# HG changeset patch # User ppericard # Date 1592956655 14400 # Node ID d0b77b92686383a66176ea7756c5fb17d7ecb20c "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty" diff -r 000000000000 -r d0b77b926863 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +our General Public Licenses are intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + Developers that use our General Public Licenses protect your rights +with two steps: (1) assert copyright on the software, and (2) offer +you this License which gives you legal permission to copy, distribute +and/or modify the software. + + A secondary benefit of defending all users' freedom is that +improvements made in alternate versions of the program, if they +receive widespread use, become available for other developers to +incorporate. Many developers of free software are heartened and +encouraged by the resulting cooperation. However, in the case of +software used on network servers, this result may fail to come about. +The GNU General Public License permits making a modified version and +letting the public access it on a server without ever releasing its +source code to the public. + + The GNU Affero General Public License is designed specifically to +ensure that, in such cases, the modified source code becomes available +to the community. It requires the operator of a network server to +provide the source code of the modified version running there to the +users of that server. Therefore, public use of a modified version, on +a publicly accessible server, gives the public access to the source +code of the modified version. + + An older license, called the Affero General Public License and +published by Affero, was designed to accomplish similar goals. This is +a different license, not a version of the Affero GPL, but Affero has +released a new version of the Affero GPL which permits relicensing under +this license. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU Affero General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based +on the Program. + + To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + + A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + + The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + + The Corresponding Source for a work in source code form is that +same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + + When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + + A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + + If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + + The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + + All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + + If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + + A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Remote Network Interaction; Use with the GNU General Public License. + + Notwithstanding any other provision of this License, if you modify the +Program, your modified version must prominently offer all users +interacting with it remotely through a computer network (if your version +supports such interaction) an opportunity to receive the Corresponding +Source of your version by providing access to the Corresponding Source +from a network server at no charge, through some standard or customary +means of facilitating copying of software. This Corresponding Source +shall include the Corresponding Source for any work covered by version 3 +of the GNU General Public License that is incorporated pursuant to the +following paragraph. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the work with which it is combined will remain governed by version +3 of the GNU General Public License. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU Affero General Public License from time to time. Such new versions +will be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU Affero General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU Affero General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU Affero General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero 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 Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff -r 000000000000 -r d0b77b926863 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,70 @@ +# galaxy-mixomics-blocksplsda +Galaxy wrappers for the block.splsda, plotIndiv and plotVar functions from the mixOmics R package + +# Install for developers + +Clone repository + +``` +$ git clone --recurse-submodules https://gitlab.com/bilille/galaxy-mixomics-blocksplsda.git +``` + +Add `galaxy-mixomics-blocksplsda` repository to `$GALAXYDIR/tools` directory. + +Edit `$GALAXYDIR/config/tool_conf.xml` and add: + +``` +
+
+``` + +# Preparing Galaxy conda manual environment for visCorVar + +Activate Galaxy self-installed conda (for your shell; bash here) and reload terminal + +``` +$ . $GALAXYDIR/database/dependencies/_conda/bin/conda init bash +``` + +Create and activate conda environment for visCorVar package + +``` +$ conda create --name __viscorvar@0.1 && conda activate __viscorvar@0.1 +``` + +Install dependencies + +``` +$ conda install bioconductor-mixomics r-rdpack r-igraph +``` + +Manually install visCorVar package from repository + +``` +$ R + +> install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.1.tar.gz", repos=NULL) +> library(visCorVar) +``` + + + + + + + + + + + + + + diff -r 000000000000 -r d0b77b926863 additional_functions_block_splsda.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/additional_functions_block_splsda.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,104 @@ +#' @title Check if a block contains missing values +#' @description Check if a block contains missing values +#' @param list_X type : list of matrix. This list is used to perform the data integration. +#' @details This function checks if a block contains missing values. +#' @return type : boolean. If at least one block contains missing values, +#' this function returns TRUE, otherwise this function returns FALSE. +#' @examples +#' X1 = matrix(1:9, nrow = 3, ncol = 3) +#' X2 = matrix(10:18, nrow = 3, ncol = 3) +#' list_X = list() +#' list_X[[1]] = X1 +#' list_X[[2]] = X2 +#' names(list_X) = c("X1", "X2") +#' boolean_block_missing_values = blockMissingValues(list_X) +#' @export +blockMissingValues <-function(list_X) +{ + name_blocks = names(list_X) + name_blocks_missing_values = c() + boolean_block_missing_values = FALSE + + for(i in 1:length(list_X)) + { + X_i = list_X[[i]] + name_block_i = name_blocks[i] + + vec = sapply(1:dim(X_i)[2], FUN = function(j){ + res = any(is.na(X_i[, j])) + + return(res) + }) + + if(any(vec)) + { + name_blocks_missing_values = c(name_blocks_missing_values, name_block_i) + + } + + } # End for(i in 1:length(list_X)). + + if(length(name_blocks_missing_values) != 0) + { + stop(paste("The data integration can not be performed if a block contains missing values : ", paste(name_blocks_missing_values, collapse = ", "), " contains missing values. ")) + boolean_block_missing_values = TRUE + + } + + return(boolean_block_missing_values) + +} + + +#' @title Determination of selected variables for all components +#' @description The function unionSelectBlockVariables determines, for each block, the selected block variables +#' for all components. +#' @param res_block_splsda type : sgccda. This parameter is the output of block.splsda function +#' mixOmics. +#' @details For each block, the function unionSelectBlockVariables returns 1 if the block variable is selected for +#' at least one component. Otherwise, this function returns 0. +#' @return type : list of matrix. For each block, if the block variable is selected, the value 1 is associated with +#' this block variable. Otherwise the value 0 is associated with this block variable. +#' @examples +#' data(res_data_integration) +#' list_union_selected_block_variables = unionSelectBlockVariables(res_data_integration) +#' @export +unionSelectBlockVariables <-function(res_block_splsda) +{ + ncomp = res_block_splsda$ncomp[1] + + names_blocks = names(res_block_splsda$loadings) + index_Y = which(names_blocks == "Y") + names_blocks = names_blocks[ - index_Y] + list_select_block_variables = list() + + for(i in 1:length(names_blocks)) + { + mat_loadings_i = res_block_splsda$loadings[[i]] + index_i = c() + + for(j in 1:ncomp) + { + loadings_i_j = mat_loadings_i[, j] + index_i_j = which(loadings_i_j != 0) + + index_i = c(index_i, index_i_j) + + } # End for(j 1:ncomp). + + index_i = unique(index_i) + + mat_select_block_variables = matrix(0, + nrow = dim(mat_loadings_i)[1], + ncol = 1) + mat_select_block_variables[index_i, 1] = rep(1, length(index_i)) + rownames(mat_select_block_variables) = rownames(mat_loadings_i) + + list_select_block_variables[[i]] = mat_select_block_variables + + } # End for(i in 1:length(names_blocks)). + + names(list_select_block_variables) = names_blocks + + return(list_select_block_variables) +} diff -r 000000000000 -r d0b77b926863 circleCor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circleCor.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,84 @@ + + + plots a correlation circle for the datasets whose correlation circles can be superimposed. This correlation circle contains the selected variables of these datasets which are included in a rectangle and the response variables. + + + bioconductor-mixomics + + r-argparse + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r d0b77b926863 circleCor_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circleCor_wrapper.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,131 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the circleCor function') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--blocks_vec', dest='blocks_vec', required=TRUE, help="Blocks vector") +parser$add_argument('--responses_var', dest='responses_var', required=TRUE, help="Responses variables") +parser$add_argument('--x_min', dest='x_min', type='double', required=TRUE, help="X min") +parser$add_argument('--x_max', dest='x_max', type='double', required=TRUE, help="X max") +parser$add_argument('--y_min', dest='y_min', type='double', required=TRUE, help="Y min") +parser$add_argument('--y_max', dest='y_max', type='double', required=TRUE, help="Y max") +parser$add_argument('--output_var', dest='output_var', required=TRUE, help="Output variables file") +parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") + +args <- parser$parse_args() + +## Print parameters +print("Input RData:") +print(args$input_rdata) +print("Blocks vector:") +print(args$blocks_vec) +print("Response variables:") +print(args$responses_var) +print("X min:") +print(args$x_min) +print("X max:") +print(args$x_max) +print("Y min:") +print(args$y_min) +print("Y max:") +print(args$y_max) +print("Output variables file:") +print(args$output_var) +print("Output PDF file:") +print(args$output_pdf) + +names_blocks = strsplit(args$blocks_vec, ",")[[1]] +names_response_variables = strsplit(args$responses_var, ",")[[1]] + +print("names_blocks:") +print(names_blocks) +print("names_response_variables:") +print(names_response_variables) + +## Loading libraries +# suppressPackageStartupMessages(require(ellipse)) +# suppressPackageStartupMessages(require(grDevices)) +# suppressPackageStartupMessages(require(RColorBrewer)) +# suppressPackageStartupMessages(require(mixOmics)) +## Loading local functions +# source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") +install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL) +suppressPackageStartupMessages(require(visCorVar)) +print("visCorVar has been loaded") + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +# Loading input Rdata file +# loads res_matCorAddVar object +load(args$input_rdata) + +mat_cor_comp1 = res_matCorAddVar$mat_cor_comp1 +mat_cor_comp2 = res_matCorAddVar$mat_cor_comp2 +cutoff_comp = res_matCorAddVar$cutoff_comp +comp = res_matCorAddVar$comp +list_vec_index_block_select = res_matCorAddVar$list_vec_index_block_select +list_vec_names_blocks = res_matCorAddVar$list_vec_names_blocks +list_cor_comp_selected_var_resp_var = res_matCorAddVar$list_cor_comp_selected_var_resp_var +res_compute_cor_var_interest = res_matCorAddVar$res_compute_cor_var_interest +res_block_splsda = res_matCorAddVar$res_block_splsda + +# +print("mat_cor_comp1:") +print(mat_cor_comp1) +print("mat_cor_comp2:") +print(mat_cor_comp2) +print("cutoff_comp:") +print(cutoff_comp) +print("comp:") +print(comp) +print("list_vec_index_block_select:") +print(list_vec_index_block_select) +print("list_vec_names_blocks:") +print(list_vec_names_blocks) +print("list_cor_comp_selected_var_resp_var:") +print(list_cor_comp_selected_var_resp_var) +print("res_compute_cor_var_interest:") +print(res_compute_cor_var_interest) + +# Open output pdf file +pdf(args$output_pdf, width=8, height=7) +mar = c(5, 5, 2, 8) +par(mar = mar) + +selected_variables = circleCor(list_dataframe_cor_comp_var_global = list_cor_comp_selected_var_resp_var, + list_vec_index_block_select = list_vec_index_block_select, + mat_cor_comp1 = mat_cor_comp1, + mat_cor_comp2 = mat_cor_comp2, + names_blocks = names_blocks, + names_response_variables = names_response_variables, + comp = comp, + cutoff = 0.85, + min.X = args$x_min, + max.X = args$x_max, + min.Y = args$y_min, + max.Y = args$y_max, + # vec_col = vec_col, + rad.in = 0.5, + cex = 0.7, + cex_legend = 0.8, + pos = c(1.2, 0), + pch = 20) + +dev.off() + +write(selected_variables, file=args$output_var, ncolumns=1) \ No newline at end of file diff -r 000000000000 -r d0b77b926863 computeMatSimilarity.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeMatSimilarity.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,39 @@ + + + performs the computation of the similarities. The similarity between two variables is an approximation of the correlation between these two variables. + + + bioconductor-mixomics + r-argparse + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r d0b77b926863 computeMatSimilarity_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeMatSimilarity_wrapper.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,53 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the computeMatSimilarity function') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file") + +args <- parser$parse_args() + +## Print parameters +print("Input RData:") +print(args$input_rdata) +print("Output RData:") +print(args$output_rdata) + +## Loading libraries +# suppressPackageStartupMessages(require(mixOmics)) + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +## Loading local functions +# source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") +install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL) +suppressPackageStartupMessages(require(visCorVar)) +print("visCorVar has been loaded") + +# Loading input Rdata file +# loads res_matCorAddVar object +load(args$input_rdata) + +# Run main function +res_compute_mat_similarity = computeMatSimilarity(res_matCorAddVar = res_matCorAddVar) + +liste_mat_similarity_group = res_compute_mat_similarity$liste_mat_similarity_group +res_matCorAddVar = res_compute_mat_similarity$res_matCorAddVar + +save(res_compute_mat_similarity, + file = args$output_rdata) \ No newline at end of file diff -r 000000000000 -r d0b77b926863 matCorAddVar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matCorAddVar.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,60 @@ + + + determine the correlation circles that can be overlaid and compute the correlations + + + bioconductor-mixomics + r-argparse + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r d0b77b926863 matCorAddVar_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matCorAddVar_wrapper.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,115 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Compute the matCorEtBlockSelect and addVariablesReponses functions') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--cutoff_comp', dest='cutoff_comp', type='double', required=TRUE, help="") +parser$add_argument('--interest_var_file', dest='interest_var_file', required=FALSE, help="Variables of interest file") +parser$add_argument('--block_Y_file', dest='block_Y_file', required=TRUE, help="Block Y filepath") +parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file") +parser$add_argument('--output_response_var', dest='output_response_var', required=TRUE, help="Output response variables file") +parser$add_argument('--output_blocks_comb', dest='output_blocks_comb', required=TRUE, help="Output blocks combinations file") + +args <- parser$parse_args() + +## Print parameters +print("Input RData:") +print(args$input_rdata) +print("Cutoff comp:") +print(args$cutoff_comp) +print("Variables of interest:") +print(args$interest_var_file) +print("Block Y file:") +print(args$block_Y_file) +print("Output RData:") +print(args$output_rdata) +print("Output Response variables:") +print(args$output_response_var) +print("Output Blocks combinations:") +print(args$output_blocks_comb) + +## Loading libraries +# source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") +install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL) +suppressPackageStartupMessages(require(visCorVar)) +print("visCorVar has been loaded") + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +# Loading input Rdata file +load(args$input_rdata) + +ncomp = mixomics_result$ncomp + +# Reading Block Y matrix +print("Reading Block Y") +mat_block_Y = read.table(args$block_Y_file, header=TRUE, row.names=1) +print(mat_block_Y) + +response_var = colnames(mat_block_Y) + +print("response_var:") +print(response_var) + +# Write response variables to output file +invisible(lapply(response_var, write, file=args$output_response_var, append=TRUE, ncolumns=1)) + +# Reading var of intereset file +interest_var_vec = NULL +if (args$interest_var_file != 'None') { + interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]]) +} + +# +comp = 1:2 + +# Running main function +res_matCorAddVar = matCorAddVar(res_block_splsda = mixomics_result, + block_Y = mat_block_Y, + cutoff_comp = args$cutoff_comp, + var_interest = interest_var_vec, + comp = comp) + +# +mat_cor_comp1 = res_matCorAddVar$mat_cor_comp1 +mat_cor_comp2 = res_matCorAddVar$mat_cor_comp2 +list_vec_index_block_select = res_matCorAddVar$list_vec_index_block_select +list_vec_names_blocks = res_matCorAddVar$list_vec_names_blocks +list_cor_comp_selected_var_resp_var = res_matCorAddVar$list_cor_comp_selected_var_resp_var +res_compute_cor_var_interest = res_matCorAddVar$res_compute_cor_var_interest + +# +print("mat_cor_comp1:") +print(mat_cor_comp1) +print("mat_cor_comp2:") +print(mat_cor_comp2) +print("list_vec_index_block_select:") +print(list_vec_index_block_select) +print("list_vec_names_blocks:") +print(list_vec_names_blocks) +print("list_cor_comp_selected_var_resp_var:") +print(list_cor_comp_selected_var_resp_var) +print("res_compute_cor_var_interest:") +print(res_compute_cor_var_interest) + +# Write all possible blocks combinations to output file +invisible(lapply(list_vec_names_blocks, write, file=args$output_blocks_comb, append=TRUE, ncolumns=100, sep=",")) + +# Save all objects in Rdata output file +save(res_matCorAddVar, + file = args$output_rdata) diff -r 000000000000 -r d0b77b926863 mixomics_blocksplsda.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_blocksplsda.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,268 @@ + + + performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis + + + bioconductor-mixomics + r-argparse + + + + + + + + + + + + + + + + + + +
+ + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1371/journal.pcbi.1005752 + + + \ No newline at end of file diff -r 000000000000 -r d0b77b926863 mixomics_blocksplsda_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_blocksplsda_script.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,233 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the mixOmics block.splsda function') + +parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE, + help="Block name + nb variables to select + data matrix file + variables metadata file") +parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE, + help="Samples metadata file") +parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer', + default=0, help="Sample description column number") +parser$add_argument('--ncomp', dest='ncomp', type='integer', default=2, + help="Number of components to include in the model") +parser$add_argument('--correlation', dest='correlation', action="store_true", + help="Add correlation between all blocks") +parser$add_argument('--scheme', dest='scheme', default="horst", help="Scheme") +parser$add_argument('--mode', dest='mode', default="regression", help="Mode") +parser$add_argument('--maxiter', dest='maxiter', type='integer', default=100, + help="Maximum number of iterations") +parser$add_argument('--scale', dest='scale', action="store_true", + help="Each block is standardized to zero means and unit variances") +parser$add_argument('--check_missing_values', dest='check_missing_values', action="store_true", + help="Check for missing values and raise an error") +parser$add_argument('--init', dest='init', default="svd", + help="Init (svd or svd.single)") +parser$add_argument('--tol', dest='tol', type='double', default=1e-06, + help="Convergence stopping value") +parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true", + help="Should be set in particular for data with many zero values") +parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file") +parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file") +parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory") + +args <- parser$parse_args() + +## Print parameters +print("Blocks:") +print(args$blocks_list) +print("Sample metadata file:") +print(args$sample_metadata_in) +print("Sample description column number:") +print(args$sample_description_col) +print("Number of components:") +print(args$ncomp) +print("Compute correlation between all blocks:") +print(args$correlation) +print("Scheme:") +print(args$scheme) +print("Mode:") +print(args$mode) +print("Max nb of iterations:") +print(args$maxiter) +print("Scale:") +print(args$scale) +print("Check for missing values:") +print(args$check_missing_values) +print("Tol:") +print(args$tol) +print("near.zero.var:") +print(args$nearzerovar) +print("Output Rdata file:") +print(args$rdata_out) +print("Output sample metadata file:") +print(args$sample_metadata_out) +print("Output variable metadata directory:") +print(args$variable_metadata_outdir) + +## Loading libraries +suppressPackageStartupMessages(require(mixOmics)) + +## Read sample metadata file and set description factor matrix +sample_metadata <- read.table(args$sample_metadata_in, sep='\t', header=TRUE, row.names=1) +sample_metadata_names <- row.names(sample_metadata) +# print(sample_metadata_names) + +# print("Sample metadata matrix:") +# print(head(sample_metadata)) + +description_column <- ncol(sample_metadata) +if(args$sample_description_col > 0) +{ + description_column <- args$sample_description_col +} + +Y <- factor(sample_metadata[[description_column]]) + +print("Y factor matrix:") +print(Y) + +## Read and prepare block datasets +list_X <- c() +keepX <- c() + +for(i in 1:nrow(args$blocks_list)) +{ + # Read block input parameters + block_name <- args$blocks_list[i,1] + block_keep <- strtoi(args$blocks_list[i,2]) + block_data_matrix_filename <- args$blocks_list[i,3] + # block_meta_var <- args$blocks_list[i,4] + + print(sprintf("Processing block %s", block_name)) + + # Store block data matrices + block_data_matrix <- t(read.table(block_data_matrix_filename, sep='\t', header=TRUE, row.names=1)) # transpose the matrix so that the samples become rows and the variables become columns + block_data_matrix_names <- row.names(block_data_matrix) + # print(block_data_matrix_names) + + if(!identical(sample_metadata_names, block_data_matrix_names)) + { + stop("Sample names must be the same and in the same order in the sample metadata matrix and the block data matrix") + } + + list_X[[block_name]] <- block_data_matrix + + # Set the nb of variables to keep + nb_variables = ncol(list_X[[block_name]]) + if(block_keep > 0) + { + keepX[[block_name]] <- rep(block_keep, args$ncomp) + } + else + { + keepX[[block_name]] <- rep(nb_variables, args$ncomp) + } + print(sprintf("Block %s contains %d variables and %d will be selected", block_name, nb_variables, block_keep)) +} + +# print(list_X) + +## Generate design matrix +block_nb <- nrow(args$blocks_list) + +design <- matrix(0, nrow = block_nb, ncol = block_nb) + +if(args$correlation) +{ + design <- matrix(1, nrow = block_nb, ncol = block_nb) + diag(design) <- 0 +} + +# print("Design matrix:") +# print(design) + +################### +## Main function ## +################### + +mixomics_result <- block.splsda(X = list_X, + Y = Y, + ncomp = args$ncomp, + keepX = keepX, + design = design, + scheme = args$scheme, + mode = args$mode, + scale = args$scale, + init = args$init, + tol = args$tol, + max.iter = args$maxiter, + near.zero.var = args$nearzerovar, + all.outputs = TRUE) + +print("Block.splsda object:") +print(mixomics_result) +print(attributes(mixomics_result)) + +## Save output Rdata file +save(mixomics_result, file=args$rdata_out) + +## Save output sample metadata file +# print("Block.splsda variates:") +# print(mixomics_result$variates) + +for(block_name in names(mixomics_result$variates)) +{ + # print(block_name) + # print(mixomics_result$variates[[block_name]]) + + # Format the column names to add the block name and replace spaces + colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_") + # print(mixomics_result$variates[[block_name]]) + + # Append the new columns to the sample metadata matrix + sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]]) +} + +# print(sample_metadata) + +write.table(sample_metadata, file = args$sample_metadata_out, quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA) + +## Save output variable metadata files in output directory +# print("Block.splsda loadings:") +# print(mixomics_result$loadings) + +for(i in 1:nrow(args$blocks_list)) +{ + # Read again block input parameters + block_name <- args$blocks_list[i,1] + # block_keep <- strtoi(args$blocks_list[i,2]) + # block_data_matrix_filename <- args$blocks_list[i,3] + block_meta_var <- args$blocks_list[i,4] + + print(sprintf("Saving block %s output metavar", block_name)) + + meta_variable <- mixomics_result$loadings[[block_name]] + # print(head(meta_variable)) + + # Format the column names to add the block name and replace spaces + colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_") + + # Read input block variable metadata files if provided (optional) + if(block_meta_var != "None") + { + input_meta_variable <- read.table(block_meta_var, sep='\t', header=TRUE, row.names=1) + # print(head(input_meta_variable)) + + # Append the new columns to the variable metadata matrix + meta_variable <- cbind2(input_meta_variable, meta_variable) + } + + # print(head(meta_variable)) + + block_meta_var_output_filename <- paste("mixomics_blocksplsda_block_", block_name, "_variable_metadata.tsv", sep="") + write.table(meta_variable, file = paste(args$variable_metadata_outdir,block_meta_var_output_filename, sep='/'), quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA) +} \ No newline at end of file diff -r 000000000000 -r d0b77b926863 mixomics_plotindiv.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotindiv.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,111 @@ + + + provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA) + + + bioconductor-mixomics + r-argparse + + + + + + + + + + + + +
+ + +
+ + + + + + + + + + + + + + + + + + + 10.1371/journal.pcbi.1005752 + + + \ No newline at end of file diff -r 000000000000 -r d0b77b926863 mixomics_plotindiv_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotindiv_script.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,53 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the mixOmics plotIndiv function') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend") +parser$add_argument('--ellipse', dest='ellipse', action="store_true", help="Plot ellipse plots") +parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") + +args <- parser$parse_args() + +## Print parameters +print("Input RData:") +print(args$input_rdata) +print("Plot legend:") +print(args$legend) +print("Plot ellipse plots:") +print(args$ellipse) +print("Output PDF file:") +print(args$output_pdf) + +# loading libraries +suppressPackageStartupMessages(require(mixOmics)) + +load(args$input_rdata) + +pdf(args$output_pdf) + +# plotIndiv(mixomics_result, +# legend = args$legend, +# ellipse = args$ellipse) + +for(k in 1:(length(mixomics_result$names[[3]])-1)) +{ + name_block = mixomics_result$names[[3]][k] + + try(plotIndiv(mixomics_result, + blocks = k, + legend = args$legend, + ellipse = args$ellipse), + silent = FALSE) +} + +dev.off() \ No newline at end of file diff -r 000000000000 -r d0b77b926863 mixomics_plotvar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotvar.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,112 @@ + + + provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA + + + bioconductor-mixomics + r-argparse + + + + + + + + + + + + +
+ + +
+ + + + + + + + + + + + + + + + + + + 10.1371/journal.pcbi.1005752 + + + \ No newline at end of file diff -r 000000000000 -r d0b77b926863 mixomics_plotvar_script.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotvar_script.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,56 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Main Function ## + +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the mixOmics plotVar function') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend") +parser$add_argument('--cutoff', dest='cutoff', type='double', required=TRUE, help="Cutoff (0..1)") +parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") + +args <- parser$parse_args() + +## +print("Input RData:") +print(args$input_rdata) +print("Plot legend:") +print(args$legend) +print("Cutoff:") +print(args$cutoff) +print("Output PDF file:") +print(args$output_pdf) + +# loading libraries +suppressPackageStartupMessages(require(mixOmics)) + +load(args$input_rdata) + +pdf(args$output_pdf) + +# plotVar(mixomics_result, +# legend = args$legend, +# cutoff = args$cutoff) + +for(k in 1:(length(mixomics_result$names[[3]])-1)) +{ + name_block = mixomics_result$names[[3]][k] + + # We're still continuing even if a graph is empty + try(plotVar(mixomics_result, + blocks = k, + legend = args$legend, + cutoff = args$cutoff), + silent = FALSE) + +} + +dev.off() \ No newline at end of file diff -r 000000000000 -r d0b77b926863 networkVar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/networkVar.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,64 @@ + + + creates a network between selected variables of datasets and the response variables. In the network, the similarity between two variables is associated with the link between these two variables. + + + bioconductor-mixomics + r-igraph + r-argparse + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r d0b77b926863 networkVar_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/networkVar_wrapper.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,81 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the networkVar function') + +parser$add_argument('--mat_similarity_rdata', dest='mat_similarity_rdata', required=TRUE, help="matSimilarity RData file") +parser$add_argument('--var_list_file', dest='var_list_file', required=TRUE, help="Variables list file") +# parser$add_argument('--interest_var_file', dest='interest_var_file', required=FALSE, help="Variables of interest file") +parser$add_argument('--response_var', dest='response_var', required=TRUE, help="Response variables") +parser$add_argument('--output_graph', dest='output_graph', required=TRUE, help="Output graphml") + +args <- parser$parse_args() + +## Print parameters +print("matSimilarity RData file:") +print(args$mat_similarity_rdata) +print("Variables list file:") +print(args$var_list_file) +# print("Variables of interest:") +# print(args$interest_var_file) +print("Response variables:") +print(args$response_var) +print("Output graphml:") +print(args$output_graph) + +## Loading libraries +# suppressPackageStartupMessages(require(mixOmics)) +suppressPackageStartupMessages(require(igraph)) + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +## Loading local functions +# source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") +install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL) +suppressPackageStartupMessages(require(visCorVar)) +print("visCorVar has been loaded") + +# Loading input Rdata file +# loads res_compute_mat_similarity object +load(args$mat_similarity_rdata) + +# +names_block_variables = as.character(read.table(args$var_list_file, header=FALSE)[[1]]) +names_response_variables = strsplit(args$response_var, ",")[[1]] + +# interest_var_vec = NULL +# if (args$interest_var_file != 'None') { +# interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]]) +# } + +print("names_block_variables:") +print(names_block_variables) +# print("interest_var_vec:") +# print(interest_var_vec) +print("names_response_variables:") +print(names_response_variables) + +res_networkVar = networkVar(res_compute_mat_similarity = res_compute_mat_similarity, + names_block_variables = names_block_variables, + names_response_variables = names_response_variables, + cutoff = 0) + +print("networkVar() completed") +print("res_networkVar:") +print(res_networkVar) + +write.graph(res_networkVar$gR, file = args$output_graph, format = "graphml") \ No newline at end of file diff -r 000000000000 -r d0b77b926863 test-data/in_block1_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_block1_data.tabular Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,7 @@ + "A1" "A2" "B1" "B2" +"var1" 1 2 3 4 +"var2" 1.5 2.5 3.5 4.5 +"var3" 2.5 2 2.5 2 +"var4" 5 4 3 2 +"var5" 1.001 1.01 1.1 1 +"var6" 10 13 11 10 diff -r 000000000000 -r d0b77b926863 test-data/in_block2_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_block2_data.tabular Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,7 @@ + "A1" "A2" "B1" "B2" +"var1" 2 3 4 5 +"var2" 2.5 1 2.5 4 +"var3" 2.5 2 2.5 2 +"var4" 6 5 3 2 +"var5" 10.001 10.01 10.1 10 +"var6" 20 23 21 20 diff -r 000000000000 -r d0b77b926863 test-data/in_sample_meta.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_sample_meta.tabular Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,5 @@ + "Y" +"A1" "catA" +"A2" "catA" +"B1" "catB" +"B2" "catB" diff -r 000000000000 -r d0b77b926863 test-data/out_plotIndiv.pdf Binary file test-data/out_plotIndiv.pdf has changed diff -r 000000000000 -r d0b77b926863 test-data/out_plotVar.pdf Binary file test-data/out_plotVar.pdf has changed diff -r 000000000000 -r d0b77b926863 test-data/out_rdata.rdata Binary file test-data/out_rdata.rdata has changed diff -r 000000000000 -r d0b77b926863 test-data/out_sample_meta.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_sample_meta.tabular Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,5 @@ +"" "Y" "block.splsda_Block1_comp1" "block.splsda_Block1_comp2" "block.splsda_Block2_comp1" "block.splsda_Block2_comp2" "block.splsda_Y_comp1" "block.splsda_Y_comp2" +"A1" "catA" 1.85013467343542 0.422684485040581 1.28016568038406 0.405956759170116 1.22474487139159 0.0342790721507239 +"A2" "catA" 1.07324868851916 -0.960001503242697 1.53872954309497 -0.749531756995324 1.22474487139159 -0.16259622770647 +"B1" "catB" -1.0856729590951 1.64317643604658 -1.01949098398762 1.60513370686125 -1.22474487139159 0.374128476201717 +"B2" "catB" -1.83771040285949 -1.10585941784446 -1.79940423949142 -1.26155870903602 -1.22474487139159 -0.245811320645977