diff tsv_to_biom.xml @ 0:59bc96331073 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tsv_to_biom.xml	Thu Feb 28 10:14:49 2019 -0500
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+<?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="3.1">
+	<description>Converts a TSV file in a BIOM file.</description>
+        <requirements>
+                <requirement type="package" version="3.1.0">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/10-biom2tsv.tsv" />
+			<param name="multi_affi_file" value="references/10-biom2tsv-affiliation_multihit.tsv" />
+			<param name="extract_fasta" value="true"/>
+			<output name="biom_file" file="references/12-tsv2biom.biom" compare="sim_size" delta="0"/>
+			<output name="sequence_file" file="references/12-tsv2biom.fasta" />
+		</test>
+	</tests>
+	<help>
+.. image:: static/images/frogs_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 &lt;http://biom-format.org/&gt;`_).
+
+**Sequence file [optional]**:
+
+ By checking the "Extract seed FASTA file" option, the sequences will be extract from TSV to create a file in `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_ 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: [e-mail]
+
+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>