Mercurial > repos > lecorguille > package_r_camera_1_22_0

changeset 0:4386042cb931 draft

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planemo upload
author lecorguille
date Fri, 07 Aug 2015 10:36:42 -0400
parents
children 818457f556cc
files tool_dependencies.xml
diffstat 1 files changed, 113 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Aug 07 10:36:42 2015 -0400
@@ -0,0 +1,113 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.2">
+        <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="netcdf" version="4.3.3.1">
+        <repository changeset_revision="36e1b1104eb2" name="package_netcdf_4_3_3_1" owner="lecorguille" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="camera" version="1.22.0">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.1.2" />
+                    </repository>
+                    <repository changeset_revision="36e1b1104eb2" name="package_netcdf_4_3_3_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="netcdf" version="4.3.3.1" />
+                    </repository>
+                    
+                    
+                    <package>http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocGenerics_0.14.0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.1/bioc/src/contrib/Biobase_2.28.0.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_xcms_1_44_0/Rcpp_0.12.0.tar.gz</package>
+                    <package>http://www.bioconductor.org/packages/3.1/bioc/src/contrib/ProtGenerics_1.0.0.tar.gz</package>
+
+                    <package>http://www.bioconductor.org/packages/3.1/bioc/src/contrib/zlibbioc_1.14.0.tar.gz</package>
+                    <package>http://www.bioconductor.org/packages/3.1/bioc/src/contrib/mzR_2.2.1.tar.gz</package>
+
+                    <package>http://www.bioconductor.org/packages/3.1/bioc/src/contrib/xcms_1.44.0.tar.gz</package>
+                    
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/MASS_7.3-43.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/magrittr_1.5.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/registry_0.3.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/digest_0.6.8.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/stringi_0.5-5.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/stringr_1.0.0.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/xtable_1.7-4.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/pkgmaker_0.22.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/rngtools_1.2.4.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/gridBase_0.4-7.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/colorspace_1.2-6.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/RColorBrewer_1.1-2.tar.gz </package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/iterators_1.0.7.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/foreach_1.4.2.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/doParallel_1.0.8.tar.gz </package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/plyr_1.8.3.tar.gz </package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/gtable_0.1.2.tar.gz </package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/reshape2_1.4.1.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/dichromat_2.0-0.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/munsell_0.4.2.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/labeling_0.3.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/scales_0.2.5.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/proto_0.3-10.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/ggplot2_1.0.1.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/NMF_0.20.6.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/irlba_1.0.3.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/igraph_1.0.1.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.0/bioc/src/contrib/graph_1.44.1.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.0/bioc/src/contrib/RBGL_1.42.0.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/Formula_1.2-1.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/lattice_0.20-33.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/latticeExtra_0.6-26.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/acepack_1.3-3.3.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/gridExtra_2.0.0.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/Hmisc_3.16-0.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.0/bioc/src/contrib/CAMERA_1.22.0.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/survival_2.38-3.tar.gz</package>
+                    <package>http://bioconductor.org/packages/3.0/bioc/src/contrib/multtest_2.22.0.tar.gz</package>
+                    
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/snow_0.3-13.tar.gz</package>
+                    <package>http://application.sb-roscoff.fr/download/w4m/cran-archive/package_r_camera_1_22_0/batch_1.1-4.tar.gz</package>
+
+
+<!--attached base packages:
+[1] parallel  stats     graphics  grDevices utils     datasets  methods  
+[8] base     
+
+other attached packages:
+[1] CAMERA_1.22.0       igraph_0.7.1        xcms_1.42.0        
+[4] mzR_2.0.0           Rcpp_0.11.5         Biobase_2.26.0     
+[7] BiocGenerics_0.12.1
+
+loaded via a namespace (and not attached):
+ [1] acepack_1.3-3.3     cluster_2.0.1       codetools_0.2-10   
+ [4] colorspace_1.2-5    digest_0.6.8        foreign_0.8-63     
+ [7] Formula_1.2-0       ggplot2_1.0.0       graph_1.44.1       
+[10] grid_3.1.1          gtable_0.1.2        Hmisc_3.15-0       
+[13] lattice_0.20-30     latticeExtra_0.6-26 MASS_7.3-39        
+[16] munsell_0.4.2       nnet_7.3-9          plyr_1.8.1         
+[19] proto_0.3-10        RBGL_1.42.0         RColorBrewer_1.1-2 
+[22] reshape2_1.4.1      rpart_4.1-9         scales_0.2.4       
+[25] splines_3.1.1       stats4_3.1.1        stringr_0.6.2      
+[28] survival_2.38-1     tcltk_3.1.1         tools_3.1.1 -->
+
+
+                </action>
+            </actions>
+        </install>
+        <readme>
+http://bioconductor.org/packages/release/bioc/html/CAMERA.html
+
+Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments
+
+Author: Carsten Kuhl, Ralf Tautenhahn, Steffen Neumann {ckuhl|sneumann}@ipb-halle.de, rtautenh@scripps.edu 
+
+Galaxy integration: ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff - part of Workflow4Metabolomics.org [W4M]
+Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
+
+Thanks to https://testtoolshed.g2.bx.psu.edu/repository?repository_id=dd467491fd861a73
+        </readme>
+    </package>
+</tool_dependency>