diff STACKS_prepare_population_map.xml @ 0:d6ba40f6c824

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+<tool id="STACKSpreparepopmap" name="STACKS : Prepare population map file " >
+  <description>for STACKS denovomap and refmap</description>
+
+<configfiles>
+<configfile name="fastq_files">
+#for $input in $fastq_file:
+${input.display_name}::${input}
+#end for
+</configfile>
+<configfile name="sam_files">
+#if str( $options_target.options_target_selector ) == "refmap":
+#for $input in $options_target.sam_file:
+${input.display_name}::${input}
+#end for
+#end if
+</configfile>
+</configfiles>  
+
+<command interpreter="python">
+STACKS_prepare_population_map.py
+-f $fastq_files
+#if str( $options_target.options_target_selector ) == "refmap":
+-s $sam_files
+#end if
+-t $info_file
+-o $output
+-d $__new_file_path__
+</command>
+
+<inputs>	
+<conditional name="options_target">
+	<param name="options_target_selector" type="select" label="Select your target">
+		<option value="denovo" selected="true">STACKS De Novo map</option>
+		<option value="refmap">STACKS Reference map</option>
+	</param>
+	<when value="denovo">
+	</when>
+	<when value="refmap">
+		<param name="sam_file" format="sam,zip,tar.gz" type="data" multiple="true" label="SAM files generated by your alignment" help="SAM/ZIP/TAR.GZ files." />
+	</when>
+
+</conditional>
+	<param name="fastq_file" format="fastq,fasta,zip,tar.gz" type="data" multiple="true" label="Fastq files generated by STACKS : Process radtags tool" help="FASTQ/FASTA/ZIP/TAR.GZ files." />
+	<param name="info_file" format="tabular,txt" type="data" label="File with population information" help="File looks like : barcode TAB population " />		
+		
+
+</inputs>
+<outputs>
+
+    <data format="tabular" name="output" label="population_map.txt with ${tool.name} on ${on_string}" />
+
+</outputs>
+<help>
+
+.. class:: infomark
+
+**What it does**
+
+This program will prepare a population map dataset from a 2 columns file containing relation between barcode and population. 
+
+--------
+
+**Created by:**
+
+Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko
+
+--------
+
+**Example:**
+
+Input files:
+
+- FASTQ, FASTA, zip, tar.gz
+
+
+- File with population informations:
+
+This file must have exactly 2 columns, separated by a tab, the first with barcode, second with population name or ID ::
+
+	CGATA	pop1
+	CGGCG	pop1
+	GAAGC	pop1
+	GAGAT	pop1
+	CGATA	pop2 
+	CGGCG	pop2
+	GAAGC	pop2
+	GAGAT	pop2
+
+
+Output file:
+
+- Population map::
+
+    indv_01    1
+    indv_02    1
+    indv_03    1
+    indv_04    2
+    indv_05    2
+    indv_06    2
+
+WARNING : the file name in the population map output may be different from the history file name. Don't worry about this, it's safe.
+
+
+Instructions to add the functionality of archives management in Galaxy on the `eBiogenouest HUB wiki &lt;https://www.e-biogenouest.org/wiki/ManArchiveGalaxy&gt;`_ .
+
+--------
+
+**Project links:**
+
+`STACKS website &lt;http://creskolab.uoregon.edu/stacks/&gt;`_ .
+
+`STACKS manual &lt;http://creskolab.uoregon.edu/stacks/stacks_manual.pdf&gt;`_ .
+
+`STACKS google group &lt;https://groups.google.com/forum/#!forum/stacks-users&gt;`_ .
+
+--------
+
+**References:**
+
+-J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013.
+
+-J. Catchen, S. Bassham, T. Wilson, M. Currey, C. O'Brien, Q. Yeates, and W. Cresko. The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Molecular Ecology. 2013.
+
+-J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1:171-182, 2011.
+
+-A. Amores, J. Catchen, A. Ferrara, Q. Fontenot and J. Postlethwait. Genome evolution and meiotic maps by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication. Genetics, 188:799'808, 2011.
+
+-P. Hohenlohe, S. Amish, J. Catchen, F. Allendorf, G. Luikart. RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow trout and westslope cutthroat trout. Molecular Ecology Resources, 11(s1):117-122, 2011.
+
+-K. Emerson, C. Merz, J. Catchen, P. Hohenlohe, W. Cresko, W. Bradshaw, C. Holzapfel. Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Science, 107(37):16196-200, 2010.
+
+--------
+
+**Integrated by:**
+
+Yvan Le Bras and Cyril Monjeaud 
+
+GenOuest Bio-informatics Core Facility
+
+UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)
+
[e-mail]
+
+If you use this tool in Galaxy, please cite :
+
+`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_
+
+
+</help>
+<citations>
+    <citation type="doi">10.1111/mec.12354</citation>
+    <citation type="doi">10.1111/mec.12330</citation>
+    <citation type="doi">10.1534/g3.111.000240</citation>
+    <citation type="doi">10.1534/genetics.111.127324</citation>
+    <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation>
+    <citation type="doi">10.1073/pnas.1006538107</citation>
+
+    <citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
+    author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
+    title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
+    booktitle = {JOBIM 2013 Proceedings},
+    year = {2013},
+    url = {https://www.e-biogenouest.org/resources/128},
+    pages = {97-106}
+    }</citation>
+</citations>
+</tool>
+