Mercurial > repos > frogs > frogs_2_0_0
diff tsv_to_biom.xml @ 0:76c750c5f0d1 draft default tip
planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
| author | frogs |
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| date | Thu, 25 Oct 2018 05:01:13 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tsv_to_biom.xml Thu Oct 25 05:01:13 2018 -0400 @@ -0,0 +1,145 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2016 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<tool id="FROGS_tsv_to_biom" name="FROGS TSV_to_BIOM" version="2.0.0"> + <description>Converts a TSV file in a BIOM file.</description> + <requirements> + <requirement type="package" version="2.0.1">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + tsv_to_biom.py + --input-tsv $tsv_file + --output-biom $biom_file + #if $multi_affi_file + --input-multi-affi $multi_affi_file + #end if + #if $extract_fasta + --output-fasta $sequence_file + #end if + </command> + <inputs> + <!-- Files --> + <param format="tabular" name="tsv_file" type="data" label="Abundance TSV File" help="Your FROGS abundance TSV file. Take care to keep original column names." optional="false"/> + <param format="tabular" name="multi_affi_file" type="data" label="Multi_hits TSV File" help="TSV file describing multi_hit blast results." optional="true" /> + <!-- Parameters --> + <param name="extract_fasta" type="boolean" label="Extract seeds in FASTA file" help="If there is a 'seed_sequence' column in your TSV table, you can extract seed sequences in a separated FASTA file." /> + </inputs> + <outputs> + <data format="biom1" name="biom_file" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" /> + <data format="fasta" name="sequence_file" label="${tool.name}: sequences.fasta" from_work_dir="seed.fasta" > + <filter>extract_fasta</filter> + </data> + </outputs> + <tests> + <test> + <param name="tsv_file" value="references/07-biom2tsv.tsv" /> + <param name="multi_affi_file" value="references/07-biom2tsv.multi" /> + <param name="extract_fasta" value="true"/> + <output name="biom_file" file="references/09-tsv2biom.biom" compare="sim_size" delta="0"/> + <output name="sequence_file" file="references/09-tsv2biom.fasta" /> + </test> + </tests> + <help> +.. image:: static/images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +This tool converts a TSV file in a BIOM file. + +.. class:: h3 + +Inputs + +**Abundance file**: + +The table with abundances each cluster in each sample and other details conerning the cluster (format TSV). + +Authorised column names : rdp_tax_and_bootstrap, blast_taxonomy, blast_subject, blast_perc_identity, blast_perc_query_coverage, blast_evalue, blast_aln_length, seed_id, seed_sequence, observation_name, observation_sum + +**Multiple affiliation file**: + +The file that stores the multiple blast hits. + +.. class:: h3 + +Outputs + +**Abundance file**: + + The abundance of each cluster in each sample and their metadata (format `BIOM <http://biom-format.org/>`_). + +**Sequence file [optional]**: + + By checking the "Extract seed FASTA file" option, the sequences will be extract from TSV to create a file in `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_ format. + For this option, be sure that your TSV file contains the seed_sequence column. + + +.. class:: infomark page-header h2 + +How it works + +FROGS TSV_to_BIOM detects any metadata (columns before "observation_name") and names of samples (columns after "observation_sum"). + +Then it reconstructs the BIOM abundance file : for each "observation_name" it adds the associated metadata and the count of samples. + +If blast_taxonomy is included in metadata and if blast_subject is equal to "multi-subject", it parses multi_hit TSV file. Then it extracts the list of blast_affiliations that contains the non ambiguous blast_taxonomy. + + + +.. class:: infomark page-header h2 + +Advices + +This tool is usefull if you have modified your abundance TSV file and that you want to generate rarefaction curve or sunburst with the FROGS affiliation_stat tool. + +If you modify your abundance TSV file + + * -do not modify column names + * -do not remove columns + * -take care to choose a taxonomy available in your multi_hit TSV file + * -if you delete lines of the multi_hit file, take care to not remove a complete cluster whithout removing all "multi tags" in you abundance TSV file. + * -if you want to rename a taxon level (ex : genus "Ruminiclostridium 5;" to genus "Ruminiclostridium;"), do not forget to modify also your multi_hit TSV file. + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + <citation type="doi">10.1128/AEM.01043-13</citation> + <citation type="doi">10.14806/ej.17.1.200</citation> + <citation type="doi">10.1093/bioinformatics/btr507</citation> + </citations> + +</tool>