Mercurial > repos > frogs > frogs_3_1_0
diff affiliations_stat.xml @ 0:59bc96331073 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
| author | frogs |
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| date | Thu, 28 Feb 2019 10:14:49 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/affiliations_stat.xml Thu Feb 28 10:14:49 2019 -0500 @@ -0,0 +1,175 @@ +<?xml version="1.0"?> +<!-- +# Copyright (C) 2015 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_affiliations_stat" name="FROGS Affiliations stat" version="3.1"> + <description>Process some metrics on taxonomies.</description> + <requirements> + <requirement type="package" version="3.1.0">frogs</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <command> + affiliations_stat.py + --input-biom $biom + --output-file $summary_file + --rarefaction-ranks $rarefaction_ranks + #if $affiliation.affiliation_type == "FROGS_blast" + --taxonomic-ranks Domain Phylum Class Order Family Genus Species + --multiple-tag "blast_affiliations" + --tax-consensus-tag "blast_taxonomy" + --identity-tag "perc_identity" + --coverage-tag "perc_query_coverage" + #else if $affiliation.affiliation_type == "FROGS_rdp" + --taxonomic-ranks Domain Phylum Class Order Family Genus Species + --taxonomy-tag "rdp_taxonomy" + --bootstrap-tag "rdp_bootstrap" + #else + --taxonomic-ranks $affiliation.taxonomic_ranks + --taxonomy-tag "$affiliation.taxonomy_tag" + #if $affiliation.bootstrap_tag + --bootstrap-tag "$affiliation.bootstrap_tag" + #end if + #if $affiliation.identity_tag and $affiliation.coverage_tag + --identity-tag "$affiliation.identity_tag" + --coverage-tag "$affiliation.coverage_tag" + #end if + #end if + </command> + <inputs> + <!-- Files --> + <param format="biom1" name="biom" type="data" label="Abundance file" help="OTUs abundances and affiliations (format: BIOM)." optional="false" /> + <!-- Parameters --> + <param name="rarefaction_ranks" type="text" label="Rarefaction ranks" help="The ranks that will be evaluated in rarefaction. Each rank is separated by one space." optional="false" value="Class Order Family Genus Species" size="80" /> + <conditional name="affiliation"> + <param name="affiliation_type" type="select" label="Affiliation processed" help="Select the type of affiliation processed. If your affiliation has been processed with an external tool: use 'Custom'."> + <option value="FROGS_blast" selected="true">FROGS blast</option> + <option value="FROGS_rdp">FROGS rdp</option> + <option value="custom">Custom</option> + </param> + <when value="FROGS_blast"></when> + <when value="FROGS_rdp"></when> + <when value="custom"> + <param name="taxonomic_ranks" type="text" label="Taxonomic ranks" help="The ordered taxonomic ranks levels stored in BIOM. Each rank is separated by one space." optional="false" value="Domain Phylum Class Order Family Genus Species" size="80" /> + <param name="taxonomy_tag" type="text" label="Taxonomy tag" help="The metadata title in BIOM for the taxonomy." optional="false" value="taxonomy" size="20" /> + <param name="bootstrap_tag" type="text" label="Bootstrap tag" help="The metadata title in BIOM for the taxonomy bootstrap." value="" size="20" /> + <param name="identity_tag" type="text" label="Identity tag" help="The metadata tag used in BIOM file to store the alignment identity." value="" size="20" /> + <param name="coverage_tag" type="text" label="Coverage tag" help="The metadata tag used in BIOM file to store the alignment OTUs coverage." value="" size="20" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="html" name="summary_file" label="${tool.name}: summary.html" from_work_dir="summary.html"/> + </outputs> + <tests> + <test> + <param name="biom" value="references/06-affiliation.biom" /> + <param name="rarefaction_ranks" value="Family Genus Species" /> + <conditional name="affiliation"> + <param name="affiliation_type" value="FROGS_blast" /> + <param name="taxonomic_ranks" value="Domain Phylum Class Order Family Genus Species" /> + <param name="taxonomy_tag" value="blast_taxonomy" /> + <param name="identity_tag" value="perc_identity" /> + <param name="coverage_tag" value="perc_query_coverage" /> + <!-- pas de parametre dans le formulaire pour multiple-tag, uniquement une option dans la ligne de commande --> + </conditional> + <output name="summary_file" file="references/09-affiliationsStat.html" compare="sim_size" delta="0" /> + <!-- log-file option presente dans la ligne de commande dans le test.sh n'apparait pas du tout ici --> + </test> + </tests> + <help> + +.. image:: static/images/frogs_images/FROGS_logo.png + :height: 144 + :width: 110 + + +.. class:: infomark page-header h2 + +What it does + +FROGS Affiliations stat computes several metrics and generates a HTML file describing OTUs based on their taxonomies and the quality of the affiliations. + + +.. class:: infomark page-header h2 + +Input/output + +.. class:: h3 + +Input + +**Abundance file**: + +The abundance and affiliation of each OTUs in each sample (format `BIOM <http://biom-format.org/>`_). This file can be produced by FROGS Affiliation OTU. + +The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format. + +.. class:: h3 + +Output + +**Summary file** (summary.html): + + OTUs taxonomies and affiliations metrics (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + + *-Taxonomy distribution*: display the distribution of each taxon and the rarefaction for each taxonomic rank and for each sample + + .. image:: static/images/frogs_images/FROGS_affiliation_stat_taxonomies.png + :height: 380 + :width: 650 + + .. image:: static/images/frogs_images/FROGS_affiliation_stat_rarefaction.png + :height: 380 + :width: 550 + + .. image:: static/images/frogs_images/FROGS_affiliation_stat_sunburst.png + :height: 380 + :width: 430 + + -Bootstrap distribution: display for affiliation methods with bootstrap the bootstrap on each taxonomic rank + + .. image:: static/images/frogs_images/FROGS_affiliation_stat_bootstrap.png + :height: 380 + :width: 650 + + -Alignment distribution: display for affiliation methods with alignment the distribution of identity/covrage + + .. image:: static/images/frogs_images/FROGS_affiliation_stat_alignment.png + :height: 380 + :width: 650 + + + +---- + +**Contact** + +Contacts: frogs@inra.fr + +Repository: https://github.com/geraldinepascal/FROGS +website: http://frogs.toulouse.inra.fr/ + +Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.* + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx791</citation> + </citations> + +</tool>