Mercurial > repos > abims-sbr > concatphyl
changeset 10:5cae58aa1181 draft default tip
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
| author | lecorguille |
|---|---|
| date | Mon, 24 Sep 2018 03:59:21 -0400 |
| parents | ff1a3a790363 |
| children | |
| files | ConcatPhyl.xml macros.xml |
| diffstat | 2 files changed, 8 insertions(+), 17 deletions(-) [+] |
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--- a/ConcatPhyl.xml Tue Jul 03 10:55:20 2018 -0400 +++ b/ConcatPhyl.xml Mon Sep 24 03:59:21 2018 -0400 @@ -160,12 +160,12 @@ <param name="out" type="select" label="What format of file do you want for your output (concatenation of the sequences) ? "> <option value="nothing">No output</option> - <option value="fasta">Fasta format</option> + <option value="fasta" selected="true">Fasta format</option> <option value="phylip">Phylip format</option> <option value="nexus">Nexus format</option> </param> - <param name="raxml1" type="boolean" label="Do you want the output of RAxML : best tree ? " /> + <param name="raxml1" type="boolean" checked="True" label="Do you want the output of RAxML : best tree ? " /> <param name="raxml3" type="boolean" label="Do you want the output of RAxML : bi-partition ? " /> <param name="raxml4" type="boolean" label="Do you want the output of RAxML : bootstrap ? " help="Only if the option 'rapid bootsptrap' is chosen. When you don't want to choose your options, this output is accessible"/> @@ -285,18 +285,6 @@ <![CDATA[ -.. class:: infomark - -**Authors** -The run RAxML was written by Alexandros Stamatakis. -The script was written by Eric Fontanillas. - -.. class:: infomark - -**Galaxy integration** by Julie Baffard and ABiMS team. - --------- - **Description** This tool takes files containing fasta sequences (from the CDS_Search in the AdaptSearch suite) and run RAxML to build a phylogeny. @@ -413,6 +401,8 @@ </help> - <expand macro="citations" /> + <citations> + <citation type="doi">10.1093/bioinformatics/btu033</citation> + </citations> </tool>
--- a/macros.xml Tue Jul 03 10:55:20 2018 -0400 +++ b/macros.xml Mon Sep 24 03:59:21 2018 -0400 @@ -7,13 +7,14 @@ <token name="@HELP_AUTHORS@"> .. class:: infomark -**Authors** Eric Fontanillas creates the scripts of this pipeline. +**Authors** Eric Fontanillas created the version 1 of this pipeline. Victor Mataigne developped version 2. .. class:: infomark -**Galaxy integration** ABiMS TEAM +**Galaxy integration** Julie Baffard and ABiMS TEAM, Roscoff Marine Station | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. + | Credits : Gildas le Corguillé, Misharl Monsoor ---------------------------------------------------