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author | iuc |
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date | Mon, 10 Jul 2017 16:39:15 -0400 |
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<tool id="qiime_make_otu_table" name="Make OTU table" version="@WRAPPER_VERSION@.0"> <description>Make an OTU table from an OTU map and a taxonomy assignment file</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <version_command>make_otu_table.py --version</version_command> <command detect_errors="aggressive"><![CDATA[ make_otu_table.py --otu_map_fp '$otu_map_fp' --output_biom_fp '$output_biom_fp' #if $taxonomy --taxonomy '$taxonomy' #end if #if $exclude_otus_fp --exclude_otus_fp '$exclude_otus_fp' #end if #if $mapping_fp --mapping_fp '$mapping_fp' #end if ]]></command> <inputs> <param argument="--otu_map_fp" type="data" format="tabular,txt,biom" label="OTU map" help="An OTU map file generated by the pick_otus.py script" /> <param argument="--taxonomy" type="data" format="txt" optional="True" label="Taxonomy assignment" help="Text file generated by the assign_taxonomy.py script and contains the assignments of taxons to sequences" /> <param argument="--exclude_otus_fp" type="data" format="tabular,fasta,txt" optional="True" label="List of OTU identifiers to reject" help="A text file listing OTU identifiers that should not be included in the OTU table (generated by the identify_chimeric_seqs.py script) or a failure file in fasta format (generated by the align_seqs.py script)" /> <param argument="--mapping_fp" type="data" format="tabular,txt" optional="True" label="Validated mapping file" help="A mapping file in tabular format verified by the validate_mapping_file.py script" /> </inputs> <outputs> <data name="output_biom_fp" format="biom1" label="${tool.name} on ${on_string}: OTU table (biom format)"/> </outputs> <tests> <!-- Qiime make_otu_table.py generates a binary file that can't be compared directly with diff --> <!-- In addition, the files generated by 2 different executions of make_otu_table with the same input data are different --> <!-- As a consequence, standard comparisons based on "diff" or md5 checksums/SHA hash are impossible --> <!-- The following tests are then based on a comparison of file sizes with a maximum delta of 0 bytes --> <test> <param name="otu_map_fp" value="make_otu_table/otu_map.txt" /> <param name="taxonomy" value="make_otu_table/tax_assignments.txt" /> <param name="exclude_otus_fp" value="make_otu_table/chimeric_seqs.txt" /> <param name="mapping_fp" value="make_otu_table/mapping_file.txt" /> <output name="output_biom_fp" file="make_otu_table/OTU_table_chimeric.biom" compare="sim_size" /> </test> <test> <param name="otu_map_fp" value="make_otu_table/otu_map.txt" /> <param name="taxonomy" value="make_otu_table/tax_assignments.txt" /> <param name="exclude_otus_fp" value="make_otu_table/pynast_failures.fna" /> <param name="mapping_fp" value="make_otu_table/mapping_file.txt" /> <output name="output_biom_fp" file="make_otu_table/OTU_table_pynast.biom" compare="sim_size" /> </test> </tests> <help><![CDATA[ **What it does** The script `make_otu_table.py <http://qiime.org/scripts/make_otu_table.html>`_ tabulates the number of times an OTU is found in each sample, and adds the taxonomic predictions for each OTU in the last column if a taxonomy file is supplied. The output of `make_otu_table.py <http://qiime.org/scripts/make_otu_table.html>`_ is a `biom file <http://biom-format.org/>`_, where the columns correspond to Samples and rows correspond to OTUs and the number of times a sample appears in a particular OTU. More information about this tool is available on `QIIME documentation <http://qiime.org/scripts/make_otu_table.html>`_. ]]></help> <citations> <expand macro="citations"/> </citations> </tool>