information, see summarize_taxa_ in the Qiime documentation. - -Updated and validated 01/19/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA - -Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN - - .. _summarize_taxa: http://qiime.org/scripts/summarize_taxa.html - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 supervised_learning.xml --- a/supervised_learning.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ - - Run supervised classification using OTUs as predictors and a mapping file category as class labels. - - supervised_learning.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - supervised_learning.py - --input_data=$input_data - --mapping_file=$mapping_file - --category=$category - --output_dir=$__new_file_path__ - --method=$method - $force - --param_file=$param_file - $show_params - --filter_type=$filter_type - --filter_min=$filter_min - --filter_max=$filter_max - --filter_step=$filter_step - --filter_reps=$filter_reps - $keepfiles - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 transform_coordinate_matrices.xml --- a/transform_coordinate_matrices.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - Transform 2 coordinate matrices - - transform_coordinate_matrices.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - transform_coordinate_matrices.py - --input_fps=$input_fps - --output_dir=$__new_file_path__ - --random_trials=$random_trials - --num_dimensions=$num_dimensions - --sample_id_map_fp=$sample_id_map_fp - $store_trial_details - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 tree_compare.xml --- a/tree_compare.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ - - Compare jackknifed/bootstrapped trees - - tree_compare.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - tree_compare.py - --master_tree=$master_tree - --support_dir=$support_dir - --output_dir=$__new_file_path__ - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 trflp_file_to_otu_table.xml --- a/trflp_file_to_otu_table.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - - Convert TRFLP text file to an OTU table - - trflp_file_to_otu_table.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - trflp_file_to_otu_table.py - --input_path=$input_path - --output_path=$output_path - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 trim_sff_primers.xml --- a/trim_sff_primers.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ - - Trim sff primers - - trim_sff_primers.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - trim_sff_primers.py - --libdir=$libdir - --input_map=$input_map - --sfffile_path=$sfffile_path - --sffinfo_path=$sffinfo_path - $use_sfftools - $debug - - - - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 truncate_fasta_qual_files.xml --- a/truncate_fasta_qual_files.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ - - Generates filtered fasta and quality score files by truncating at the specified base position. - - truncate_fasta_qual_files.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - truncate_fasta_qual_files.py - --fasta_fp=$fasta_fp - --qual_fp=$qual_fp - --base_pos=$base_pos - --output_dir=$__new_file_path__ - - - - - - - - - - - - - - - - diff -r 2e14fb0fd792 -r 3b1401bf4cb1 upgma_cluster.xml --- a/upgma_cluster.xml Wed Jun 06 16:23:12 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ - - Build a UPGMA tree comparing samples - - upgma_cluster.py - - - qiime_wrapper.py - --galaxy_tmpdir='$__new_file_path__' - upgma_cluster.py - --input_path=$input_path - --output_path=$output_path - - - - - - - - - - - - - -