Mercurial > repos > iuc > qiime_make_otu_table
comparison make_otu_table.xml @ 0:e00b6983b175 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit d41cdeeec9fd0eb5612df0d5af63a979d1c9ec87
author | iuc |
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date | Mon, 10 Jul 2017 16:39:15 -0400 |
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1 <tool id="qiime_make_otu_table" name="Make OTU table" version="@WRAPPER_VERSION@.0"> | |
2 <description>Make an OTU table from an OTU map and a taxonomy assignment file</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <version_command>make_otu_table.py --version</version_command> | |
8 <command detect_errors="aggressive"><![CDATA[ | |
9 make_otu_table.py | |
10 --otu_map_fp '$otu_map_fp' | |
11 --output_biom_fp '$output_biom_fp' | |
12 #if $taxonomy | |
13 --taxonomy '$taxonomy' | |
14 #end if | |
15 #if $exclude_otus_fp | |
16 --exclude_otus_fp '$exclude_otus_fp' | |
17 #end if | |
18 #if $mapping_fp | |
19 --mapping_fp '$mapping_fp' | |
20 #end if | |
21 ]]></command> | |
22 <inputs> | |
23 <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" /> | |
24 <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" /> | |
25 <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)" /> | |
26 <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" /> | |
27 </inputs> | |
28 <outputs> | |
29 <data name="output_biom_fp" format="biom1" label="${tool.name} on ${on_string}: OTU table (biom format)"/> | |
30 </outputs> | |
31 <tests> | |
32 <!-- Qiime make_otu_table.py generates a binary file that can't be compared directly with diff --> | |
33 <!-- In addition, the files generated by 2 different executions of make_otu_table with the same input data are different --> | |
34 <!-- As a consequence, standard comparisons based on "diff" or md5 checksums/SHA hash are impossible --> | |
35 <!-- The following tests are then based on a comparison of file sizes with a maximum delta of 0 bytes --> | |
36 <test> | |
37 <param name="otu_map_fp" value="make_otu_table/otu_map.txt" /> | |
38 <param name="taxonomy" value="make_otu_table/tax_assignments.txt" /> | |
39 <param name="exclude_otus_fp" value="make_otu_table/chimeric_seqs.txt" /> | |
40 <param name="mapping_fp" value="make_otu_table/mapping_file.txt" /> | |
41 <output name="output_biom_fp" file="make_otu_table/OTU_table_chimeric.biom" compare="sim_size" /> | |
42 </test> | |
43 <test> | |
44 <param name="otu_map_fp" value="make_otu_table/otu_map.txt" /> | |
45 <param name="taxonomy" value="make_otu_table/tax_assignments.txt" /> | |
46 <param name="exclude_otus_fp" value="make_otu_table/pynast_failures.fna" /> | |
47 <param name="mapping_fp" value="make_otu_table/mapping_file.txt" /> | |
48 <output name="output_biom_fp" file="make_otu_table/OTU_table_pynast.biom" compare="sim_size" /> | |
49 </test> | |
50 </tests> | |
51 <help><![CDATA[ | |
52 **What it does** | |
53 | |
54 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 | |
55 sample, and adds the taxonomic predictions for each OTU in the last column if a taxonomy file is supplied. | |
56 | |
57 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 | |
58 Samples and rows correspond to OTUs and the number of times a sample appears in a particular OTU. | |
59 | |
60 More information about this tool is available on | |
61 `QIIME documentation <http://qiime.org/scripts/make_otu_table.html>`_. | |
62 ]]></help> | |
63 <citations> | |
64 <expand macro="citations"/> | |
65 </citations> | |
66 </tool> |