Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate README.rst @ 47:1bc0077b2c91 draft

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author pjbriggs
date Tue, 17 Dec 2019 09:12:13 +0000
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1 Amplicon_analysis-galaxy
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2 ========================
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4 A Galaxy tool wrapper to Mauro Tutino's ``Amplicon_analysis`` pipeline
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5 script at https://github.com/MTutino/Amplicon_analysis
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7 The pipeline can analyse paired-end 16S rRNA data from Illumina Miseq
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8 (Casava >= 1.8) and performs the following operations:
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10 * QC and clean up of input data
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11 * Removal of singletons and chimeras and building of OTU table
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12 and phylogenetic tree
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13 * Beta and alpha diversity of analysis
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15 Usage documentation
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16 ===================
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18 Usage of the tool (including required inputs) is documented within
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19 the ``help`` section of the tool XML.
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21 Installing the tool in a Galaxy instance
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22 ========================================
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24 The following sections describe how to install the tool files,
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25 dependencies and reference data, and how to configure the Galaxy
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26 instance to detect the dependencies and reference data correctly
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27 at run time.
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29 1. Install the tool from the toolshed
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30 -------------------------------------
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32 The core tool is hosted on the Galaxy toolshed, so it can be installed
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33 directly from there (this is the recommended route):
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35 * https://toolshed.g2.bx.psu.edu/view/pjbriggs/amplicon_analysis_pipeline/
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36
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37 Alternatively it can be installed manually; in this case there are two
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38 files to install:
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40 * ``amplicon_analysis_pipeline.xml`` (the Galaxy tool definition)
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41 * ``amplicon_analysis_pipeline.py`` (the Python wrapper script)
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43 Put these in a directory that is visible to Galaxy (e.g. a
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44 ``tools/Amplicon_analysis/`` folder), and modify the ``tools_conf.xml``
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45 file to tell Galaxy to offer the tool by adding the line e.g.::
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47 <tool file="Amplicon_analysis/amplicon_analysis_pipeline.xml" />
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49 2. Install the reference data
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50 -----------------------------
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52 The script ``References.sh`` from the pipeline package at
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53 https://github.com/MTutino/Amplicon_analysis can be run to install
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54 the reference data, for example::
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55
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56 cd /path/to/pipeline/data
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57 wget https://github.com/MTutino/Amplicon_analysis/raw/master/References.sh
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58 /bin/bash ./References.sh
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60 will install the data in ``/path/to/pipeline/data``.
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61
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62 **NB** The final amount of data downloaded and uncompressed will be
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63 around 9GB.
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65 3. Configure reference data location in Galaxy
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66 ----------------------------------------------
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68 The final step is to make your Galaxy installation aware of the
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69 location of the reference data, so it can locate them both when the
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70 tool is run.
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72 The tool locates the reference data via an environment variable called
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73 ``AMPLICON_ANALYSIS_REF_DATA_PATH``, which needs to set to the parent
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74 directory where the reference data has been installed.
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76 There are various ways to do this, depending on how your Galaxy
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77 installation is configured:
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79 * **For local instances:** add a line to set it in the
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80 ``config/local_env.sh`` file of your Galaxy installation (you
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81 may need to create a new empty file first), e.g.::
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82
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83 export AMPLICON_ANALYSIS_REF_DATA_PATH=/path/to/pipeline/data
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84
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85 * **For production instances:** set the value in the ``job_conf.xml``
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86 configuration file, e.g.::
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87
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88 <destination id="amplicon_analysis">
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89 <env id="AMPLICON_ANALYSIS_REF_DATA_PATH">/path/to/pipeline/data</env>
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90 </destination>
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91
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92 and then specify that the pipeline tool uses this destination::
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93
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94 <tool id="amplicon_analysis_pipeline" destination="amplicon_analysis"/>
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96 (For more about job destinations see the Galaxy documentation at
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97 https://docs.galaxyproject.org/en/master/admin/jobs.html#job-destinations)
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98
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99 4. Enable rendering of HTML outputs from pipeline
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100 -------------------------------------------------
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101
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102 To ensure that HTML outputs are displayed correctly in Galaxy
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103 (for example the Vsearch OTU table heatmaps), Galaxy needs to be
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104 configured not to sanitize the outputs from the ``Amplicon_analysis``
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105 tool.
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106
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107 Either:
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108
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109 * **For local instances:** set ``sanitize_all_html = False`` in
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110 ``config/galaxy.ini`` (nb don't do this on production servers or
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111 public instances!); or
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112
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113 * **For production instances:** add the ``Amplicon_analysis`` tool
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114 to the display whitelist in the Galaxy instance:
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115
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116 - Set ``sanitize_whitelist_file = config/whitelist.txt`` in
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117 ``config/galaxy.ini`` and restart Galaxy;
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118 - Go to ``Admin>Manage Display Whitelist``, check the box for
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119 ``Amplicon_analysis`` (hint: use your browser's 'find-in-page'
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120 search function to help locate it) and click on
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121 ``Submit new whitelist`` to update the settings.
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122
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123 Additional details
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124 ==================
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125
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126 Some other things to be aware of:
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127
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128 * Note that using the Silva database requires a minimum of 18Gb RAM
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129
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130 Known problems
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131 ==============
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132
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133 * Only the ``VSEARCH`` pipeline in Mauro's script is currently
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134 available via the Galaxy tool; the ``USEARCH`` and ``QIIME``
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135 pipelines have yet to be implemented.
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136 * The images in the tool help section are not visible if the
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137 tool has been installed locally, or if it has been installed in
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138 a Galaxy instance which is served from a subdirectory.
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139
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140 These are both problems with Galaxy and not the tool, see
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141 https://github.com/galaxyproject/galaxy/issues/4490 and
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142 https://github.com/galaxyproject/galaxy/issues/1676
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143
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144 Appendix: installing the dependencies manually
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145 ==============================================
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146
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147 If the tool is installed from the Galaxy toolshed (recommended) then
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148 the dependencies should be installed automatically and this step can
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149 be skipped.
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150
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151 Otherwise the ``install_amplicon_analysis_deps.sh`` script can be used
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152 to fetch and install the dependencies locally, for example::
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153
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154 install_amplicon_analysis.sh /path/to/local_tool_dependencies
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155
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156 (This is the same script as is used to install dependencies from the
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157 toolshed.) This can take some time to complete, and when completed will
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158 have created a directory called ``Amplicon_analysis-1.2.3`` containing
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159 the dependencies under the specified top level directory.
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160
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161 **NB** The installed dependencies will occupy around 2.6G of disk
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162 space.
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163
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164 You will need to make sure that the ``bin`` subdirectory of this
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165 directory is on Galaxy's ``PATH`` at runtime, for the tool to be able
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166 to access the dependencies - for example by adding a line to the
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167 ``local_env.sh`` file like::
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168
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169 export PATH=/path/to/local_tool_dependencies/Amplicon_analysis-1.2.3/bin:$PATH
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170
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171 History
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172 =======
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173
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174 ========== ======================================================================
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175 Version Changes
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176 ---------- ----------------------------------------------------------------------
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177 1.3.5.0 Updated to Amplicon_Analysis_Pipeline version 1.3.5.
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178 1.2.3.0 Updated to Amplicon_Analysis_Pipeline version 1.2.3; install
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179 dependencies via tool_dependencies.xml.
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180 1.2.2.0 Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
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181 jackknifed analysis which is not captured by Galaxy tool)
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182 1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds
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183 option to use the Human Oral Microbiome Database v15.1, and
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184 updates SILVA database to v123)
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185 1.1.0 First official version on Galaxy toolshed.
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186 1.0.6 Expand inline documentation to provide detailed usage guidance.
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187 1.0.5 Updates including:
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188
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189 - Capture read counts from quality control as new output dataset
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190 - Capture FastQC per-base quality boxplots for each sample as
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191 new output dataset
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192 - Add support for -l option (sliding window length for trimming)
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193 - Default for -L set to "200"
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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194 1.0.4 Various updates:
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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195
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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196 - Additional outputs are captured when a "Categories" file is
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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197 supplied (alpha diversity rarefaction curves and boxplots)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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198 - Sample names derived from Fastqs in a collection of pairs
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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199 are trimmed to SAMPLE_S* (for Illumina-style Fastq filenames)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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200 - Input Fastqs can now be of more general ``fastq`` type
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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201 - Log file outputs are captured in new output dataset
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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202 - User can specify a "title" for the job which is copied into
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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203 the dataset names (to distinguish outputs from different runs)
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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204 - Improved detection and reporting of problems with input
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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205 Metatable
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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206 1.0.3 Take the sample names from the collection dataset names when
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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207 using collection as input (this is now the default input mode);
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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208 collect additional output dataset; disable ``usearch``-based
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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209 pipelines (i.e. ``UPARSE`` and ``QIIME``).
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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210 1.0.2 Enable support for FASTQs supplied via dataset collections and
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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211 fix some broken output datasets.
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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212 1.0.1 Initial version
098ad1dd7760 planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
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213 ========== ======================================================================