Mercurial > repos > bcclaywell > microbiome_pplacer_suite

changeset 1:c8cc6529038c draft

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Uploaded
author bcclaywell
date Thu, 26 Feb 2015 19:30:44 -0500
parents d4690e65afcd
children ce6db18f5fd3
files bootstrap-wrapper.sh bootstrap.py bootstrap.xml classification-wrapper.sh classification.xml datatypes_conf.xml decorate-wrapper.sh decorate.xml filter-wrapper.sh filter.xml macros.xml pplacer-wrapper.sh pplacer.py pplacer.xml preclassification-wrapper.sh preclassification.xml preprocessing-wrapper.sh preprocessing.xml refpkgzip_to_refpkg.xml render_datatable-wrapper.sh render_datatable.py render_datatable.xml taxtastic.py usearch-wrapper.sh usearch.xml util.sh xlsx_to_csv.xml
diffstat 27 files changed, 0 insertions(+), 1512 deletions(-) [+]
line wrap: on
line diff
--- a/bootstrap-wrapper.sh	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-#!/bin/bash
-
-source $(dirname $0)/util.sh
-source $1
-
-python $(dirname $0)/bootstrap.py \
-    --plate ${PLATE_ID} \
-    ${JUNIOR} \
-    --zone ${ZONE_ID} \
-    --barcodes ${BARCODES} \
-    --labels ${LABELS} \
-    --metadata ${METADATA} \
-    - < ${SAMPLE_INFO}
--- a/bootstrap.py	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-import csv
-import sys
-import os
-import argparse
-
-def warning(*objs):
-    print("WARNING: ", *objs, file=sys.stderr)
-
-def main(arguments):
-
-    parser = argparse.ArgumentParser(arguments, description=__doc__,
-                                     formatter_class=argparse.RawDescriptionHelpFormatter)
-    parser.add_argument('infile', help = "CSV input",
-                        type = argparse.FileType('r'), default = sys.stdin)
-    parser.add_argument('--junior', help = "use junior run specimen naming convention", action = 'store_true')
-    parser.add_argument('--plate', help = "plate number", type = int, required = True)
-    parser.add_argument('--zone', help = "zone number", type = int, required = True)
-    parser.add_argument('--barcodes', help = "name of barcodes file",
-                        type = argparse.FileType('w'), default = 'barcodes.csv')
-    parser.add_argument('--labels', help = "name of labels file",
-                        type = argparse.FileType('w'), default = 'labels.csv')
-    parser.add_argument('--metadata', help = "name of metadata template file",
-                        type = argparse.FileType('w'), default = 'metadata.csv')
-
-    args = parser.parse_args(arguments)
-
-    label_key = 'sampleid'
-    primer_key = 'reverse'
-    barcode_key = 'barcode'
-    zone_key = 'zone'
-
-    fstr = "j{plate_id}{primer_id}" if args.junior else "p{plate_id}z{zone_id}{primer_id}"
-
-    reader = csv.DictReader(sys.stdin)
-
-    barcodes = csv.writer(args.barcodes)
-    labels = csv.writer(args.labels)
-    metadata = csv.writer(args.metadata)
-
-    barcodes.writerow(['stub', 'barcode'])
-    labels.writerow(['specimen', 'label'])
-    metadata.writerow(['specimen', 'plate', 'zone', 'label', 'primer'])
-
-    seen_labels = {}
-    seen_primers = {}
-
-    # TODO: add checks for duplicates, empty fields, etc., and bail if something goes wrong
-    for i, d in enumerate(reader):
-        if not all (k in d for k in (label_key, primer_key, barcode_key)):
-            return "Expected columns not found"
-
-        if zone_key in d and d[zone_key] != str(args.zone):
-            continue
-
-        label = d[label_key]
-        primer = d[primer_key]
-        barcode = d[barcode_key]
-        zone = args.zone
-
-        if not all((label, primer, barcode)):
-            # only print a warning if at least one of the fields is non-empty
-            if any((label, primer, barcode)):
-                warning("Missing required field on row {}, skipping".format(i+2))
-            continue
-
-        if label in seen_labels:
-            return "Duplicate label '{}' found on rows {} and {}".format(label, seen_labels[label]+2, i+2)
-
-        if primer in seen_primers:
-            return "Duplicate primer '{}' found on rows {} and {}".format(primer, seen_primers[primer]+2, i+2)
-
-        seen_labels[label] = i
-        seen_primers[primer] = i
-
-        specimen = fstr.format(plate_id=args.plate, zone_id=zone, primer_id=primer.strip().lower().replace('-',''))
-        barcodes.writerow([specimen, barcode])
-        labels.writerow([specimen, label])
-        metadata.writerow([specimen, args.plate, zone, label, primer])
-
-if __name__ == '__main__':
-    sys.exit(main(sys.argv[1:]))
--- a/bootstrap.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
-<tool id="PHYLO_bootstrap" name="Prepare data" version="1.1.0">
-  <description>for analysis</description>
-  <requirements>
-    <requirement type="package">yapp_env</requirement>
-  </requirements>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <version_command>echo "bootstrap script 1.1.0"</version_command>
-  <command interpreter="bash">
-    bootstrap-wrapper.sh $config
-  </command>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
-  <inputs>
-    <param name="plate_id" type="integer" value="1" label="Plate number"/>
-    <conditional name="run_type">
-      <param name="run_type_select" type="select" label="Run type">
-        <option value="junior">Junior</option>
-        <option value="senior">Senior</option>
-      </param>
-      <when value="junior"></when>
-      <when value="senior">
-        <param name="zone_id" type="integer" value="1" label="Zone number"/>
-      </when>
-    </conditional>
-    <param name="sample_info" type="data" format="csv" label="Sample information"/>
-  </inputs>
-  <outputs>
-    <data format="csv" name="barcodes" label="Specimen-to-barcode map"/>
-    <data format="csv" name="labels" label="Specimen-to-label map"/>
-    <data format="csv" name="metadata" label="Metadata template"/>
-  </outputs>
-  <configfiles>
-    <configfile name="config">
-PLATE_ID="${plate_id}"
-#if $run_type.run_type_select == "senior"
-JUNIOR=""
-ZONE_ID="${run_type.zone_id}"
-#else
-JUNIOR="--junior"
-ZONE_ID="1"
-#end if
-SAMPLE_INFO="${sample_info}"
-
-BARCODES="${barcodes}"
-LABELS="${labels}"
-METADATA="${metadata}"
-    </configfile>
-  </configfiles>
-  <!-- The contents of the help tag is parsed as reStructuredText. Please see
-       help-template.rst for examples of commonly-used sections in other Galaxy
-       tools. -->
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool parses sample information and creates a mapping of samples to
-barcodes. The sample information file must contain the columns ``sampleid``,
-``barcode``, and ``reverse``, and can optionally contain a ``zone`` column
-also.
-
-  </help>
-</tool>
--- a/classification-wrapper.sh	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-#!/bin/bash
-
-source $(dirname $0)/util.sh
-source $1
-
-classif_table.py \
-    --specimen-map ${SPLIT_MAP} \
-    --metadata-map ${LABEL_MAP} \
-    --rank ${WANT_RANK} \
-    --tallies-wide ${TALLIES_WIDE} \
-    --by-specimen ${BY_SPECIMEN} \
-    ${CLASS_DB} \
-    ${BY_TAXON}
--- a/classification.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,104 +0,0 @@
-<tool id="PHYLO_classification" name="Output classifications" version="2.1.0">
-  <description>in tabular format</description>
-  <requirements>
-    <requirement type="package">yapp_env</requirement>
-  </requirements>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <version_command>echo "guppy $(guppy --version)"</version_command>
-  <command interpreter="bash">
-    classification-wrapper.sh ${config}
-  </command>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
-  <inputs>
-    <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/>
-    <param name="label_map" type="data" format="csv" label="Specimen-to-label map"/>
-    <param name="class_db" type="data" format="sqlite3" label="Placement database"/>
-    <param name="want_rank" type="select" label="Desired classification rank">
-      <option value="species" selected="true">Species</option>
-      <option value="genus">Genus</option>
-      <option value="family">Family</option>
-      <option value="order">Order</option>
-      <option value="class">Class</option>
-      <option value="phylum">Phylum</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="by_taxon" format="csv" label="By-taxon classification"/>
-    <data name="by_specimen" format="csv" label="By-specimen classification"/>
-    <data name="tallies_wide" format="csv" label="Tallies-wide classification"/>
-  </outputs>
-  <configfiles>
-    <configfile name="config">
-SPLIT_MAP="${split_map}"
-LABEL_MAP="${label_map}"
-CLASS_DB="${class_db}"
-WANT_RANK="${want_rank}"
-
-BY_TAXON="${by_taxon}"
-BY_SPECIMEN="${by_specimen}"
-TALLIES_WIDE="${tallies_wide}"
-    </configfile>
-  </configfiles>
-  <!-- The contents of the help tag is parsed as reStructuredText. Please see
-       help-template.rst for examples of commonly-used sections in other Galaxy
-       tools. -->
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool outputs the classifications made by ``pplacer`` to a tabular format
-appropriate for use with R.
-
------
-
-**Example**
-
-The classifications are simply done by containment. Say clade A of the
-reference tree is the smallest such that contains a given placement. The most
-specific classification for that read will be the lowest common ancestor of the
-taxonomic classifications for the leaves of A. If the desired classification is
-more specific than that, then we get a disconnect between the desired and the
-actual classification. For example, if we try to classify at the species level
-and the clade LCA is a genus, then we will get a genus name. If there is
-uncertainty in read placement, then there is uncertainty in classification.
-
-For example, here is a classification list made for one read using the tabular
-output. The columns are as follows: read name, attempted rank for
-classification, actual rank for classification, taxonomic identifier, and
-confidence. You can see that in this example, there is some uncertainty at and
-below species, but only one classification at the genus level::
-
-    GLKT0ZE01CQ2BU                      root          root       1          1
-    GLKT0ZE01CQ2BU                below_root    below_root  131567          1
-    GLKT0ZE01CQ2BU              superkingdom  superkingdom       2          1
-    GLKT0ZE01CQ2BU        below_superkingdom  superkingdom       2          1
-    GLKT0ZE01CQ2BU  below_below_superkingdom  superkingdom       2          1
-    GLKT0ZE01CQ2BU               superphylum  superkingdom       2          1
-    GLKT0ZE01CQ2BU                    phylum        phylum    1239          1
-    GLKT0ZE01CQ2BU                 subphylum        phylum    1239          1
-    GLKT0ZE01CQ2BU                     class         class  186801          1
-    GLKT0ZE01CQ2BU                  subclass         class  186801          1
-    GLKT0ZE01CQ2BU                     order         order  186802          1
-    GLKT0ZE01CQ2BU               below_order         order  186802          1
-    GLKT0ZE01CQ2BU         below_below_order         order  186802          1
-    GLKT0ZE01CQ2BU                  suborder         order  186802          1
-    GLKT0ZE01CQ2BU                    family        family  186804          1
-    GLKT0ZE01CQ2BU              below_family        family  186804          1
-    GLKT0ZE01CQ2BU                     genus         genus    1257          1
-    GLKT0ZE01CQ2BU             species_group         genus    1257          1
-    GLKT0ZE01CQ2BU          species_subgroup         genus    1257          1
-    GLKT0ZE01CQ2BU                   species         genus    1257  0.0732247
-    GLKT0ZE01CQ2BU                   species       species    1261   0.853561
-    GLKT0ZE01CQ2BU                   species       species  341694   0.073214
-    GLKT0ZE01CQ2BU             below_species         genus    1257  0.0732247
-    GLKT0ZE01CQ2BU             below_species       species    1261   0.853561
-    GLKT0ZE01CQ2BU             below_species       species  341694   0.073214
-
-  </help>
-</tool>
--- a/datatypes_conf.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-  <datatype_files>
-    <datatype_file name="pplacer.py"/>
-    <datatype_file name="taxtastic.py"/>
-  </datatype_files>
-  <registration>
-    <datatype extension="jplace" type="galaxy.datatypes.pplacer:Jplace" mimetype="application/json" display_in_upload="True"/>
-    <datatype extension="refpkg" type="galaxy.datatypes.taxtastic:Refpkg" display_in_upload="False"/>
-    <datatype extension="refpkg.zip" type="galaxy.datatypes.taxtastic:RefpkgZip" mimetype="application/zip" display_in_upload="True">
-      <converter file="refpkgzip_to_refpkg.xml" target_datatype="refpkg" depends_on="unzip"/>
-    </datatype>
-    <datatype extension="xlsx" type="galaxy.datatypes.taxtastic:OfficeXlsx" mimetype="application/zip" display_in_upload="True">
-      <converter file="xlsx_to_csv.xml" target_datatype="csv"/>
-    </datatype>
-  </registration>
-  <sniffers>
-    <sniffer type="galaxy.datatypes.pplacer:Jplace"/>
-    <sniffer type="galaxy.datatypes.taxtastic:RefpkgZip"/>
-    <sniffer type="galaxy.datatypes.taxtastic:OfficeXlsx"/>
-  </sniffers>
-</datatypes>
--- a/decorate-wrapper.sh	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-source $(dirname $0)/util.sh
-source $1
-
-csvcut -c "specimen,${COLUMNS}" ${METADATA} | \
-    csvjoin -c "specimen" ${GROUP_BY_SPECIMEN} - > ${DECORATED_GROUP_BY_SPECIMEN}
-
-# drop duplicate columns (thanks, Erick!)
-#csvcut -c $(head -n 1 addresses.csv | sed "s/,/\n/g" | sort |uniq | paste -s -d",")
--- a/decorate.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<tool id="PHYLO_decorate" name="Decorate" version="1.0.0">
-  <description>classification results with sample metadata</description>
-  <requirements>
-    <requirement type="package">yapp_env</requirement>
-  </requirements>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <version_command>echo "decorate script 1.0.0"</version_command>
-  <command interpreter="bash">
-    decorate-wrapper.sh ${config}
-  </command>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
-  <inputs>
-    <param name="group_by_specimen" type="data" format="csv" label="Grouped-by-specimen classification"/>
-    <param name="metadata" type="data" format="csv" label="Sample metadata"/>
-    <param name="columns" type="text" label="Comma-separated metadata columns" area="True" size="5x40"/>
-  </inputs>
-  <outputs>
-    <data name="decorated_group_by_specimen" format="csv" label="Decorated grouped-by-specimen classification"/>
-  </outputs>
-  <configfiles>
-    <configfile name="config">
-GROUP_BY_SPECIMEN="${group_by_specimen}"
-METADATA="${metadata}"
-COLUMNS="${columns}"
-
-DECORATED_GROUP_BY_SPECIMEN="${decorated_group_by_specimen}"
-    </configfile>
-  </configfiles>
-  <!-- The contents of the help tag is parsed as reStructuredText. Please see
-       help-template.rst for examples of commonly-used sections in other Galaxy
-       tools. -->
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool joins the classifications made by ``pplacer`` with arbitrary sample
-metadata.
-
-  </help>
-</tool>
--- a/filter-wrapper.sh	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-#!/bin/bash
-
-source $(dirname $0)/util.sh
-source $1
-
-INPUT_QUAL=$(extify qual ${INPUT_QUAL})
-BARCODES=$(extify csv ${BARCODES})
-RAW_SEQS=$(extify fasta ${RAW_SEQS})
-
-seqmagick quality-filter \
-    --input-qual ${INPUT_QUAL} \
-    --barcode-file ${BARCODES} \
-    --primer "${PRIMER}" \
-    --report-out ${FILTER_REPORT} \
-    --details-out ${FILTER_DETAILS} \
-    --map-out ${SPLIT_MAP} \
-    --barcode-header \
-    --min-length ${MIN_LENGTH} \
-    --min-mean-quality ${MIN_QUALITY} \
-    --quality-window 30 \
-    --quality-window-prop 0.9 \
-    --quality-window-mean-qual 15 \
-    ${RAW_SEQS} \
-    filtered.fasta
-
-if [[ ${REVERSE_COMPLEMENT} == "TRUE" ]]; then
-    seqmagick mogrify \
-        --reverse-complement \
-        filtered.fasta
-fi
-
-mv filtered.fasta ${FILTERED_SEQS}
-
-# TODO: separate tool for concatenating seq data (and reverse complementing them?)
-#cat [12]*Reads.fasta | seqmagick convert --input-format fasta - combined.fasta --reverse-complement
-#cat [12]*.map.csv > combined.map.csv
-
-sequencing_quality_report.py ${PLATE_JSON} -t "Sequencing quality report" -o ${SQR_DIR}
-
-cat <<EOF > ${SQR}
-<!DOCTYPE HTML>
-<html lang="en-US">
-  <head/>
-  <body>
-    <a href="index.html">Sequencing quality report</a>
-  </body>
-</html>
-EOF
--- a/filter.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-<tool id="PHYLO_filter" name="Filter and trim" version="1.2.0">
-  <description>sequences</description>
-  <requirements>
-    <requirement type="package">yapp_env</requirement>
-  </requirements>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <version_command>seqmagick --version</version_command>
-  <command interpreter="bash">
-    filter-wrapper.sh ${config}
-  </command>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
-  <inputs>
-    <!-- TODO: can take either fasta+qual or fastq -->
-    <param name="plate_id" type="integer" value="1" label="Plate number"/>
-    <param name="zone_id" type="integer" value="1" label="Zone number"/>
-    <param name="raw_seqs" type="data" format="fasta" label="Unfiltered sequences"/>
-    <param name="input_qual" type="data" format="qual" label="Sequence quality data"/>
-    <!-- TODO: handle MID format for multi-sample sequencing; see http://qiime.org/scripts/split_libraries.html -->
-    <param name="barcodes" type="data" format="csv" label="Barcodes"/>
-    <param name="primer" type="text" label="Primer" value="GCGGACTACCVGGGTATCTAAT" area="True" size="1x40"/>
-    <param name="min_length" type="integer" min="100" max="1000" value="350" label="Minimum sequence length"/>
-    <param name="min_quality" type="integer" min="0" max="63" value="35" label="Minimum mean sequence quality"/>
-    <param name="reverse_complement" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Reads uniformly correspond to negative strands"/>
-  </inputs>
-  <outputs>
-    <data name="filtered_seqs" format="fasta" label="Filtered sequences"/>
-    <data name="filter_report" format="tabular" label="Filtering report"/>
-    <data name="filter_details" format="data" label="Filtering details"/>
-    <data name="split_map" format="csv" label="Read-to-specimen map"/>
-    <data name="seq_qual_report" format="html" label="Sequence quality report"/>
-  </outputs>
-  <configfiles>
-    <configfile name="plate_json">
-{
-  "plate": ${plate_id},
-  "name": "Plate ${plate_id}",
-  "zones": [
-    {
-      "zone": ${zone_id},
-      "cleaning_stats": "${filter_details}"
-    }
-  ]
-}
-    </configfile>
-    <configfile name="config">
-RAW_SEQS="${raw_seqs}"
-INPUT_QUAL="${input_qual}"
-BARCODES="${barcodes}"
-PRIMER="${primer}"
-MIN_LENGTH="${min_length}"
-MIN_QUALITY="${min_quality}"
-REVERSE_COMPLEMENT="${reverse_complement}"
-PLATE_JSON="${plate_json}"
-
-FILTERED_SEQS="${filtered_seqs}"
-FILTER_REPORT="${filter_report}"
-FILTER_DETAILS="${filter_details}"
-SPLIT_MAP="${split_map}"
-SQR="${seq_qual_report}"
-SQR_DIR="${seq_qual_report.files_path}"
-    </configfile>
-  </configfiles>
-  <!-- The contents of the help tag is parsed as reStructuredText. Please see
-       help-template.rst for examples of commonly-used sections in other Galaxy
-       tools. -->
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool truncates and removes sequences that don’t match a set of quality
-criteria, as well as mapping sequence barcodes to specimens. It takes input
-sequences in FASTA format and a quality file, and outputs the filtered
-sequences as well as a filtering summary and a sequence quality report.
-
-The default quality filter settings are:
-
-+---------------------------+------+
-|parameter                  |value |
-+===========================+======+
-|--min-length               |350   |
-+---------------------------+------+
-|--min-mean-quality         |35    |
-+---------------------------+------+
-|--quality-window           |30    |
-+---------------------------+------+
-|--quality-window-prop      |0.9   |
-+---------------------------+------+
-|--quality-window-mean-qual |15    |
-+---------------------------+------+
-
-See seqmagick's `quality filter documentation`_ for full explanations of these
-parameters.
-
-.. _quality filter documentation: http://fhcrc.github.io/seqmagick/quality_filter.html
-
-  </help>
-</tool>
--- a/macros.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<macros>
-  <macro name="basic_errors">
-    <exit_code range="1:" level="fatal"/>
-    <regex match="error" level="fatal"/>
-    <regex match="traceback" level="fatal"/>
-    <regex match="warning" level="warning"/>
-  </macro>
-</macros>
--- a/pplacer-wrapper.sh	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-#!/bin/bash
-
-source $(dirname $0)/util.sh
-source $1
-
-QUERY_SEQS=$(extify fasta ${QUERY_SEQS})
-PPLACER_DEFAULT_ARGS="-j ${GALAXY_SLOTS:-4} -p --inform-prior --prior-lower 0.01 --map-identity"
-
-pplacer \
-    ${PPLACER_DEFAULT_ARGS} \
-    -c ${REFPKG} \
-    -o ${PLACED_SEQS} \
-    ${QUERY_SEQS}
--- a/pplacer.py	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-import json
-from galaxy.datatypes.data import Text
-from galaxy.datatypes.images import Html
-
-class Jplace(Text):
-    file_ext = "jplace"
-
-    def sniff(self, filename):
-        try:
-            with open(filename, "r") as f:
-                data = json.load(f)
-                if all (k in data for k in ("version", "tree", "placements", "fields")):
-                    return True
-        except:
-            pass
-
-        return False
-
-    def get_mime(self):
-        return "application/json"
-
-class AutoPrimaryComposite(Html):
-    composite_type = "auto_primary_file"
-
-    def __init__(self, **kwd):
-        Html.__init__(self, **kwd)
-
-    def regenerate_primary_file(self,dataset):
-        """
-        cannot do this until we are setting metadata
-        """
-        bn = dataset.metadata.base_name
-        efp = dataset.extra_files_path
-        flist = os.listdir(efp)
-        rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name,dataset.name)]
-        for i,fname in enumerate(flist):
-            sfname = os.path.split(fname)[-1]
-            f,e = os.path.splitext(fname)
-            rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) )
-        rval.append( '</ul></body></html>' )
-        f = file(dataset.file_name,'w')
-        f.write("\n".join( rval ))
-        f.write('\n')
-        f.close()
-
-    def set_meta(self, dataset, **kwd):
-        Html.set_meta(self, dataset, **kwd)
-        self.regenerate_primary_file(dataset)
-
-    def get_mime(self):
-        return "text/html"
-
-class BasicHtmlComposite(Html):
-    composite_type = "basic"
--- a/pplacer.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-<tool id="PHYLO_pplacer" name="Place aligned sequences" version="1.0.0">
-  <description>on a reference tree</description>
-  <requirements>
-    <requirement type="package">yapp_env</requirement>
-  </requirements>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <version_command>echo "pplacer $(pplacer --version)"</version_command>
-  <command interpreter="bash">
-    pplacer-wrapper.sh ${config}
-  </command>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
-  <inputs>
-    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
-    <param name="query_seqs" type="data" format="fasta" label="Query alignment"/>
-  </inputs>
-  <outputs>
-    <data name="placed_seqs" format="jplace" label="Placed sequences"/>
-  </outputs>
-  <configfiles>
-    <configfile name="config">
-REFPKG="${refpkg.extra_files_path}"
-QUERY_SEQS="${query_seqs}"
-
-PLACED_SEQS="${placed_seqs}"
-    </configfile>
-  </configfiles>
-  <!-- The contents of the help tag is parsed as reStructuredText. Please see
-       help-template.rst for examples of commonly-used sections in other Galaxy
-       tools. -->
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool places query sequences on a fixed reference phylogenetic tree
-according to a reference alignment, producing taxonomic annotations which can
-be used for classification and visualization.
-
------
-
-**Citation**
-
-Matsen F, Kodner R, Armbrust E V: **pplacer: linear time maximum-likelihood and
-Bayesian phylogenetic placement of sequences onto a fixed reference tree**. BMC
-Bioinformatics 2010, **11**:1.
-
-  </help>
-</tool>
--- a/preclassification-wrapper.sh	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-#!/bin/bash
-
-source $(dirname $0)/util.sh
-source $1
-
-PLACED_SEQS=$(extify jplace ${PLACED_SEQS})
-NBC_SEQS=$(extify fasta ${NBC_SEQS})
-
-guppy redup \
-    -m \
-    -d ${DEDUP_INFO} \
-    -o ${REDUPED_SEQS} \
-    ${PLACED_SEQS}
-
-REDUPED_SEQS=$(extify jplace ${REDUPED_SEQS})
-
-rppr prep_db \
-    -c ${REFPKG} \
-    --sqlite ${CLASS_DB}
-
-guppy classify \
-    -c ${REFPKG} \
-    -j ${GALAXY_SLOTS:-4} \
-    --pp \
-    --sqlite ${CLASS_DB} \
-    --classifier hybrid2 \
-    --nbc-sequences ${NBC_SEQS} \
-    ${REDUPED_SEQS}
-
-multiclass_concat.py --dedup-info ${DEDUP_INFO} ${CLASS_DB}
--- a/preclassification.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-<tool id="PHYLO_preclassification" name="Generate database" version="1.2.0">
-  <description>for classification</description>
-  <requirements>
-    <requirement type="package">yapp_env</requirement>
-  </requirements>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <version_command>echo "guppy $(guppy --version)"</version_command>
-  <command interpreter="bash">
-    preclassification-wrapper.sh ${config}
-  </command>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
-  <inputs>
-    <param name="dedup_info" type="data" format="csv" label="Deduplication info"/>
-    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
-    <param name="nbc_seqs" type="data" format="fasta" label="Query alignment" help="The query alignment specified here should be the same as the one passed to pplacer."/>
-    <param name="placed_seqs" type="data" format="jplace" label="Placements"/>
-  </inputs>
-  <outputs>
-    <data name="reduped_seqs" format="jplace" label="Reduped placements"/>
-    <data name="class_db" format="sqlite3" label="Placement database"/>
-  </outputs>
-  <configfiles>
-    <configfile name="config">
-DEDUP_INFO="${dedup_info}"
-REFPKG="${refpkg.extra_files_path}"
-NBC_SEQS="${nbc_seqs}"
-PLACED_SEQS="${placed_seqs}"
-
-REDUPED_SEQS="${reduped_seqs}"
-CLASS_DB="${class_db}"
-    </configfile>
-  </configfiles>
-  <!-- The contents of the help tag is parsed as reStructuredText. Please see
-       help-template.rst for examples of commonly-used sections in other Galaxy
-       tools. -->
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool outputs the classifications made by ``pplacer`` to a database for use
-in taxonomic classification.
-
-  </help>
-</tool>
--- a/preprocessing-wrapper.sh	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-#!/bin/bash
-
-source $1
-
-deduplicate_sequences.py \
-    --split-map ${SPLIT_MAP} \
-    --deduplicated-sequences-file ${DEDUP_INFO} \
-    ${INPUT_SEQS} \
-    ${DEDUP_SEQS}
-
-# adapted from yapp/bin/refpkg_align
-ref_sto=$(taxit rp ${REFPKG} aln_sto)
-profile=$(taxit rp ${REFPKG} profile)
-
-sto=$(mktemp -u).sto
-
-cmalign --cpu ${GALAXY_SLOTS:-4} -o "$sto" --sfile "${ALIGNED_SCORES}" --noprob --dnaout "$profile" "${DEDUP_SEQS}" | grep -E '^#'
-
-esl-alimerge --dna --outformat afa "$ref_sto" "$sto" | \
-    seqmagick convert --output-format fasta --dash-gap - "${ALIGNED_SEQS}"
--- a/preprocessing.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-<tool id="PHYLO_preprocessing" name="Preprocess sequences" version="2.0.0">
-  <description>in preparation for phylogenetic placement</description>
-  <requirements>
-    <requirement type="package">yapp_env</requirement>
-  </requirements>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <version_command>echo "guppy $(guppy --version)"</version_command>
-  <command interpreter="bash">
-    preprocessing-wrapper.sh ${config}
-  </command>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
-  <inputs>
-    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
-    <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
-    <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/>
-  </inputs>
-  <outputs>
-    <data name="dedup_seqs" format="fasta" label="Deduplicated sequences"/>
-    <data name="dedup_info" format="csv" label="Deduplication info"/>
-    <data name="aligned_seqs" format="fasta" label="Aligned sequences"/>
-    <data name="aligned_scores" format="txt" label="Alignment scores"/>
-  </outputs>
-  <configfiles>
-    <configfile name="config">
-REFPKG="${refpkg.extra_files_path}"
-INPUT_SEQS="${input_seqs}"
-SPLIT_MAP="${split_map}"
-
-DEDUP_SEQS="${dedup_seqs}"
-DEDUP_INFO="${dedup_info}"
-ALIGNED_SEQS="${aligned_seqs}"
-ALIGNED_SCORES="${aligned_scores}"
-    </configfile>
-  </configfiles>
-  <!-- The contents of the help tag is parsed as reStructuredText. Please see
-       help-template.rst for examples of commonly-used sections in other Galaxy
-       tools. -->
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool aligns query sequences with the reference sequences used to make the
-reference tree contained in the reference package and then merges the query and
-reference sequences.
-
-  </help>
-</tool>
--- a/refpkgzip_to_refpkg.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-<tool id="CONVERTER_refpkgzip_to_refpkg" name="Convert zipped refpkg to refpkg" version="1.0.0">
-  <command>unzip -o -j $input -d $output.files_path</command>
-  <inputs>
-    <param name="input" type="data" format="refpkg.zip" label="Zipped refpkg"/>
-  </inputs>
-  <outputs>
-    <data name="output" format="refpkg"/>
-  </outputs>
-  <help>
-  </help>
-</tool>
--- a/render_datatable-wrapper.sh	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-#!/bin/bash
-
-source $(dirname $0)/util.sh
-source $1
-
-mkdir -p ${OUTPUT_DIR}
-
-python $(dirname $0)/render_datatable.py \
-    < ${INPUT} \
-    > ${OUTPUT_DIR}/index.html
-
-cat <<EOF > ${OUTPUT}
-<!DOCTYPE HTML>
-<html lang="en-US">
-  <head/>
-  <body>
-    <a href="index.html">Generated table</a>
-  </body>
-</html>
-EOF
--- a/render_datatable.py	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,412 +0,0 @@
-#!/usr/bin/env python
-
-import csv
-import itertools
-import string
-import sys
-
-input = sys.stdin
-start_lines = input.readlines(10)
-all_input = itertools.chain(iter(start_lines), input)
-
-def detect_delimiter(iterable, char_set):
-    matches = (c for c in char_set if c in iterable)
-    return next(matches, None)
-
-def detect_csv_dialect(sample):
-    try:
-        return csv.Sniffer().sniff(sample)
-    except:
-        return None
-
-delimiter = detect_delimiter(start_lines[0], list('\t, '))
-reader = None
-
-if delimiter in list('\t,'):
-    # try to detect csv dialect, which should neatly handle quoted separators and stuff
-    dialect = detect_csv_dialect(''.join(start_lines))
-    if dialect:
-        reader = csv.reader(all_input, dialect)
-
-if not reader:
-    if delimiter in list(string.whitespace):
-        # use str.split() with no arguments to split on arbitrary whitespace strings
-        reader = (line.strip().split() for line in all_input)
-    else:
-        reader = all_input
-
-print """\
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-    <meta http-equiv="content-type" content="text/html; charset=UTF-8"></meta>
-    <link href="http://netdna.bootstrapcdn.com/twitter-bootstrap/2.3.2/css/bootstrap-combined.no-icons.min.css" rel="stylesheet">
-    <style>
-div.dataTables_length label {
-	float: left;
-	text-align: left;
-}
-
-div.dataTables_length select {
-	width: 75px;
-}
-
-div.dataTables_filter label {
-	float: right;
-}
-
-div.dataTables_info {
-	padding-top: 8px;
-}
-
-div.dataTables_paginate {
-	float: right;
-	margin: 0;
-}
-
-table.table {
-	clear: both;
-	margin-bottom: 6px !important;
-	max-width: none !important;
-}
-
-table.table thead .sorting,
-table.table thead .sorting_asc,
-table.table thead .sorting_desc,
-table.table thead .sorting_asc_disabled,
-table.table thead .sorting_desc_disabled {
-	cursor: pointer;
-	*cursor: hand;
-}
-
-
-table.table thead .sorting { background: url('images/sort_both.png') no-repeat center right; }
-
-//table.table thead .sorting_asc { background: url('images/sort_asc.png') no-repeat center right; }
-//table.table thead .sorting_desc { background: url('images/sort_desc.png') no-repeat center right; }
-table.table thead .sorting_asc { background: url('http://cdn3.iconfinder.com/data/icons/fatcow/16x16_0140/bullet_arrow_up.png') no-repeat center right; }
-table.table thead .sorting_desc { background: url('http://cdn3.iconfinder.com/data/icons/fatcow/16x16_0140/bullet_arrow_down.png') no-repeat center right; }
-
-table.table thead .sorting_asc_disabled { background: url('images/sort_asc_disabled.png') no-repeat center right; }
-table.table thead .sorting_desc_disabled { background: url('images/sort_desc_disabled.png') no-repeat center right; }
-
-table.dataTable th:active {
-	outline: none;
-}
-
-/* Scrolling */
-div.dataTables_scrollHead table {
-	margin-bottom: 0 !important;
-	border-bottom-left-radius: 0;
-	border-bottom-right-radius: 0;
-}
-
-div.dataTables_scrollHead table thead tr:last-child th:first-child,
-div.dataTables_scrollHead table thead tr:last-child td:first-child {
-	border-bottom-left-radius: 0 !important;
-	border-bottom-right-radius: 0 !important;
-}
-
-div.dataTables_scrollBody table {
-	border-top: none;
-	margin-bottom: 0 !important;
-}
-
-div.dataTables_scrollBody tbody tr:first-child th,
-div.dataTables_scrollBody tbody tr:first-child td {
-	border-top: none;
-}
-
-div.dataTables_scrollFoot table {
-	border-top: none;
-}
-
-
-
-
-/*
- * TableTools styles
- */
-.table tbody tr.active td,
-.table tbody tr.active th {
-	background-color: #08C;
-	color: white;
-}
-
-.table tbody tr.active:hover td,
-.table tbody tr.active:hover th {
-	background-color: #0075b0 !important;
-}
-
-.table-striped tbody tr.active:nth-child(odd) td,
-.table-striped tbody tr.active:nth-child(odd) th {
-	background-color: #017ebc;
-}
-
-table.DTTT_selectable tbody tr {
-	cursor: pointer;
-	*cursor: hand;
-}
-
-div.DTTT .btn {
-	color: #333 !important;
-	font-size: 12px;
-}
-
-div.DTTT .btn:hover {
-	text-decoration: none !important;
-}
-
-
-ul.DTTT_dropdown.dropdown-menu a {
-	color: #333 !important; /* needed only when demo_page.css is included */
-}
-
-ul.DTTT_dropdown.dropdown-menu li:hover a {
-	background-color: #0088cc;
-	color: white !important;
-}
-
-/* TableTools information display */
-div.DTTT_print_info.modal {
-	height: 150px;
-	margin-top: -75px;
-	text-align: center;
-}
-
-div.DTTT_print_info h6 {
-	font-weight: normal;
-	font-size: 28px;
-	line-height: 28px;
-	margin: 1em;
-}
-
-div.DTTT_print_info p {
-	font-size: 14px;
-	line-height: 20px;
-}
-
-
-
-/*
- * FixedColumns styles
- */
-div.DTFC_LeftHeadWrapper table,
-div.DTFC_LeftFootWrapper table,
-table.DTFC_Cloned tr.even {
-	background-color: white;
-}
-
-div.DTFC_LeftHeadWrapper table {
-	margin-bottom: 0 !important;
-	border-top-right-radius: 0 !important;
-	border-bottom-left-radius: 0 !important;
-	border-bottom-right-radius: 0 !important;
-}
-
-div.DTFC_LeftHeadWrapper table thead tr:last-child th:first-child,
-div.DTFC_LeftHeadWrapper table thead tr:last-child td:first-child {
-	border-bottom-left-radius: 0 !important;
-	border-bottom-right-radius: 0 !important;
-}
-
-div.DTFC_LeftBodyWrapper table {
-	border-top: none;
-	margin-bottom: 0 !important;
-}
-
-div.DTFC_LeftBodyWrapper tbody tr:first-child th,
-div.DTFC_LeftBodyWrapper tbody tr:first-child td {
-	border-top: none;
-}
-
-div.DTFC_LeftFootWrapper table {
-	border-top: none;
-}
-    </style>
-    <script type="text/javascript" language="javascript" src="http://ajax.aspnetcdn.com/ajax/jQuery/jquery-2.0.0.min.js"></script>
-    <script type="text/javascript" language="javascript" src="http://ajax.aspnetcdn.com/ajax/jquery.dataTables/1.9.4/jquery.dataTables.min.js"></script>
-    <script type="text/javascript" charset="utf-8">
-/* Set the defaults for DataTables initialisation */
-$.extend( true, $.fn.dataTable.defaults, {
-	"sDom": "<'row-fluid'<'span6'l><'span6'f>r>t<'row-fluid'<'span6'i><'span6'p>>",
-	"sPaginationType": "bootstrap",
-	"oLanguage": {
-		"sLengthMenu": "_MENU_ records per page"
-	}
-} );
-
-
-/* Default class modification */
-$.extend( $.fn.dataTableExt.oStdClasses, {
-	"sWrapper": "dataTables_wrapper form-inline"
-} );
-
-
-/* API method to get paging information */
-$.fn.dataTableExt.oApi.fnPagingInfo = function ( oSettings )
-{
-	return {
-		"iStart":         oSettings._iDisplayStart,
-		"iEnd":           oSettings.fnDisplayEnd(),
-		"iLength":        oSettings._iDisplayLength,
-		"iTotal":         oSettings.fnRecordsTotal(),
-		"iFilteredTotal": oSettings.fnRecordsDisplay(),
-		"iPage":          oSettings._iDisplayLength === -1 ?
-			0 : Math.ceil( oSettings._iDisplayStart / oSettings._iDisplayLength ),
-		"iTotalPages":    oSettings._iDisplayLength === -1 ?
-			0 : Math.ceil( oSettings.fnRecordsDisplay() / oSettings._iDisplayLength )
-	};
-};
-
-
-/* Bootstrap style pagination control */
-$.extend( $.fn.dataTableExt.oPagination, {
-	"bootstrap": {
-		"fnInit": function( oSettings, nPaging, fnDraw ) {
-			var oLang = oSettings.oLanguage.oPaginate;
-			var fnClickHandler = function ( e ) {
-				e.preventDefault();
-				if ( oSettings.oApi._fnPageChange(oSettings, e.data.action) ) {
-					fnDraw( oSettings );
-				}
-			};
-
-			$(nPaging).addClass('pagination').append(
-				'<ul>'+
-					'<li class="prev disabled"><a href="#">&larr; '+oLang.sPrevious+'</a></li>'+
-					'<li class="next disabled"><a href="#">'+oLang.sNext+' &rarr; </a></li>'+
-				'</ul>'
-			);
-			var els = $('a', nPaging);
-			$(els[0]).bind( 'click.DT', { action: "previous" }, fnClickHandler );
-			$(els[1]).bind( 'click.DT', { action: "next" }, fnClickHandler );
-		},
-
-		"fnUpdate": function ( oSettings, fnDraw ) {
-			var iListLength = 5;
-			var oPaging = oSettings.oInstance.fnPagingInfo();
-			var an = oSettings.aanFeatures.p;
-			var i, ien, j, sClass, iStart, iEnd, iHalf=Math.floor(iListLength/2);
-
-			if ( oPaging.iTotalPages < iListLength) {
-				iStart = 1;
-				iEnd = oPaging.iTotalPages;
-			}
-			else if ( oPaging.iPage <= iHalf ) {
-				iStart = 1;
-				iEnd = iListLength;
-			} else if ( oPaging.iPage >= (oPaging.iTotalPages-iHalf) ) {
-				iStart = oPaging.iTotalPages - iListLength + 1;
-				iEnd = oPaging.iTotalPages;
-			} else {
-				iStart = oPaging.iPage - iHalf + 1;
-				iEnd = iStart + iListLength - 1;
-			}
-
-			for ( i=0, ien=an.length ; i<ien ; i++ ) {
-				// Remove the middle elements
-				$('li:gt(0)', an[i]).filter(':not(:last)').remove();
-
-				// Add the new list items and their event handlers
-				for ( j=iStart ; j<=iEnd ; j++ ) {
-					sClass = (j==oPaging.iPage+1) ? 'class="active"' : '';
-					$('<li '+sClass+'><a href="#">'+j+'</a></li>')
-						.insertBefore( $('li:last', an[i])[0] )
-						.bind('click', function (e) {
-							e.preventDefault();
-							oSettings._iDisplayStart = (parseInt($('a', this).text(),10)-1) * oPaging.iLength;
-							fnDraw( oSettings );
-						} );
-				}
-
-				// Add / remove disabled classes from the static elements
-				if ( oPaging.iPage === 0 ) {
-					$('li:first', an[i]).addClass('disabled');
-				} else {
-					$('li:first', an[i]).removeClass('disabled');
-				}
-
-				if ( oPaging.iPage === oPaging.iTotalPages-1 || oPaging.iTotalPages === 0 ) {
-					$('li:last', an[i]).addClass('disabled');
-				} else {
-					$('li:last', an[i]).removeClass('disabled');
-				}
-			}
-		}
-	}
-} );
-
-
-/*
- * TableTools Bootstrap compatibility
- * Required TableTools 2.1+
- */
-if ( $.fn.DataTable.TableTools ) {
-	// Set the classes that TableTools uses to something suitable for Bootstrap
-	$.extend( true, $.fn.DataTable.TableTools.classes, {
-		"container": "DTTT btn-group",
-		"buttons": {
-			"normal": "btn",
-			"disabled": "disabled"
-		},
-		"collection": {
-			"container": "DTTT_dropdown dropdown-menu",
-			"buttons": {
-				"normal": "",
-				"disabled": "disabled"
-			}
-		},
-		"print": {
-			"info": "DTTT_print_info modal"
-		},
-		"select": {
-			"row": "active"
-		}
-	} );
-
-	// Have the collection use a bootstrap compatible dropdown
-	$.extend( true, $.fn.DataTable.TableTools.DEFAULTS.oTags, {
-		"collection": {
-			"container": "ul",
-			"button": "li",
-			"liner": "a"
-		}
-	} );
-}
-
-
-/* Table initialisation */
-$(document).ready(function() {
-	$('#from_csv').dataTable( {
-		"sDom": "<'row'<'span6'l><'span6'f>r>t<'row'<'span6'i><'span6'p>>",
-		"sPaginationType": "bootstrap",
-		"oLanguage": {
-			"sLengthMenu": "_MENU_ records per page"
-		}
-	} );
-} );
-    </script>
-  </head>
-  <body>
-    <div class="container" style="margin-top: 10px">
-      <table cellpadding="0" cellspacing="0" border="0" class="table table-striped table-bordered" id="from_csv">
-        <thead>\
-"""
-
-for i, row in enumerate(reader):
-    if i == 0:
-        print "<tr><th>" + "</th><th>".join(row) + "</th></tr>"
-    else:
-        print "<tr><td>" + "</td><td>".join(row) + "</td></tr>"
-
-    if i == 0:
-        print "</thead><tbody>"
-
-print """\
-        </tbody>
-      </table>
-    </div>
-  </body>
-</html>\
-"""
--- a/render_datatable.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-<tool id="PHYLO_render_datatable" name="Render CSV file" version="1.1.0">
-  <description>as an interactive HTML table</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <command interpreter="bash">
-    render_datatable-wrapper.sh $config
-  </command>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
-  <inputs>
-    <param name="input" type="data" format="csv" label="CSV file"/>
-  </inputs>
-  <outputs>
-    <data format="html" name="output" label="Generated table"/>
-  </outputs>
-  <configfiles>
-    <configfile name="config">
-INPUT="${input}"
-
-OUTPUT="${output}"
-OUTPUT_DIR="${output.files_path}"
-    </configfile>
-  </configfiles>
-  <!-- The contents of the help tag is parsed as reStructuredText. Please see
-       help-template.rst for examples of commonly-used sections in other Galaxy
-       tools. -->
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool reformats a CSV file, like this::
-
-    "seqname","accession","tax_id","species_name","is_type"
-    "FM872653","FM872653","308994","Dialister propionicifaciens",0.0
-    "AY331416","AY331416","239137","Candidate Division TM7 oral",0.0
-    "DQ666092","DQ666092","95818_1","Candidate Division TM7 vaginal",0.0
-    "S002223913","GQ900631","186802_3","bacterium BVAB3-Strain 1",0.0
-    ...
-
-into an interactive HTML table.
-
-[placeholder]
-
-+-------------+-----------+----------+---------------------------------------+----------+
-|  seqname    | accession | tax_id   | species_name                          | is_type  |
-+=============+===========+==========+=======================================+==========+
-|  FM872653   | FM872653  | 308994   | Dialister propionicifaciens           | 0.0      |
-+-------------+-----------+----------+---------------------------------------+----------+
-|  AY331416   | AY331416  | 239137   | Candidate Division TM7 oral           | 0.0      |
-+-------------+-----------+----------+---------------------------------------+----------+
-|  DQ666092   | DQ666092  | 95818_1  | Candidate Division TM7 vaginal        | 0.0      |
-+-------------+-----------+----------+---------------------------------------+----------+
-|  S002223913 | GQ900631  | 186802_3 | bacterium BVAB3-Strain 1              | 0.0      |
-+-------------+-----------+----------+---------------------------------------+----------+
-
-...
-
-  </help>
-</tool>
--- a/taxtastic.py	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
-import os
-import zipfile
-from galaxy.datatypes.binary import Binary
-from galaxy.datatypes.data import Text
-
-class Refpkg(Text):
-    composite_type = "basic"
-
-    def __init__(self, **kwd):
-        Text.__init__(self, **kwd)
-        self.add_composite_file("CONTENTS.json")
-
-    def get_mime(self):
-        return "application/json"
-
-class RefpkgZip(Binary):
-    file_ext = "refpkg.zip"
-
-    def __init__(self, **kwd):
-        Binary.__init__(self, **kwd)
-
-    def sniff(self, filename):
-        if not zipfile.is_zipfile(filename):
-            return False
-        contains_contents_file = False
-        zip_file = zipfile.ZipFile(filename, "r")
-        for name in zip_file.namelist():
-            if os.path.basename(name) == "CONTENTS.json":
-                contains_contents_file = True
-                break
-        zip_file.close()
-        if not contains_contents_file:
-            return False
-        return True
-
-    def get_mime(self):
-        return "application/zip"
-
-class OfficeXlsx(Binary):
-    file_ext = "xlsx"
-
-    def __init__(self, **kwd):
-        Binary.__init__(self, **kwd)
-
-    # TODO: this should check for an xl/ directory also
-    def sniff(self, filename):
-        if not zipfile.is_zipfile(filename):
-            return False
-        contains_contents_file = False
-        zip_file = zipfile.ZipFile(filename, "r")
-        for name in zip_file.namelist():
-            if os.path.basename(name) == "[Content_Types].xml":
-                contains_contents_file = True
-                break
-        zip_file.close()
-        if not contains_contents_file:
-            return False
-        return True
-
-    def get_mime(self):
-        return "application/zip"
-
-Binary.register_sniffable_binary_format("refpkg.zip", "refpkg.zip", RefpkgZip)
-Binary.register_sniffable_binary_format("xlsx", "xlsx", OfficeXlsx)
--- a/usearch-wrapper.sh	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-#!/bin/bash
-
-source $(dirname $0)/util.sh
-source $1
-
-RDP_SEQS="/shared/silo_researcher/Matsen_F/MatsenGrp/micro_refset/rdp/10_31/tax_filter/filtered/rdp_10_31.filter.fasta"
-RDP_SEQINFO="/shared/silo_researcher/Matsen_F/MatsenGrp/micro_refset/rdp/10_31/tax_filter/filtered/rdp_10_31.filter.seq_info.csv"
-
-sqlite3 -csv -header ${CLASS_DB} <<EOF > usearch_meta.csv
-SELECT pn.name, CAST(pn.mass AS INT) count, tax_id, tax_name, taxa.rank
-  FROM multiclass_concat
-    JOIN taxa USING (tax_id)
-    JOIN placement_names pn USING (placement_id, name)
-    WHERE want_rank = 'species';
-EOF
-
-romp -v usearch_clusters \
-    --usearch-quietly \
-    --query-group tax_id \
-    --query-duplication count \
-    --database-name seqname \
-    --database-group tax_id \
-    ${INPUT_SEQS} \
-    usearch_meta.csv \
-    ${RDP_SEQS} \
-    ${RDP_SEQINFO} \
-    ${USEARCH_HITS} \
-    ${USEARCH_GROUPS}
--- a/usearch.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-<tool id="PHYLO_usearch" name="Analyze sequences" version="1.1.0">
-  <description>with USEARCH</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <version_command>/home/matsengrp/local/bin/usearch6_64 --version</version_command>
-  <command interpreter="bash">
-    usearch-wrapper.sh $config
-  </command>
-  <stdio>
-    <expand macro="basic_errors"/>
-  </stdio>
-  <inputs>
-    <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
-    <param name="class_db" type="data" format="sqlite3" label="Placement database"/>
-  </inputs>
-  <outputs>
-    <data format="csv" name="usearch_hits" label="USEARCH hits"/>
-    <data format="csv" name="usearch_groups" label="USEARCH groups"/>
-  </outputs>
-  <configfiles>
-    <configfile name="config">
-INPUT_SEQS="${input_seqs}"
-CLASS_DB="${class_db}"
-
-USEARCH_HITS="${usearch_hits}"
-USEARCH_GROUPS="${usearch_groups}"
-    </configfile>
-  </configfiles>
-  <!-- The contents of the help tag is parsed as reStructuredText. Please see
-       help-template.rst for examples of commonly-used sections in other Galaxy
-       tools. -->
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool queries large sequence databases for target sequences and assigns
-those sequences to clusters.
-
------
-
-**Citation**
-
-Edgar, R C: **Search and clustering orders of magnitude faster than
-BLAST**. Bioinformatics 2010, **26**:19.
-
-  </help>
-</tool>
--- a/util.sh	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-#!/bin/bash
-
-extify() {
-    local REQ_EXT=$1
-    shift
-
-    local OUTPUT=""
-    local FILE
-    for FILE in $*; do
-        local BASENAME=$(basename ${FILE})
-        local EXT=${BASENAME##*.}
-        if [[ ${EXT} != ${REQ_EXT} ]]; then
-            local LINK="${BASENAME%%.*}.${REQ_EXT}"
-            if [[ ! -f ${LINK} ]]; then
-                ln -s ${FILE} ${LINK}
-            fi
-            FILE="${LINK}"
-        fi
-        OUTPUT="${OUTPUT} ${FILE}"
-    done
-
-    echo ${OUTPUT}
-}
-
-# from http://www.linuxjournal.com/content/use-date-command-measure-elapsed-time
-timer() {
-    if [[ $# -eq 0 ]]; then
-        echo $(date '+%s')
-    else
-        local  stime=$1
-        etime=$(date '+%s')
-
-        if [[ -z "$stime" ]]; then stime=$etime; fi
-
-        dt=$((etime - stime))
-        ds=$((dt % 60))
-        dm=$(((dt / 60) % 60))
-        dh=$((dt / 3600))
-        printf '%d:%02d:%02d' $dh $dm $ds
-    fi
-}
-
-on_exit() {
-    echo "Elapsed time: $(timer ${START_TIME})"
-}
-
-set -eux
-
-xargs -n 1 -0 < /proc/self/environ > env.log
-
-START_TIME=$(timer)
-trap on_exit EXIT
--- a/xlsx_to_csv.xml	Thu Feb 26 18:16:36 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<tool id="CONVERTER_xlsx_to_csv" name="Convert xlsx to csv" version="1.0.0">
-  <requirements>
-    <requirement type="package">yapp_env</requirement>
-  </requirements>
-  <command>in2csv -f xlsx $input > $output</command>
-  <inputs>
-    <param name="input" type="data" format="xlsx" label="Excel spreadsheet"/>
-  </inputs>
-  <outputs>
-    <data name="output" format="csv"/>
-  </outputs>
-  <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool converts a spreadsheet in Microsoft Excel 2007 (.xlsx) format to CSV.
-
-  </help>
-</tool>